title: P3248_356

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_366

status: Public on Dec 31 2021

type: SRA

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
full-lenght RNA-seq
P3248.tsv

library_source: transcriptomic

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Mouse: Gencode release 21, assembly GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 22 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent Technologies). 140 pg of the amplified cDNA were fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit. Sequencing of Nextera® libraries from 384 cells was carried out in one lane on a Illumina HiSeq2500 v4.
Full-length single-cell RNA sequencing libraries were prepared using the Smart-seq2 protocol
single cell RNA-seq (scRNA-seq)

tag: protocol

tag: cell type

value: Glioblastoma

tag: treatment

value: PDGFR


title: P3248_353

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_354

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_380

description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


title: P3248_359

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_352

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_351

description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


title: P3248_348

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_347

description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


title: P3248_363

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_342

description:
full-lenght RNA-seq
P3248.tsv


title: P3248_341

description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


title: P3248_343

description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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full-lenght RNA-seq
P3248.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv

source_name: empty


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3213.tsv

value: EGFR


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3247.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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P3213.tsv


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full-lenght RNA-seq
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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


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description:
full-lenght RNA-seq
P3213.tsv


title: P3213_028

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_002

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_384

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_018

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_379

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_378

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_015

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_026

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_017

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_376

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_014

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_011

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_370

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_010

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_009

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_368

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_007

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_006

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_361

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_004

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_371

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_003

description:
full-lenght RNA-seq
P3213.tsv


title: P3213_001

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_383

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_382

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_381

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_357

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_355

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_377

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_375

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_362

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_372

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_369

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_373

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_380

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_365

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_374

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_363

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_351

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_364

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_360

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_367

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_349

description:
full-lenght RNA-seq
P3212.tsv


title: P3213_050

description:
full-lenght RNA-seq
P3213.tsv


title: P3212_359

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_358

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_345

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_366

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_356

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_354

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_348

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_347

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_350

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_346

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_341

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_340

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_344

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_343

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_352

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_338

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_342

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_337

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_336

description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


title: P3212_317

description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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full-lenght RNA-seq
P3212.tsv


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full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


title: P3212_300

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_301

description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


title: P3212_299

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_298

description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


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full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


title: P3212_292

description:
full-lenght RNA-seq
P3212.tsv


title: P3212_291

description:
full-lenght RNA-seq
P3212.tsv


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description:
full-lenght RNA-seq
P3212.tsv


title: P3149_383

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_381

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_378

description:
full-lenght RNA-seq
P3149.tsv

source_name: S93B3(M3)_P3 Core


title: P3212_304

description:
full-lenght RNA-seq
P3212.tsv


title: P3149_382

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_380

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_377

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_384

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_379

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_375

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_374

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_370

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_371

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3212.tsv


title: P3149_373

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_372

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


title: P3149_367

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_369

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_366

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_365

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_363

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_364

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_362

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_359

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_361

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_376

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_360

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_355

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


title: P3149_352

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


title: P3149_348

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_343

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_350

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_351

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


title: P3149_353

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


title: P3149_336

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3149.tsv


title: P3149_329

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_328

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_326

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_321

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_327

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_317

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_319

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_345

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_322

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_318

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_323

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_325

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_312

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_337

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_316

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_320

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_309

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_315

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_313

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_311

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_314

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_303

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_305

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_324

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_300

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_298

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_306

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_304

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_310

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_301

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_307

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_308

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_297

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_291

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_293

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_290

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3149_289

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_292

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_296

description:
full-lenght RNA-seq
P3149.tsv


title: P3149_294

description:
full-lenght RNA-seq
P3149.tsv


title: P3148_286

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_288

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_282

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_281

description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3149_299

description:
full-lenght RNA-seq
P3149.tsv


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description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3148_277

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_275

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_272

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_284

description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3148_271

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_269

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_283

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_265

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_273

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_263

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_268

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_267

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_257

description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3148_266

description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3148_260

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_253

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_259

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_261

description:
full-lenght RNA-seq
P3148.tsv


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description:
full-lenght RNA-seq
P3148.tsv


title: P3148_255

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_252

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_274

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_251

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_250

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_249

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_243

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_258

description:
full-lenght RNA-seq
P3148.tsv


title: P3149_295

description:
full-lenght RNA-seq
P3149.tsv


title: P3148_242

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_241

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_244

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_245

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_248

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_239

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_238

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_236

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_235

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_234

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_246

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_233

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_237

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_232

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_230

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_240

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_228

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_229

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_227

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_231

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_247

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_225

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_224

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_223

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_222

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_221

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_226

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_220

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_219

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_218

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_217

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_213

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_214

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_212

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_211

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_208

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_209

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_207

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_210

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_196

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_206

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_201

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_203

description:
full-lenght RNA-seq
P3148.tsv


title: P3147_191

description:
full-lenght RNA-seq
P3147.tsv


title: P3148_216

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_215

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_197

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_200

description:
full-lenght RNA-seq
P3148.tsv


title: P3147_189

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_188

description:
full-lenght RNA-seq
P3147.tsv


title: P3148_193

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_199

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_195

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_204

description:
full-lenght RNA-seq
P3148.tsv


title: P3147_190

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_192

description:
full-lenght RNA-seq
P3147.tsv


title: P3148_202

description:
full-lenght RNA-seq
P3148.tsv


title: P3147_183

description:
full-lenght RNA-seq
P3147.tsv

source_name: S93B3(M3)_P4 Core


title: P3147_181

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_180

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_187

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_186

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_184

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_185

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_179

description:
full-lenght RNA-seq
P3147.tsv


title: P3148_194

description:
full-lenght RNA-seq
P3148.tsv


title: P3148_198

description:
full-lenght RNA-seq
P3148.tsv


title: P3147_178

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_171

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_175

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_168

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_174

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_165

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_169

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_173

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_162

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_167

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_170

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_157

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_158

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_177

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_166

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_182

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_153

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_161

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_156

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_159

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_151

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_176

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_154

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_172

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_152

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_155

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_164

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_163

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_160

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_150

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_146

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_147

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_145

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_148

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_149

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_142

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_143

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_138

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_134

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_140

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_139

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_136

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_132

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_133

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_144

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_128

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_127

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_135

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_129

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_125

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_130

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_131

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_124

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_123

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_126

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_122

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_120

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_137

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_118

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_141

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_117

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_116

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_114

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_113

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_112

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_111

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_109

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_110

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_106

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_105

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_104

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_107

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_103

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_102

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_099

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_100

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_098

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_121

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_097

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_108

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_101

description:
full-lenght RNA-seq
P3147.tsv


title: P3147_119

description:
full-lenght RNA-seq
P3147.tsv


title: P3146_095

description:
full-lenght RNA-seq
P3146.tsv


title: P3146_096

description:
full-lenght RNA-seq
P3146.tsv


title: P3146_092

description:
full-lenght RNA-seq
P3146.tsv


title: P3146_093

description:
full-lenght RNA-seq
P3146.tsv


title: P3146_091

description:
full-lenght RNA-seq
P3146.tsv


title: P3147_115

description:
full-lenght RNA-seq
P3147.tsv


title: P3146_090

description:
full-lenght RNA-seq
P3146.tsv


title: P3146_089

description:
full-lenght RNA-seq
P3146.tsv

source_name: S93B3(M3)_P2 Core


title: P3146_088

description:
full-lenght RNA-seq
P3146.tsv


title: P3146_085

description:
full-lenght RNA-seq
P3146.tsv


title: P2774_156

description:
full-lenght RNA-seq
P2774.tsv

source_name: S94F1_P2 Inv


title: P2774_155

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_153

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_152

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_149

description:
full-lenght RNA-seq
P2774.tsv

source_name: S94F1_P2 Core


title: P2774_147

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_151

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_150

description:
full-lenght RNA-seq
P2774.tsv


title: P3146_087

description:
full-lenght RNA-seq
P3146.tsv


title: P2774_145

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_146

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_148

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_144

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_140

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_139

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_141

description:
full-lenght RNA-seq
P2774.tsv


title: P3146_094

description:
full-lenght RNA-seq
P3146.tsv


title: P2774_138

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_137

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_135

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_134

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_136

description:
full-lenght RNA-seq
P2774.tsv


title: P3146_086

description:
full-lenght RNA-seq
P3146.tsv


title: P2774_133

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_132

description:
full-lenght RNA-seq
P2774.tsv


title: P3148_205

description:
full-lenght RNA-seq
P3148.tsv


title: P2774_128

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_130

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_129

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_143

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_142

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_125

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_131

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_127

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_122

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_124

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_121

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_123

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_117

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_120

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_118

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_115

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_126

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_116

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_114

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_113

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_112

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_110

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_111

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_109

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_108

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_105

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_103

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_104

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_106

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_107

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_099

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_101

description:
full-lenght RNA-seq
P2774.tsv


title: Dhcr24TG

city: New Haven

first: Xinbo

last: Zhang

state: Connecticut

address: Rm320, 10 Amistad St

department: Comparative Medicine

country: USA

institute: Yale University

data_processing:
Reads were aligned against mouse genome mm9 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 5% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Genome_build: mmp9
Supplementary_files_format_and_content: Cell-gene-barcode matrices

molecule: total RNA

source_name: Aorta

growth_protocol: WT and Dhcr24TG mice (8 weeks old, male) were i.p injected with PCSK9 adeno-associated virus (AAV8-Pcsk9) at 1.0x1011 vector genome copies per mouse.

extract_protocol:
Atherosclerotic aorta was digested with 1 mg/ml Collagenase  A for 7 min (Roche, Cat 11088785103) at 37 °C to remove the adventitia under microscope. Aortic tissue  was cut into small pieces and subjected to enzymatic digestion with 1.5 mg/ml Collagenase A and 0.5  mg/ml Elastase (Worthington, Cat LS006365) for 40 min at 37 °C while shaking. Viable CD45+CD11B+  cells were sorted by FACS Aria III (BD Biosciences) with gating on live, single cells using ive/dead viability dye eFluor 450  (Thermo Fisher Scientific).
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using the V2 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

treatment_protocol: Two weeks after AAV8-Pcsk9 injection, animals were maintained in a Western-type diet for 16 weeks.

value: CD45+CD11B+ Cell

tag: strain

tag: tissue

value: Aorta

tag: genotype

value: AAV8-Pcsk9 + Western diet for 16  weeks


title: P2774_119

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_098

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_102

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_097

description:
full-lenght RNA-seq
P2774.tsv


title: P2774_100

description:
full-lenght RNA-seq
P2774.tsv


title: wild type

value: WT


title: IL1-61

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Mice dosed every 4 days for 28 days

data_processing:
Quality control: FASTQC v0.11.3
Removal of adaptors: Trimmomatic v0.33
Removal of artifacts: FASTX v0.0.14
Alignment: TopHat2 v2.1.0
Conversion to SAM format: SAMTools v1.2.0
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Proximal Ileal epithelium

extract_protocol:
Intestinal epithelium scrapings were homogenized in TRIzol (Ambion, Waltham, MA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified using a Nano-drop spectrophotometer (Thermo Scientific, Wilmington, DE) at 260 nm and purity was assessed by calculating the A260/A280 ratio. RNA quality was analyzed using the Caliper LabChip GX (Perkin Elmer, Waltham, MA).
Libraries were were prepared using the Ovation Mouse RNA-Seq System 1-16 sample preparation kit (NuGen, San Carlos, CA), with an additional DNase step. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Male C57BL/6 mice were gavaged with sesame oil vehicle, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

value: Proximal Ileal epithelium

tag: Sex

value: Male

value: days

value: degree fahrenheit

value: percent

value: Innovive disposable cage

tag: bedding

value: ALPHA-dri bedding

tag: water

value: Aquavive water

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vendor

value: Accustandard

value: Sesame oil

value: oral gavage

tag: dose

value: Microgram per Kilogram

value: day

value: NuGen Ovation Mouse RNA-Seq System 1-16 sample preparation kit


title: IL1-07

description: Mice dosed every 4 days for 28 days


title: IL1-53

description: Mice dosed every 4 days for 28 days


title: IL1-55

description: Mice dosed every 4 days for 28 days


title: IL1-68

description: Mice dosed every 4 days for 28 days


title: IL1-62

description: Mice dosed every 4 days for 28 days


title: Col-67

description: Mice dosed every 4 days for 28 days

source_name: Colonic epithelium

treatment_protocol: Male C57BL/6 mice were gavaged with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

value: Colonic epithelium


title: IL1-52

description: Mice dosed every 4 days for 28 days

value: Proximal Ileal epithelium


title: IL1-72

description: Mice dosed every 4 days for 28 days

value: Male


title: Col-66

description: Mice dosed every 4 days for 28 days

value: days


title: IL1-65

description: Mice dosed every 4 days for 28 days

value: degree fahrenheit


title: IL1-06

description: Mice dosed every 4 days for 28 days

value: percent


title: Col-51

description: Mice dosed every 4 days for 28 days

value: Innovive disposable cage


title: Col-41

description: Mice dosed every 4 days for 28 days

value: ALPHA-dri bedding


title: Col-43

description: Mice dosed every 4 days for 28 days

value: Aquavive water


title: IL1-59

description: Mice dosed every 4 days for 28 days

value: Harlan Teklad 22/5 Rodent Diet 8940


title: Col-65

description: Mice dosed every 4 days for 28 days

value: Harlan Teklad


title: Col-33

description: Mice dosed every 4 days for 28 days

value: Accustandard


title: Col-59

description: Mice dosed every 4 days for 28 days

value: Sesame oil


title: Col-52

description: Mice dosed every 4 days for 28 days

value: oral gavage


title: Col-58

description: Mice dosed every 4 days for 28 days

value: Microgram per Kilogram


title: Col-57

description: Mice dosed every 4 days for 28 days

value: day


title: Col-11

description: Mice dosed every 4 days for 28 days

value: NuGen Ovation Mouse RNA-Seq System 1-16 sample preparation kit


title: Col-14

description: Mice dosed every 4 days for 28 days

value: Colonic epithelium


title: Col-04

description: Mice dosed every 4 days for 28 days


title: Col-02

description: Mice dosed every 4 days for 28 days


title: P2774_154

description:
full-lenght RNA-seq
P2774.tsv

value: Glioblastoma

value: EGFR


title: Col-03

description: Mice dosed every 4 days for 28 days

value: Male

value: days


title: Col-44

description: Mice dosed every 4 days for 28 days

value: degree fahrenheit

value: percent


title: Col-49

description: Mice dosed every 4 days for 28 days

value: Innovive disposable cage

value: ALPHA-dri bedding


title: IL1-03

description: Mice dosed every 4 days for 28 days

value: Proximal Ileal epithelium

value: Aquavive water

value: Harlan Teklad 22/5 Rodent Diet 8940


title: Col-34

description: Mice dosed every 4 days for 28 days

value: Harlan Teklad

value: Accustandard

value: Sesame oil


title: Col-28

description: Mice dosed every 4 days for 28 days

value: oral gavage

value: Microgram per Kilogram

value: day


title: pH_BMP2ADV590 Rep 2

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQC (v0.11.5) quality control
bbduk (v35.92) adapter trimming and filtering
STAR (v2.5.2a) genome alignment
HTSeq-count (v0.6.0) feature counting
DESeq2 (v3.11) differential expression
Genome_build: GRCm38

source_name: Mouse embryonic cells

growth_protocol: DMEM HG, 10% FCS, 1% L-Glutamine, until 80% confluence

extract_protocol:
Three days post transfection, total RNA was harvested using TriFast reagent (manufacturer's instructions were followed)
mRNA libraries were generated from 100ng total RNA input using Quant Seq 3’mRNA Library Prep Kit FWD for Illumina (Lexogen, Austria) according to the manufactures declaration. Libraries were amplified with 16 cycles using barcoded Illumina reverse primer (i7 index primer) in combination with Illumina forward primer.

treatment_protocol: Transfection of 0.5µg pDNA per square cm using TurboFect polymer transfection reagent (manufacturer's instructions were followed), medium exchanged 4hrs post transfection

tag: morphology

value: fibroblast

value: embryo

tag: disease

value: sarcoma

tag: transfection

value: non-viral, transient


title: pH_BMP2ADV148b Rep 2


title: Col-27

description: Mice dosed every 4 days for 28 days

value: Colonic epithelium

value: Male

value: days

value: degree fahrenheit

value: NuGen Ovation Mouse RNA-Seq System 1-16 sample preparation kit


title: Col-09

description: Mice dosed every 4 days for 28 days

value: percent

value: Innovive disposable cage

value: ALPHA-dri bedding

value: Aquavive water


title: Col-20

description: Mice dosed every 4 days for 28 days

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

value: Sesame oil


title: Col-19

description: Mice dosed every 4 days for 28 days

value: oral gavage

value: Microgram per Kilogram

value: day


title: pH_BMP2ADV20a Rep 1

value: fibroblast

value: embryo

value: sarcoma

value: non-viral, transient


title: Col-35

description: Mice dosed every 4 days for 28 days

value: Colonic epithelium

value: Male

value: days

value: degree fahrenheit


title: Ms1608-Normal

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
The sequences were aligned to the GRCm38 reference genome using RNA-Star (v2.4.2a; https://github.com/alexdobin/STAR).
The gene expression was normalized and calculated as FPKM (Fragments Per Kilobase Million) values by Cufflinks (v2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) with Gencode M5 gene annotations (https://www.gencodegenes.org/mouse/release_M5.html).
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each sample

source_name: Heart tissue from normal LV

extract_protocol:
3 weeks after the MI surgery, mice were euthanized and perfused with PBS supplemented with EDTA, and hearts were harvested. Infarcted tissue was dissected under a stereomicroscope, and digested with DMEM medium with collagenase-II (5 mg/ml, Invitrogen 17101-015) and DNase (1 mg/ml, Sigma D4527). Single cell suspension was prepared after filtering with a mesh strainer (100-micron pores). Cells were incubated with anti-F4/80 antibody (Miltenyl Biotec, #130-102-327), and tdTomato+F4/80- cells were sorted by using a flow cytometer (BD FACS Aria). RNA was extracted using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions, followed by RNA purification using a RNeasy Plus Mini Kit (Qiagen). cDNA was obtained by reverse transcription with Superscript III (Thermo Fisher, 18080044), and a second complementary cDNA strand was synthesized by DNA polymerase (10 U/ul, Thermo Fisher, 18010025), followed by in vitro RNA transcription using a MEGASCRIPT T7 KIT (Thermo Fisher, AMB13345) and RNA purification using a MEGACLEAR KIT (Thermo Fisher, AM1908). Quality control was validated using a RNA Nano assay chips with a 2100 Bioanalyzer (Agilent)
The library was constructed according to a TruSeq protocol (Agilent), followed by sequencing (100 PE, about 10 megabyte reads for each sample) with a 2500 Illumina sequencer at the Children’s Hospital of Philadelphia/Beijing Genomics Institute core facility (CHOP/BGI).

treatment_protocol: MI was induced by ligation of left anterior descending (LAD) coronary artery in Tie2-Cre;Rosa-LSL-tdTomato mice (6-8 weeks old).

value: Normal LV tissue

value: Without MI surgery


title: Col-25

description: Mice dosed every 4 days for 28 days

value: percent

value: Innovive disposable cage

value: ALPHA-dri bedding

value: Aquavive water

value: Harlan Teklad 22/5 Rodent Diet 8940

value: NuGen Ovation Mouse RNA-Seq System 1-16 sample preparation kit


title: Ms1537-Normal


title: pH_BMP2ADV590 Rep 3


title: pH_BMP2ADV590 Rep 1


title: Ms1537-MI

source_name: Heart tissue from MI region

value: MI tissue

value: With MI surgery


title: pH_BMP2ADV Rep 1

value: fibroblast

value: embryo


title: Ms1535-Normal


title: wound healing tissue single cell RNA seq

city: Gangnam-gu

first: Seok-Hyung

last: Kim

state: Seoul

address: 81, Irwon-ro

department: Department of Pathology

country: South Korea

institute: Samsung Medical Center

data_processing:
Using CellRanger 2.1.0 pipelines sequence reads were performd alignment using STAR, filtering, barcode counting, and UMI counting
The raw gene expression count matrix from the CellRanger pipeline was filtered using the Seurat R package (version 4.0.0) and selected according to the following criteria: cells with > 1000 UMI counts, > 200 genes, and < 6,000 genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: wound healing tissue

growth_protocol: To avoid distortion of the data by multiple passages using medium containing serum, these cells were not sub-cultured more than two times (2 passage).

extract_protocol:
After resuspension in 1× PBS, all single-cell suspensions were loaded into a 10x Chromium Controller (10x Genomics, USA). Barcoded sequencing libraries were generated using Chromium Single Cell 3’ Library & Gel Bead kits v2 (cat# PN-120237, 10x Genomics, USA) and sequenced on a Hiseq 2500 platform (Illumina, USA).
Chromium Single Cell 3’ Library & Gel Bead Kit v2 (cat# PN-120237) Chromium Single Cell A Chip Kit (cat# PN-120236) Chromium i7 Multiplex Kit (cat# PN-120262) Following the manufacturer’s instructions, barcoded sequencing libraries were generated using Chromium Single Cell 3’ v2 kits. Sequencing was performed on Illumina Hiseq2500

treatment_protocol: Adult wild-type (WT) mice (BALB/c) were used for this study. 12mm biopsy punch skin wounds were placed on the side of dorsal of mice. The wound was covered with a transparent semi-occlusive dressing (Tegaderm, 3M, Saint Paul, MN, USA) to prevent desiccation. After 10 days (at day10 post wound), tissues of wound area were excised. These tissues were cut into small pieces, minced with scalpels and dissociated with D/F12 serum medium containing collagenase I in a 37'C for 12hrs using a shaker. Cells from wound tissue were transferred to a 50ml tube, and the dead cells were removed using ficoll seperation.

value: BALB/c

value: single cells of wound tissue


title: Ms1535-MI


title: pH_BMP2ADV148b Rep 1

value: sarcoma

value: non-viral, transient


title: Col-18

description: Mice dosed every 4 days for 28 days

value: Colonic epithelium

value: Male

value: days

value: degree fahrenheit

value: Harlan Teklad

value: Accustandard

value: Sesame oil

value: oral gavage

value: Microgram per Kilogram

value: day


title: pH_BMP2ADV20a Rep 3


title: pH_BMP2ADV20a Rep 2


title: pH_BMP2ADV Rep 2


title: Ms1608-MI

value: MI tissue

value: With MI surgery


title: 8C-KO1_3+28_24h

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig, Count table (.txt)

source_name: T cells

growth_protocol: Cells were grown in full RPMI media containing 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin and 0.1% b-mercaptoethanol in an incubator at 37C and 5% CO2

extract_protocol:
Cells pellets were collected in TRIZOL and mRNA was further purified with the RNeasy Micro RNA Isolation Kit (Qiagen)
The NYU Genome Technology Center constructed the libraries followed their standard protocol

treatment_protocol: Cell were stimulated with 1 ug/ml with anti-CD3 + 1 ug/ml with anti-CD28 antibodies and treated or not with the drug DCPIB at 20 uM

value: Spleen

value: CD4+ T cells

value: CD3+CD28 stimulated for 24h


title: WT2_DCPIB_3+28_48h

value: WT

value: CD3+CD28 stimulated for 48h in the presence of 20 uM DCPIB


title: 8C-KO3_3+28_48h

value: CD3+CD28 stimulated for 48h


title: 8C-KO2_3+28_48h


title: 8C-KO3_3+28_24h


title: WT3_3+28_24h


title: WT1_3+28_24h


title: 8C-KO3_unst

value: Unstimulated cells


title: WT2_unst


title: pH_BMP2ADV148b Rep 3

value: fibroblast

value: embryo

value: sarcoma

value: non-viral, transient


title: WT3_unst


title: 8C-KO1_unst


title: 8C-KO1_3+28_48h


title: cKO-2_Tumor#2_ATAC

city: Cincinnati

first: Zaili

last: Luo

state: OH

address: 3333 Burnet Ave.

institute: CCHMC

library_source: genomic

data_processing:
none provided by the submitter
Genome_build: mm10

molecule: genomic DNA

source_name: Neural progenitor cells

growth_protocol: NPC cells were isolated from postnatal 4 days mouse cerebellum and cultured (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in  in NSC medium ( with EGF, bFGF, B27 and Lif )

extract_protocol:
Genome DNA was extracted based on the protocol of QIAamp DNA Micro Kit, and the ATAC-seq was performed by the ATAC-seq protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
WGS and ATAC-seq

treatment_protocol: no

tag: cell origin

value: Isolated the NPCs from postnatal 4 days


title: WT2_DCPIB_3+28_24h

value: CD3+CD28 stimulated for 24h in the presence of 20 uM DCPIB


title: WT3_3+28_48h


title: pH_BMP2ADV Rep 3


title: WT3_DCPIB_3+28_48h


title: WT1_3+28_48h


title: cKO-2_NPC_ATAC


title: WT1_DCPIB_3+28_48h


title: cKO_NPC_ATAC


title: cKO_Tumor#1

source_name: Neural progenitor cell tumor


title: XEN-H8_S284_002

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Base calling was performed using Off-line Basecaller (OLB) v1.9.4 provided by Illumina.
Sequences were filtered and trimmed using trim_galore version 0.6.4_ev.
Sequences were aligned and counted on mouse genome using Kallisto version 0.46.2 with mRNA database generated using RefSeq database and default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: plain text

source_name: XEN

growth_protocol: C57B6N × 129X1 F1 (#1M, #6M) ESCs were cultured in serum-free ES medium (ESM): Neurobasal:DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15 mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 3μM CHIR99021, 1μM PD0325901, 103U/ml ESGRO LIF on a gelatin-coated dish or in serum ESM (2iL): Knockout DMEM (Thermo Fisher Scientific) , 20% FBS, 1xNEAA, 0.1mM β-mercaptoethanol, 1 × penicillin-streptomycin, 3μM CHIR99021, 1μM PD0325901, and 103U/ml ESGRO LIF on mouse embryonic fibroblasts (MEF) feeder dish. CD1 TSCs (#1-4M, #2-2M, #8M, #1F, #2-3F, #2-4F) were derived in serum-free TS medium: Neurobasal: DMEMF12(1:1), 0.5 × N2 supplement (Thermo Fisher Scientific), 0.5 × B27 supplement (Thermo Fisher Scientific), 0.15mM 1-thioglycerol (Sigma), 0.05% bovine serum albumin (BSA, Sigma), 1 × glutamine-penicillin-streptomycin (Thermo Fisher Scientific), 50ng/ml human FGF4, 10μg/ml heparin, 20ng/ml human Activin A, 10μM XAV939, 10μM Y27632 on MEF feeder dish. CD1 (Clea) or PWK (BRC, RIKEN) × C57BL6N (Charles River) F1 blastocysts were collected at E3.5. CD1-Tg(CAG-EGFP) mice were kindly gifted from Prof. T. Wakayama (Yamanashi university). Culture conditions used in this study is summarized in Supplementary Table 1. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in +C10F4HPDGF medium (Suppl table 1): StemFit® Basic02, 1xpenicillin-streptomycin (Thermo Fisher Scientific), 10μM CHIR99021 (Reprocell), 50ng/ml human FGF4 (Sigma), 1ng/ml heparin (Sigma), 25ng/ml human PDGF-AA (R&D). Embryos were cultured in +C10F4HPDGF medium for at least 5 days until they formed outgrowths. The outgrowth was dissociated with 1xTrypLE™ Select (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate. After 5-7 days, PrES cell colonies reached 50-80% confluence and the cells were passaged into a 12-well MEF feeder plate. PrES cells were frozen in Cellbanker® 1plus (Zenoaq). XEN cells were derived according to a standard protocol (1) with minor modifications. CD1 blastocysts were collected at E3.5. Each blastocyst was transferred to one well of a 48-well MEF feeder plate in serum-containing ES medium: RPMI1640 (Thermo Fisher Scientific), 20% fetal bovine serum (FBS, Biosera), 1 × penicillin-streptomycin (Thermo Fisher Scientific), 1 × non-essential amino acids (NEAA, Thermo Fisher Scientific), 0.1mM β-mercaptoethanol (β-ME, Sigma), 103U/ml ESGRO LIF on a MEF feeder plate. Embryos were cultured for at least 7 days until they formed outgrowths. The outgrowth was removed by pipetting and the remaining adherent cells were continuously cultured for another 7 days. The proliferated cells were dissociated with 0.05% trypsin-EDTA (Thermo Fisher Scientific) and transferred into a new 48-well MEF feeder plate, then expanded into a 6-well plate. XEN cells were frozen in Cellbanker® 1plus (Zenoaq) and stored in a -150°C freezer (Panasonic). Removal of the primary outgrowth was not necessary when CHIR99021 (3μM) was added.

extract_protocol:
mRNA were extracted following Illumina's instructions.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combi

value: not treated

value: single cell XEN cell


title: 8C-KO2_3+28_24h


title: WT3_DCPIB_3+28_24h


title: WT2_3+28_48h


title: XEN-H7_S283_001


title: WT2_3+28_24h


title: XEN-H6_S282_002


title: WT1_DCPIB_3+28_24h


title: XEN-H5_S281_001


title: XEN-H5_S281_002


title: WT1_unst


title: XEN-H3_S279_002


title: XEN-H4_S280_002


title: XEN-H6_S282_001


title: 8C-KO2_unst


title: XEN-H2_S278_001


title: cKO_tumor#2


title: Ctrl-2_NPC_ATAC


title: XEN-H1_S277_002


title: cKO_NPC


title: Ctrl_NPC


title: XEN-H8_S284_001


title: XEN-G9_S273_001


title: cKO_Tumor#2_ATAC


title: XEN-G8_S272_001


title: XEN-G9_S273_002


title: XEN-G7_S271_002


title: XEN-G7_S271_001


title: XEN-H7_S283_002


title: XEN-G5_S269_002


title: XEN-G6_S270_001


title: XEN-H4_S280_001


title: XEN-G2_S266_002


title: XEN-H3_S279_001


title: XEN-H2_S278_002


title: Ctrl_NPC_ATAC


title: XEN-H1_S277_001


title: XEN-G12_S276_002


title: XEN-G1_S265_001


title: XEN-G10_S274_002


title: XEN-G12_S276_001


title: XEN-F9_S261_001


title: XEN-F9_S261_002


title: XEN-F7_S259_001


title: XEN-F7_S259_002


title: XEN-F6_S258_002


title: XEN-F4_S256_002


title: XEN-F4_S256_001


title: XEN-G10_S274_001


title: XEN-F2_S254_002


title: XEN-F3_S255_001


title: XEN-G6_S270_002


title: XEN-G4_S268_001


title: XEN-G4_S268_002


title: XEN-G3_S267_002


title: XEN-G8_S272_002


title: XEN-G3_S267_001


title: XEN-G11_S275_002


title: XEN-G2_S266_001


title: XEN-F11_S263_001


title: XEN-G11_S275_001


title: XEN-G1_S265_002


title: XEN-F5_S257_002


title: XEN-G5_S269_001


title: XEN-F8_S260_001


title: XEN-F5_S257_001


title: XEN-F3_S255_002


title: XEN-F6_S258_001


title: XEN-F12_S264_002


title: XEN-E8_S248_001


title: XEN-E9_S249_002


title: XEN-F2_S254_001


title: XEN-F8_S260_002


title: XEN-F1_S253_001


title: XEN-F12_S264_001


title: XEN-F10_S262_002


title: XEN-F11_S263_002


title: XEN-F10_S262_001


title: XEN-E3_S243_002


title: XEN-F1_S253_002


title: XEN-E9_S249_001


title: XEN-E4_S244_001


title: XEN-E8_S248_002


title: XEN-E2_S242_002


title: XEN-E1_S241_001


title: XEN-E2_S242_001


title: XEN-E7_S247_002


title: XEN-E12_S252_001


title: XEN-E1_S241_002


title: XEN-E7_S247_001


title: XEN-E11_S251_001


title: XEN-E5_S245_001


title: XEN-E6_S246_001


title: XEN-E5_S245_002


title: XEN-E3_S243_001


title: XEN-E6_S246_002


title: XEN-E11_S251_002


title: XEN-E10_S250_002


title: XEN-E10_S250_001


title: XEN-D8_S236_002


title: XEN-D9_S237_002


title: XEN-D8_S236_001


title: XEN-D9_S237_001


title: XEN-E4_S244_002


title: XEN-D7_S235_001


title: XEN-E12_S252_002


title: XEN-D6_S234_001


title: XEN-D6_S234_002


title: XEN-D5_S233_001


title: XEN-D5_S233_002


title: XEN-D4_S232_002


title: XEN-D4_S232_001


title: XEN-D2_S230_001


title: XEN-D12_S240_002


title: XEN-D12_S240_001


title: XEN-D1_S229_001


title: XEN-D1_S229_002


title: XEN-D2_S230_002


title: XEN-D10_S238_002


title: XEN-D3_S231_002


title: XEN-D3_S231_001


title: XEN-C9_S225_002


title: XEN-D10_S238_001


title: XEN-C8_S224_001


title: XEN-C8_S224_002


title: XEN-C7_S223_001


title: XEN-D11_S239_001


title: XEN-C9_S225_001


title: XEN-C7_S223_002


title: XEN-C6_S222_001


title: XEN-C4_S220_002


title: XEN-C4_S220_001


title: XEN-C5_S221_002


title: XEN-C6_S222_002


title: XEN-C5_S221_001


title: XEN-D11_S239_002


title: XEN-C3_S219_002


title: XEN-C2_S218_002


title: XEN-C3_S219_001


title: XEN-C2_S218_001


title: XEN-C1_S217_002


title: XEN-C1_S217_001


title: XEN-C12_S228_002


title: XEN-C10_S226_001


title: XEN-D7_S235_002


title: XEN-C11_S227_001


title: XEN-C12_S228_001


title: XEN-C11_S227_002


title: XEN-B9_S213_002


title: XEN-B8_S212_002


title: XEN-B9_S213_001


title: XEN-C10_S226_002


title: XEN-B7_S211_002


title: XEN-B6_S210_002


title: XEN-B6_S210_001


title: XEN-B5_S209_002


title: XEN-B4_S208_001


title: XEN-B3_S207_001


title: XEN-B3_S207_002


title: XEN-B2_S206_001


title: XEN-B2_S206_002


title: XEN-B1_S205_001


title: XEN-B12_S216_001


title: XEN-B12_S216_002


title: XEN-B1_S205_002


title: XEN-B4_S208_002


title: XEN-B11_S215_001


title: XEN-B10_S214_001


title: XEN-B10_S214_002


title: XEN-B7_S211_001


title: XEN-A8_S200_002


title: XEN-A9_S201_001


title: XEN-B8_S212_001


title: XEN-A9_S201_002


title: XEN-A8_S200_001


title: XEN-A7_S199_002


title: XEN-A7_S199_001


title: XEN-B5_S209_001


title: XEN-A6_S198_002


title: XEN-A5_S197_002


title: XEN-A4_S196_002


title: XEN-A4_S196_001


title: XEN-A5_S197_001


title: XEN-A2_S194_001


title: XEN-A2_S194_002


title: XEN-A3_S195_001


title: XEN-B11_S215_002


title: XEN-A10_S202_001


title: XEN-A12_S204_002


title: XEN-A11_S203_001


title: XEN-A10_S202_002


title: XEN-A12_S204_001


title: XEN-A11_S203_002


title: Undetermined_S0_001

value: undetermined


title: TS-H8_S380_002

source_name: TS

value: single cell trophoblast stem cell


title: TS-H7_S379_002


title: TS-H7_S379_001


title: TS-H5_S377_002


title: TS-H5_S377_001


title: TS-H6_S378_002


title: XEN-A1_S193_001


title: XEN-A6_S198_001


title: Undetermined_S0_002


title: TS-H8_S380_001


title: XEN-A1_S193_002


title: TS-H6_S378_001


title: TS-H3_S375_001


title: TS-H2_S374_001


title: TS-H4_S376_001


title: XEN-A3_S195_002


title: TS-H3_S375_002


title: TS-H4_S376_002


title: TS-H1_S373_002


title: TS-H2_S374_002


title: TS-H1_S373_001


title: TS-G5_S365_002


title: TS-G2_S362_002


title: TS-G3_S363_002


title: TS-G6_S366_001


title: TS-G9_S369_001


title: TS-G2_S362_001


title: TS-G12_S372_002


title: TS-G9_S369_002


title: TS-G1_S361_002


title: TS-G7_S367_001


title: TS-G5_S365_001


title: TS-G4_S364_002


title: TS-G8_S368_002


title: TS-G7_S367_002


title: TS-G4_S364_001


title: TS-G6_S366_002


title: TS-G8_S368_001


title: TS-F9_S357_001


title: TS-F9_S357_002


title: TS-G1_S361_001


title: TS-G12_S372_001


title: TS-F8_S356_002


title: TS-G3_S363_001


title: TS-G11_S371_002


title: TS-G11_S371_001


title: TS-G10_S370_002


title: TS-G10_S370_001


title: TS-F7_S355_002


title: TS-F5_S353_001


title: TS-F1_S349_001


title: TS-F2_S350_001


title: TS-F6_S354_001


title: TS-E9_S345_001


title: TS-F10_S358_001


title: TS-F12_S360_001


title: TS-F1_S349_002


title: TS-F6_S354_002


title: TS-F11_S359_001


title: TS-F3_S351_002


title: TS-F12_S360_002


title: TS-E7_S343_001


title: TS-E6_S342_001


title: TS-E4_S340_002


title: TS-F7_S355_001


title: TS-F5_S353_002


title: TS-E6_S342_002


title: TS-E2_S338_001


title: TS-F8_S356_001


title: TS-E2_S338_002


title: TS-E1_S337_001


title: TS-F4_S352_002


title: TS-E3_S339_002


title: TS-F11_S359_002


title: TS-F2_S350_002


title: TS-F4_S352_001


title: TS-E9_S345_002


title: TS-F10_S358_002


title: TS-F3_S351_001


title: TS-E8_S344_002


title: TS-E8_S344_001


title: TS-E5_S341_002


title: TS-E5_S341_001


title: TS-D5_S329_002


title: TS-E3_S339_001


title: TS-E7_S343_002


title: TS-E4_S340_001


title: TS-D3_S327_001


title: TS-D2_S326_001


title: TS-E1_S337_002


title: TS-E12_S348_002


title: TS-E12_S348_001


title: TS-E11_S347_002


title: TS-E11_S347_001


title: TS-E10_S346_002


title: TS-D12_S336_002


title: TS-D9_S333_002


title: TS-D9_S333_001


title: TS-D1_S325_002


title: TS-D12_S336_001


title: TS-D8_S332_002


title: TS-D6_S330_001


title: TS-D7_S331_001


title: TS-D4_S328_001


title: TS-D11_S335_001


title: TS-D3_S327_002


title: TS-D4_S328_002


title: TS-E10_S346_001


title: TS-D8_S332_001


title: TS-C7_S319_002


title: TS-D5_S329_001


title: TS-C9_S321_001


title: TS-D2_S326_002


title: TS-C6_S318_002


title: TS-D6_S330_002


title: TS-D1_S325_001


title: TS-C5_S317_001


title: TS-D10_S334_001


title: TS-C9_S321_002


title: TS-D11_S335_002


title: TS-C8_S320_002


title: TS-C2_S314_001


title: TS-C4_S316_002


title: TS-D7_S331_002


title: TS-D10_S334_002


title: TS-C11_S323_002


title: TS-C4_S316_001


title: TS-C7_S319_001


title: TS-C8_S320_001


title: TS-C2_S314_002


title: TS-C6_S318_001


title: TS-B9_S309_002


title: TS-B9_S309_001


title: TS-C1_S313_002


title: TS-C3_S315_001


title: TS-C1_S313_001


title: TS-C12_S324_001


title: TS-C3_S315_002


title: TS-C11_S323_001


title: TS-B8_S308_001


title: TS-B6_S306_002


title: TS-B6_S306_001


title: TS-C12_S324_002


title: TS-B5_S305_001


title: TS-C10_S322_002


title: TS-C10_S322_001


title: TS-B7_S307_001


title: TS-B3_S303_001


title: TS-C5_S317_002


title: TS-B4_S304_002


title: TS-B2_S302_001


title: TS-B2_S302_002


title: TS-B5_S305_002


title: TS-B8_S308_002


title: TS-B3_S303_002


title: TS-B7_S307_002


title: TS-B1_S301_001


title: TS-B12_S312_001


title: TS-B12_S312_002


title: TS-A9_S297_002


title: TS-B4_S304_001


title: TS-A8_S296_002


title: TS-B11_S311_001


title: TS-B10_S310_002


title: TS-A9_S297_001


title: TS-B10_S310_001


title: TS-B11_S311_002


title: TS-A7_S295_002


title: TS-A8_S296_001


title: TS-A5_S293_002


title: TS-A6_S294_002


title: TS-A7_S295_001


title: TS-A4_S292_002


title: TS-A3_S291_002


title: TS-A3_S291_001


title: TS-A6_S294_001


title: TS-A12_S300_001


title: TS-A1_S289_002


title: TS-A2_S290_001


title: TS-B1_S301_002


title: TS-A11_S299_001


title: TS-A1_S289_001


title: TS-A2_S290_002


title: TS-A12_S300_002


title: TS-A10_S298_001


title: TS-A11_S299_002


title: PrES-H7_S187_002

source_name: PrES

value: single cell PrES


title: TS-A5_S293_001


title: PrES-H6_S186_001


title: PrES-H8_S188_001


title: PrES-H4_S184_001


title: PrES-H6_S186_002


title: PrES-H5_S185_001


title: TS-A4_S292_001


title: PrES-H7_S187_001


title: PrES-H3_S183_001


title: PrES-H3_S183_002


title: PrES-H1_S181_002


title: TS-A10_S298_002


title: PrES-G9_S177_001


title: PrES-G8_S176_001


title: PrES-G9_S177_002


title: PrES-H2_S182_002


title: PrES-G8_S176_002


title: PrES-G7_S175_002


title: PrES-H1_S181_001


title: PrES-G6_S174_001


title: PrES-G7_S175_001


title: PrES-H4_S184_002


title: PrES-G5_S173_001


title: PrES-G6_S174_002


title: PrES-H8_S188_002


title: PrES-G4_S172_001


title: PrES-G5_S173_002


title: PrES-H5_S185_002


title: PrES-G3_S171_001


title: PrES-G2_S170_002


title: PrES-G4_S172_002


title: PrES-G3_S171_002


title: PrES-G2_S170_001


title: PrES-G12_S180_001


title: PrES-G11_S179_001


title: PrES-G12_S180_002


title: PrES-F9_S165_002


title: PrES-F9_S165_001


title: PrES-F8_S164_002


title: PrES-G10_S178_001


title: PrES-G10_S178_002


title: PrES-F6_S162_001


title: PrES-F8_S164_001


title: PrES-F7_S163_001


title: PrES-F7_S163_002


title: PrES-F4_S160_001


title: PrES-F5_S161_001


title: PrES-F5_S161_002


title: PrES-F4_S160_002


title: PrES-F6_S162_002


title: PrES-G1_S169_002


title: PrES-F3_S159_002


title: PrES-F1_S157_002


title: PrES-F2_S158_002


title: PrES-G11_S179_002


title: PrES-F2_S158_001


title: PrES-H2_S182_001


title: PrES-F3_S159_001


title: PrES-G1_S169_001


title: PrES-F11_S167_002


title: PrES-F11_S167_001


title: PrES-F10_S166_001


title: PrES-F12_S168_001


title: PrES-F12_S168_002


title: PrES-E9_S153_002


title: PrES-E8_S152_002


title: PrES-E7_S151_001


title: PrES-E7_S151_002


title: PrES-F1_S157_001


title: PrES-E8_S152_001


title: PrES-E9_S153_001


title: PrES-E5_S149_001


title: PrES-E4_S148_001


title: PrES-E4_S148_002


title: PrES-E6_S150_001


title: PrES-E3_S147_001


title: PrES-E2_S146_001


title: PrES-E2_S146_002


title: PrES-E1_S145_001


title: PrES-E12_S156_001


title: PrES-E5_S149_002


title: PrES-D9_S141_002


title: PrES-E10_S154_002


title: PrES-E11_S155_001


title: PrES-E12_S156_002


title: PrES-F10_S166_002


title: PrES-E11_S155_002


title: PrES-E1_S145_002


title: PrES-D9_S141_001


title: PrES-E10_S154_001


title: PrES-D8_S140_001


title: PrES-E6_S150_002


title: PrES-D8_S140_002


title: PrES-D6_S138_002


title: PrES-D7_S139_001


title: PrES-D4_S136_002


title: PrES-D5_S137_001


title: PrES-D5_S137_002


title: PrES-D6_S138_001


title: PrES-D3_S135_002


title: PrES-D2_S134_002


title: PrES-E3_S147_002


title: PrES-D1_S133_002


title: PrES-D4_S136_001


title: PrES-D2_S134_001


title: PrES-D7_S139_002


title: PrES-D3_S135_001


title: PrES-D12_S144_001


title: PrES-D1_S133_001


title: PrES-D12_S144_002


title: PrES-C6_S126_002


title: PrES-C7_S127_002


title: PrES-C5_S125_002


title: PrES-D11_S143_002


title: PrES-D10_S142_001


title: PrES-C5_S125_001


title: PrES-D11_S143_001


title: PrES-C9_S129_001


title: PrES-D10_S142_002


title: PrES-C9_S129_002


title: PrES-C2_S122_002


title: PrES-C2_S122_001


title: PrES-C7_S127_001


title: PrES-C8_S128_002


title: PrES-C6_S126_001


title: PrES-C4_S124_002


title: PrES-C12_S132_001


title: PrES-C11_S131_001


title: PrES-C3_S123_002


title: PrES-C1_S121_002


title: DNMT1_WT_H4K20me3

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

data_processing:
Library strategy: CUT&RUN
All reads were mapped to mouse genome (mm10) using the Bowtie2 alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters (macs2 callpeak -f BAMPE --keep-dup 1)
Genome_build: mm10

source_name: Dnmt1 KO ES rescued with WT hDNMT1

growth_protocol: ES cells were grown in the DMEM base medium supplemented with 15% of FBS, 1% of antibiotics, 0.1mM of β-mercaptoethanol, 0.1mM of non-essential amino acids, and 1,000 units/ml of leukemia inhibitory factor (LIF).

extract_protocol:
Cells were trypsinized with 0.05% trypsin and pellets were collected for CUT&RUN.
Ten nanograms of the purified CUT&RUN-enriched DNA was used for preparation of multiplexed sequencing libraries with the NEB Ultra II DNA Library Prep Kit per manufacturer's instructions (NEB #E7103). The libraries were sequenced on NextSeq550 system.

treatment_protocol: Cells were grown in regular medium and collected.

tag: antibody

value: Rabbit polyclonal to H4K20me3 (ab9053)

tag: genotype/variation


title: PrES-C1_S121_001


title: PrES-C3_S123_001


title: PrES-C12_S132_002


title: PrES-C8_S128_001


title: PrES-C11_S131_002


title: DNMT1_W796A_H4K20me3

source_name: Dnmt1 KO ES rescued with hDNMT1 W796A

value: W796A DNMT1


title: PrES-B8_S116_002


title: PrES-C10_S130_001


title: P2930_360

description:
full-lenght RNA-seq
P2930.tsv

tag: protocol

value: Glioblastoma

value: EGFR


title: P2930_361

description:
full-lenght RNA-seq
P2930.tsv

tag: cell type


title: P2930_357

description:
full-lenght RNA-seq
P2930.tsv

tag: treatment


title: PrES-C4_S124_001

tag: strain


title: PrES-B9_S117_001


title: siH19-2 3

type: RNA

city: Heidelberg

first: Yiqiao

state: Deutschland

address: Im Neuenheimer Feld 365

country: Germany

institute: Section Surgical Research

description: Gene expression data

hyb_protocol: Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).

label: biotin

organism: Homo sapiens

source_name: MIA-PaCa2 transfected with siH19

label_protocol: Affymetrix protocol

growth_protocol: Cells were cultured in DMEM/high glucose (Sigma, Deisenhoffen, Germany), which was supplemented with 10% FCS (Sigma) and 25mmol/L HEPES (Thermo Fisher, Dreieich, Germany)

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: FlexiTube siRNAs siH19-2, and AllStars Negative Control siRNA (QIAGEN, Hilden, Germany), 20 µg each, were transfected with lipofectamine 2000 (Thermo Fisher Scientific, Dreieich, Germany) according to the instructions of the manufacturer.

tag: pdac cell line

tag: sirna


title: PrES-B9_S117_002


title: NC 3

description: Gene expression data

scan_protocol: Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).

source_name: MIA-PaCa2 transfected with NC

value: NC


title: NC 2

description: Gene expression data

data_processing: Microarray analyses was performed at the Microarray-Analytic Center of the Medical Faculty Mannheim, using Clariom™ D Assays (Thermo Fisher Scientific, Dreieich, Germany).


title: PFC ELS Rep4

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

country: Australia

institute: The University of New South Wales

hyb_protocol: Microarray was performed at UNSW Ramaciotti Centre for Genomics according to manufacturer's protocol for Affymetrix Clariom S Arrays

data_processing: Data import from .CEL files was performed in R using the Bioconductor oligo package and pd.clariom.s.rat. Probe annotation to gene symbols was obtained from Affymetrix (Clariom_S_Rat.na36.rn6.transcript.csv, www.affymetrix.com/Auth/analysis/downloads/na36/xta/Clariom_S_Rat.na36.rn6.transcript.csv.zip).  Microarray data was quantile normalised and log2-transformed using the rma function in the Affy Bioconductor R package.

organism: Rattus norvegicus

source_name: Prefrontal cortex

extract_protocol: Tissue collection was carried out at post-natal day 91. RNA was extracted from 5 male rat PFC tissue samples per group. RNA was extracted using the Qiagen miRNeasy Mini kit with oncolumn DNase digestion using the QIAGEN RNase-Free DNase kit according to the manufacturers protocol.

treatment_protocol: Limited nesting paradigm was performed for ELS rats from post-natal day 2-9

value: Sprague-Dawley

tag: Sex

value: male

tag: tissue

value: prefrontal cortex

tag: age

value: post natal day 91

tag: condition

value: limited nesting


title: siH19-2 2

description: Gene expression data


title: PFC Con Rep5

scan_protocol: Microarray was performed at UNSW Ramaciotti Centre for Genomics according to manufacturer's protocol for Affymetrix Clariom S Arrays

value: control


title: PFC Con Rep3

label_protocol: Microarray was performed at UNSW Ramaciotti Centre for Genomics according to manufacturer's protocol for Affymetrix Clariom S Arrays


title: PFC ELS Rep3


title: siH19-2 1

description: Gene expression data


title: NC 1

description: Gene expression data


title: PFC ELS Rep1


title: PrES-B8_S116_001


title: P2930_362

description:
full-lenght RNA-seq
P2930.tsv


title: PFC Con Rep2


title: extra-cellular RNAs from MEF

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description:
all RNAs below 200 nt
167712_GTTTCGATCCCCCCCC_HVKFJBGXJ_1_20210722B_20210722

data_processing:
base-calling was performed by VBCF sequencing facility
Read 3' end adapter trimming and quality filtering was performed by Cutadapt with the following parameters (-q 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC )
Small RNA seq reads were aligned to the Hg38 or mm10 genome for libraries originating from HeLa and MEF cells, respectively, by using Bowtie2 with the following parameters (-D 15 -R 2 -N 0  -L 10 -i S,1,1.15 )
for tRNA expression and coverage data, trimmed reads were aligned to the collapsed tRNA reference genome using Bowtie2 with the following parameters (--no-unal --no-1mm-upfront -D 15 -R 2 -N 0  -L 10 -i S,1,1.15)
Biotype extraction was performed by featureCounts software by using the following parameters (-a annotation.gtf -M -O  -g 'transcript_type') and the comprehensive gene and tRNA annotation gtf files awailable from Gencode webpage
tRNA coverage data was extracted from sorted BAM files using Samtools with the apropriate parameters (Samtools depth -a)
Genome_build: mm10 and Hg38
Supplementary_files_format_and_content: tsv files containing number of reads mapping to specific tRNA clusters
Supplementary_files_format_and_content: tsv files containing coverage per position information for every tRNA cluster

source_name: MEF

growth_protocol: HeLa cultured in a humidified 5% CO2 incubator at 37°C in standard DMEM supplemented with antibiotic/antimycotics, 2 mM L-glutamine and 10% fetal bovine serum. MEF were cultured in the same medium, additionally supplemented with non-essential amino acids.

extract_protocol:
0.2 mL of cell culture medium conditioned by cells growing in a 6-well dish format (2.5 mL each well total) was collected. were Aliquots were centrifuged for one hour at 16.000x g at 4°C. Total RNA was isolated from 0.2 mL of cell culture medium using TRIzol. Samples were incubated at room temperature for five minutes and extracted with 0.2 mL chloroform, followed by precipitation with isopropanol (over-night) and centrifugation for > 20 minutes at 16.000x g at 4°C. RNA pellets were washed once with 75% ethanol, re-suspended in RNase-free water.
Libraries were prepared according to NEBNext small RNA cloning protocol (E7580S)

treatment_protocol: 70% confluent cells were treated with sodium arsenite (0.75 mM) for one hour, followed by washout and recovery in fresh medium for 24 hours

tag: cell line/type

value: MEF

tag: molecule subtype

value: small RNAs


title: PrES-C10_S130_002

value: not treated


title: P2930_359

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_358

description:
full-lenght RNA-seq
P2930.tsv


title: PFC ELS Rep5


title: P2930_355

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_356

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_354

description:
full-lenght RNA-seq
P2930.tsv


title: PFC Con Rep4


title: P2930_353

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_345

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_351

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Mammary epithelial cells rep2

type: other

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Labeled RNA was hybridized to Agilent custom UCSF miRNA v3.4 multi-species 8x15K Ink-jet arrays (Agilent). Hybridizations were performed for 16 hrs according to the manufacturers protocol (Agilent).

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent).

data_processing: Raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent)

molecule: other

source_name: Mouse Mammary epithelial cells rep2

label_protocol: miRNA was labeled with Cy3-CTP using the miRCURY LNA microRNA power labeling kit (Exiqon, Inc, Woburn, MA), according to manufacturers’ protocol

growth_protocol: To prepare embryonic lung epithelium, noon of the day when a vaginal plug was detected was considered approximately E0.5. Embryos were collected in cold 1 X phosphate buffered saline (PBS). Lungs were dissected out from embryos at the E13.5 stages. Epithelium and mesenchyme were separated as reported previously86.  For adult donor cell preparation, female mice of 10-weeks of age were sacrificed and perfused with PBS. Lungs and mammary glands were harvested, minced and dissociated in buffer [5% fetal bovine serum (FBS), insulin 5 µg/ml, Penicillin-Streptomycin 100 U/ml in DMEM/F12] containing trypsin (2 mg/ml) and collagenase A (2 mg/ml) for 45 minutes and 30 minutes, respectively, at 37ºC. Primary epithelia were purified by differential centrifugation: specifically, lung and mammary epithelia were washed in dissociation buffer without collagenase and collected using a swing-bucket centrifuge at 400 X g. The process was repeated for seven and five times for lung and mammary tissues, respectively. To prepare single cells, primary epithelia from embryonic lung and adult lung and mammary gland were washed in Hank’s (Ca2+ Mg2+ free) buffer and dissociated in 0.05% Trypsin/EDTA buffer. Cells were counted using a Hausser Scientific Hemocytometer and prepared in 50% Matrigel™ (growth factor reduced, BD Biosciences) for transplantation.

extract_protocol: Sample preparation, labeling, and array hybridizations were performed according to standard protocols from the UCSF Shared Microarray Core Facilities and Agilent Technologies. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: mammary

value: epithelial cells


title: P2930_352

description:
full-lenght RNA-seq
P2930.tsv


title: PFC ELS Rep2


title: Mouse Reprogrammed Mammary epithelial cells rep 1

value: reprogrammed mammary


title: P2930_344

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Reprogrammed Mammary epithelial cells rep 4


title: P2930_342

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_349

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Mammary epithelial cells rep4

source_name: Mouse Mammary epithelial cells rep4


title: P2930_350

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Mammary epithelial cells rep1

source_name: Mouse Mammary epithelial cells rep1


title: P2930_348

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Reprogrammed Lung epithelial cells rep 3

value: reprogrammed lung


title: P2930_346

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_347

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Reprogrammed Mammary epithelial cells rep 2


title: P2930_341

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Reprogrammed Lung epithelial cells rep 1


title: Mouse Reprogrammed Lung epithelial cells rep 2


title: P2930_343

description:
full-lenght RNA-seq
P2930.tsv


title: Mouse Lung epithelial cells rep2

source_name: Mouse Lung epithelial cells rep2

value: lung


title: Mouse Lung epithelial cells rep3

source_name: Mouse Lung epithelial cells rep3


title: PFC Con Rep1


title: P2930_339

description:
full-lenght RNA-seq
P2930.tsv

value: Glioblastoma


title: P2930_340

description:
full-lenght RNA-seq
P2930.tsv

value: EGFR


title: P2930_337

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_333

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_332

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_336

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_331

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_329

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_338

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_335

description:
full-lenght RNA-seq
P2930.tsv


title: P2930_327

description:
full-lenght RNA-seq
P2930.tsv