title: U87 scRNA-Seq U87_SC_c11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e7

status: Public on Nov 11 2021

type: SRA

city: Tucson

first: Hongxu

last: Ding

state: AZ

address: The University of Arizona

country: USA

institute: University of Arizona

description: HsMm.csv

library_source: transcriptomic

data_processing:
After demultiplexing, UMIs from the barcode read (8nt) were concatenated onto the 5’ part of corresponding mappable reads using a custom Python script.
The concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --quantMode TranscriptomeSAM so that output alignments are translated into transcript coordinates for downstream analysis, and --clip5pNbases 8 so that the UMI sequences are not mapped. All other options for STAR are set as default.
Specifically, for mix-species experiments, the concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --outFilterMultimapNmax 1 so that only reads that uniquely mapped are considered.
The mapped transcripts per gene and mapped reads per gene were quantified using a custom Python script. When measuring mapped transcripts per gene, we use hamming distance threshold 1, which means only if the hamming distance between two UMIs is greater than 1, then they are considered from different transcripts.
Genome_build: UCSC hg38 for HEK293 RNA-Seq and scRNA-Seq, and U87 scRNA-Seq.
Genome_build: Concatenated UCSC hg38 and mm10 for U87-3T3 cell mixture scRNA-Seq profiles.
Supplementary_files_format_and_content: comma separated file including umi matrix, counts matrix and cross-species matrix.

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Single cell from U87-3T3 cell mixture

extract_protocol:
published scPLATE-Seq protocol
published scPLATE-Seq protocol

tag: cell line

value: U87 and 3T3


title: U87 scRNA-Seq U87_SC_c1

description: umi0.csv, umi1.csv, counts.csv

organism: Homo sapiens

source_name: Single cell from cultured U87 cells


title: U87 scRNA-Seq U87_SC_c10

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_b8

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_b9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e5

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e6

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b5

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_b6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e4

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e11

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_b2

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e1

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b12

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_b11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e8

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b1

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_a9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d7

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_b10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d8

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_a7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d4

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_a8

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d3

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_a5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d5

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_a4

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_a3

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d1

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_a11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e10

description: HsMm.csv


title: U87 scRNA-Seq U87_SC_a2

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_a10

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_a6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2e2

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c7

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h8

description: umi0.csv, umi1.csv, counts.csv

source_name: Single cell from cultured HEK293 cells


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d9

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2d12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c2

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h6

description: umi0.csv, umi1.csv, counts.csv


title: Tumor Cells: Cisplatin_Rep2

city: San Francisco

first: David

last: Simpson

state: California

address: 1550 4th Street

institute: UCSF

data_processing:
Raw reads ( bcl files ) were demultiplex into FASTQs using Illumina’s bcl2fastq software
Samples were trimmed for adaptor sequence and remove for low-quality sequence using Trimmomatic 0.38,  then mapped to mm10 whole genome using  STAR 2.5.1b and counts were computed using the parameter --quantMode and gtf provided from genecode ( vM13)
Sequences were imported into R , scaled, filter for low counts ( < 1 cpm) and  TMM normalized using the edgeR package.
cpm data adjusted with prior.count = 2 prior to log2 transform
Genome_build: mm10
Supplementary_files_format_and_content: single tab delimited file containing normalize log2 (cpm) adjusted with prior.count=2

molecule: total RNA

organism: Mus musculus

source_name: RNA from murine primary tumor organoids

growth_protocol: KrasG12D;p53fl/fl mice were given intranasal Adenoviral Cre which activates LSL-Kras and deletes a floxed p53 allele in lung cells, leading to tumor development in 2-3 months. Lungs were dissociated into single cells, lineage depleted for CD45, CD31, and TER119 and seeded into equal parts Matrigel and 2x SCM (DMEM;F12, 10% FBS, and supplemented with N2 supplement, BPE, 10 ng/mL EGF, 10ng/mL FGF, and antibiotic/antimycotic) and overlayed with 1x SCM to grow into primary tumor spheres.

extract_protocol:
TRIzol extraction according to manufacturers protocol, followed by cleanup and Dnase treatment using the RNeasy kit columns with DNase treatment, also according to manufacturers protocol.
100-150ng RNA was used to create libraries using the Nugen Encore Complete kit (which produces rRNA depleted, strand-specific libraries).

treatment_protocol: On day 4 of growth they were treated with either 10uM Cisplatin or vehicle control (PBS) and total RNA was harvested in Trizol 36 hours later on day 6

tag: tissue

value: murine primary lung tumor organoids

tag: genotype


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c3

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h5

description: umi0.csv, umi1.csv, counts.csv


title: Tumor Cells: Cisplatin_Rep1


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h4

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h3

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_a12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h2

description: umi0.csv, umi1.csv, counts.csv


title: Tumor Cells: Untreated_Rep1


title: Tumor Cells: Untreated_Rep2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c10

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c1

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b9

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h10

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2c12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b8

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2h1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b7

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b5

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g7

description: umi0.csv, umi1.csv, counts.csv


title: mPFC Saline rep3

type: RNA

city: Torino

first: Aurora

last: Savino

state: Piemonte

address: via Nizza, 52

country: Italy

institute: Università di Torino

description:
Saline_rep3
Rat's mPFC after 90min of i.p. LSD administration

hyb_protocol: Biotin labeled cRNA was provided to Research Genetics (Huntsville, AL) for hybridization and analysis with the Affymetrix rat U34A array set.

scan_protocol: Arrays were scanned.

data_processing: The GeneChip ® Analysis software package from Affymetrix was employed by Research Genetics to identify statistically significant changes in gene expression.

label: biotin

organism: Rattus norvegicus

source_name: mPFC Saline

label_protocol: Used BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics; Farmingdale, NY) as per the manufacturer’s instructions.

growth_protocol: Male Sprague-Dawley rats (250-275g) were purchased from Harlan and maintained for at least one week prior to use. Rats were given ad libitum access to food and water and maintained on a 12 h light/dark cycle.

extract_protocol: Total RNA was extracted from the tissue of four animals pooled per treatment group. Pooling of the tissues should help average out differences in individual responses to the drug. RNA isolated from the prefrontal cortex of LSD and saline treated rats was purified using the RNeasy kit from Qiagen (Valencia, CA).

treatment_protocol: (+)-LSD tartrate was obtained from NIDA and dissolved at a concentration of 1.0 mg/ml in sterile water. Four rats were administered 1.0 mg/kg LSD i.p., and four rats were simultaneously administered i.p. saline. After 90 min the animals were decapitated. The brains were removed and the prefrontal cortex, hippocampus and midbrain were quickly dissected, frozen in liquid nitrogen, and stored at –80°C until processing.

tag: strain

value: Sprague-Dawley

tag: Sex

value: male

value: medial prefrontal cortex

tag: treatment

value: Saline


title: mPFC LSD rep2

description:
LSD_rep2
Rat's mPFC after 90min of i.p. Saline administration

source_name: mPFC LSD

value: LSD


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g6

description: umi0.csv, umi1.csv, counts.csv


title: mPFC LSD rep3

description:
LSD_rep3
Rat's mPFC after 90min of i.p. Saline administration


title: mPFC LSD rep1

description:
LSD_rep1
Rat's mPFC after 90min of i.p. Saline administration


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b3

description: HsMm.csv


title: mPFC Saline rep1

description:
Saline_rep1
Rat's mPFC after 90min of i.p. LSD administration


title: mPFC Saline rep2

description:
Saline_rep2
Rat's mPFC after 90min of i.p. LSD administration


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g5

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g8

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b2

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g3

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b11

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b1

description: HsMm.csv


title: 170od

city: Santander

first: Lucio

last: Di Filippo

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Pool of PCR products

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
CRISPResso Analysis of genome editing outcomes.
Either wild-type or integrated donor sequences are used as reference.
Genome_build: NM_145383.2 ; NM_214221.1
Supplementary_files_format_and_content: *_CRISPResso_quantification_of_editing_frequency.txt: CRISPResso quantification of editing frequency.
Supplementary_files_format_and_content: HITI_INDEL.fasta: CRISPRESSO Amplicons Reference.
Supplementary_files_format_and_content: HITI_INDEL_guides.txt: CRISPRESSO sgRNA Reference.

molecule: genomic DNA

organism: Sus scrofa

source_name: retina

extract_protocol:
Genomic DNA was extracted from frozen mouse and pig retina. 150 bp regions flanking the on-target sits of mRho/pRHO gRNAs were amplified by PCR. PCR products were pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: gRNA-treated mouse and pig retina.

value: retina

tag: breed

value: Large White

value: wild type


title: 166os

description: Pool of PCR products


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a9

description: HsMm.csv


title: 5 days post injury of 7-day differentiated myobundles

city: durham

first: Nenad

last: Bursac

address: 101 ciemas dr

institute: Duke University

data_processing:
The Cell Ranger v3 software (10x Genomics) was used to demultiplex cellular barcodes to produce raw 3’ end read profiles for individual cells, and then to perform alignment against hg38 reference genome, filtering, barcode counting, and UMI (unique molecular identifier) counting, producing a feature-barcode matrix per sample. The downstream analysis was performed using R package Seurat (v3.2)
Cells were first filtered to retain those with > 1000 UMIs, <5% mapping to mitochondrial genes, and >200 genes per cell. After standard normalization, variable features were identified using the “vst” method to identify the top 2000 genes. Clustering in Seurat (Louvain) was conducted with resolution 0.5. Cells from two clusters exhibiting both low nFeature_RNA (genes per cell) and nCount_RNA (number of molecules per cell), indicative of dead/dying cells, were filtered out. Differential gene expression between clusters was identified using the “FindMarkers” function with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: RNA-Seq

source_name: dissociated 3D engineered tissue (myobundle)

growth_protocol: 2D growth culture, 3D myobundle differentiation, melittin-injury

extract_protocol:
Single cell suspensions were loaded on the 10x Genomics Chromium Controller Single-Cell Instrument (10x Genomics) using the Chromium Single Cell 3’ Reagent V3 Kit. Cells were mixed with reverse transcription reagents, gel beads, and oil to generate single-cell gel beads in emulsions (GEM) for reverse transcription (RT). After RT, GEMs were broken and the single-stranded cDNA was purified with DynaBeads.
cDNA was amplified by PCR and the cDNA product was purified with the SPRIselect Reagent Kit (Beckman Coulter). Sequencing libraries were constructed using the reagents provided in the Chromium Single-Cell 3′ Library Kit following the user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep). scRNA libraries were sequenced with the DNBseq platform by BGI Genomics.

tag: cell type

value: Cells dissociated from myobundles (4 days growth media, melittin-injured on day 7 of differentiation, samples isolated at 5 days post-injury)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g10

description: umi0.csv, umi1.csv, counts.csv


title: U87 scRNA-Seq U87_SC_a1

description: umi0.csv, umi1.csv, counts.csv


title: 9-day differentiated myobundles

value: Cells dissociated from myobundles (4 days growth media followed by 9 days differentiation media)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2b10

description: HsMm.csv


title: 2D expanded cells

source_name: 2D expanded CD56+ myogenic cells

value: Primary CD56+ human myoblasts expanded for 5 passages with p38 inhibitor (SB203580)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g1

description: umi0.csv, umi1.csv, counts.csv


title: 3-day differentiated myobundles

value: Cells dissociated from myobundles (4 days growth media followed by 3 days differentiation media)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a7

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a6

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f8

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a4

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a3

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2g2

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a2

description: HsMm.csv


title: 2 days post injury of 7-day differentiated myobundles

value: Cells dissociated from myobundles (4 days growth media, melittin-injured on day 7 of differentiation, samples isolated at 2 days post-injury). This sample is age-matched with d9.


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f4

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a12

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a1

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f2

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h9

description: HsMm.csv


title: monocytes_repD

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

institute: Josep Carreras Research Institute (IJC)

description: Non-cultured CD14+ cells from PBMCs of a healthy donor

hyb_protocol: BS-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: iDATs were analyzed using a standard pipeline, with the shinyepico package (1.0.0) of the Bioconductor project

label: Cy5 and Cy3

source_name: Non-cultured CD14⁺ monocytes (replicate D)

label_protocol: Standard Illumina Protocol

growth_protocol: Monocytes were isolated from buffy coats by CD14 positive selection (MACS) and cultured 6 days in Roswell Park Memorial Institute (RPMI) Medium 1640 + GlutaMAX™ containing 10% fetal bovine serum, 100 units/mL penicillin, 100 mg/mL streptomycin

extract_protocol: Total DNA was isolated utilizing Maxwell® RSC Cultured Cells DNA Kit (Promega)

treatment_protocol: At the beginning of the differentiation process, 10ng/mL Granulocyte Macrophage Colony-Stimulating Factor and 10ng/mL Interleukin 4 were added to the cell medium. Moreover, cells were treated with or without Dexamethasone (100nM).

tag: individual

value: donor D

value: MO


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate2 U87_3T3_SC_C1_P2a10

description: HsMm.csv

value: U87 and 3T3


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h7

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h6

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2f12

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siMAFB_repC

description: Tolerogenic Dendritic cells transfected with siRNA against MAFB (ThermoFisher #si19279) and differentiated from monocytes for 6 days (donor C)

source_name: Tolerogenic Dendritic cells transfected with siRNA against MAFB (siMAFB)(donor C)

treatment_protocol: At the beginning of the differentiation process, 10ng/mL human Granulocyte Macrophage Colony-Stimulating Factor, 10ng/mL human Interleukin 4 and 100nM Dexamethasone were added to the cell medium.

value: donor C

value: tolDC

value: siMAFB


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h4

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e6

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siMAFB_repD

description: Tolerogenic Dendritic cells transfected with siRNA against MAFB (ThermoFisher #si19279) and differentiated from monocytes for 6 days (donor D)

source_name: Tolerogenic Dendritic cells transfected with siRNA against MAFB (siMAFB)(donor D)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e5

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siCTL_repA

description: Tolerogenic Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1)  and differentiated from monocytes for 6 days (donor A)

source_name: Tolerogenic Dendritic cells transfected with siRNA control (siCTL) (donor A)

value: donor A

value: siCTL


title: tolerogenic_dendritic_cells_siCTL_repD

description: Tolerogenic Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1)  and differentiated from monocytes for 6 days (donor D)

source_name: Tolerogenic Dendritic cells transfected with siRNA control (siCTL) (donor D)


title: tolerogenic_dendritic_cells_siMAFB_repA

description: Tolerogenic Dendritic cells transfected with siRNA against MAFB (ThermoFisher #si19279) and differentiated from monocytes for 6 days (donor A)

source_name: Tolerogenic Dendritic cells transfected with siRNA against MAFB (siMAFB)(donor A)


title: tolerogenic_dendritic_cells_repC

description: Cells obtained after culturing 6days CD14⁺ cells in RPMI + 10%FBS + GM-CSF (10ng/mL) + IL-4 (10ng/mL) + Dexamethasone (100nM)

source_name: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate C)


title: dendritic_cells_repC

description: Cells obtained after culturing 6days CD14⁺ cells in RPMI + 10%FBS + GM-CSF (10ng/mL) + IL-4 (10ng/mL)

source_name: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate C)

value: DC


title: tolerogenic_dendritic_cells_siMAFB_repB

description: Tolerogenic Dendritic cells transfected with siRNA against MAFB (ThermoFisher #si19279) and differentiated from monocytes for 6 days (donor B)

source_name: Tolerogenic Dendritic cells transfected with siRNA against MAFB (siMAFB)(donor B)

value: donor B


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h5

description: HsMm.csv

source_name: Single cell from U87-3T3 cell mixture


title: tolerogenic_dendritic_cells_siCTL_repC

description: Tolerogenic Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1)  and differentiated from monocytes for 6 days (donor C)

source_name: Tolerogenic Dendritic cells transfected with siRNA control (siCTL) (donor C)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h3

description: HsMm.csv


title: tolerogenic_dendritic_cells_repB

source_name: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate B)


title: tolerogenic_dendritic_cells_repA

source_name: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate A)


title: monocytes_repC

source_name: Non-cultured CD14⁺ monocytes (replicate C)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e3

description: umi0.csv, umi1.csv, counts.csv

source_name: Single cell from cultured HEK293 cells


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e9

description: umi0.csv, umi1.csv, counts.csv


title: monocytes_repA

source_name: Non-cultured CD14⁺ monocytes (replicate A)


title: tolerogenic_dendritic_cells_siCTL_repB

description: Tolerogenic Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1)  and differentiated from monocytes for 6 days (donor B)

source_name: Tolerogenic Dendritic cells transfected with siRNA control (siCTL) (donor B)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e4

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siCTL_repD (RNA-seq)

data_processing:
Sequenced reads were aligned to GRCh38 genome with hisat2 2.1.0 (standard options)
Aligned reads with not proper pair and secondary alignments were filtered out with samtools (samtools view -h -f 0x2 $file | samtools view -h -b -f 0x100 -U $file".filter.bam" > discarded.bam)
Reads were asigned to genes using featureCounts v1.6.4 with options -B -p
Differential expressed genes and VST values for representation were obtained from counts matrix with the R package DESeq2 (version 1.26.0). Ashr was used in the lfcShrink function.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated utilising Maxwell® RSC simplyRNA Cells Kit (Promega)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cultured monocytes were transfected for 6h with siRNAs (100nM) using Lipofectamine 3000 (1.5uL/well in p12).  Then, the medium was changed and cells were cultured in RPMI with 10ng/mL Granulocyte Macrophage Colony-Stimulating Factor and 10ng/mL Interleukin 4. Moreover, cells were treated with or without Dexamethasone (100nM).


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h2

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e8

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siMAFB_repD (RNA-seq)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e11

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1h1

description: HsMm.csv


title: tolerogenic_dendritic_cells_siMAFB_repC (RNA-seq)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e12

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siCTL_repC (RNA-seq)


title: dendritic_cells_siCTL_repD (RNA-seq)

description: Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1) and differentiated from monocytes for 6 days (donor D)

source_name: Dendritic cells transfected with siRNA control (siCTL) (donor D)


title: tolerogenic_dendritic_cells_repD

source_name: Tolerogenic Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4+Dexamethasone (replicate D)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g9

description: HsMm.csv


title: dendritic_cells_repB

source_name: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate B)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e2

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e10

description: umi0.csv, umi1.csv, counts.csv


title: tolerogenic_dendritic_cells_siCTL_repB (RNA-seq)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g8

description: HsMm.csv


title: tolerogenic_dendritic_cells_siCTL_repA (RNA-seq)

source_name: Tolerogenic Dendritic cells transfected with siRNA control (siCTL) (donor A)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g7

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2e1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g6

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d9

description: umi0.csv, umi1.csv, counts.csv


title: dendritic_cells_repA

source_name: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate A)


title: dendritic_cells_siCTL_repA (RNA-seq)

description: Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1) and differentiated from monocytes for 6 days (donor A)

source_name: Dendritic cells transfected with siRNA control (siCTL) (donor A)


title: dendritic_cells_repD

source_name: Dendritic cells differentiated from monocytes 6 days with GM-CSF+IL-4 (replicate D)


title: monocytes_repB

source_name: Non-cultured CD14⁺ monocytes (replicate B)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d7

description: umi0.csv, umi1.csv, counts.csv


title: dendritic_cells_siCTL_repB (RNA-seq)

description: Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1) and differentiated from monocytes for 6 days (donor B)

source_name: Dendritic cells transfected with siRNA control (siCTL) (donor B)


title: tolerogenic_dendritic_cells_siMAFB_repB (RNA-seq)

source_name: Tolerogenic Dendritic cells transfected with siRNA against MAFB (siMAFB)(donor B)


title: tolerogenic_dendritic_cells_siMAFB_repA (RNA-seq)

source_name: Tolerogenic Dendritic cells transfected with siRNA against MAFB (siMAFB)(donor A)


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d6

description: umi0.csv, umi1.csv, counts.csv


title: thp_2

city: Charleston

first: Zhenwu

last: Luo

state: SC

address: 173 Ashley Ave

department: Immunology & Microbiology

institute: Medical University of South Carolina

data_processing:
Trimmomatic (v0.39)42 was used to remove adaptors and trim low-quality bases.
The quality of the processed reads was checked using FastQC before and after preprocessing.
Remove reads containing adaptors; Remove reads containing N > 10% (N represents base that could not be determined); The Qscore (Quality value) of over 50% bases of the read is <= 5.
STAR (v2.7) was performed using the default parameters to build the indexes of the reference genome and align the paired-end clean reads to the reference genome.
Genome_build: GENCODE v38
Supplementary_files_format_and_content: readcount were generated using STAR

source_name: THP-1 cell

growth_protocol: THP-1 cells (5 x 105 cells per well) were seeded in 2 ml RPMI-1640 medium containing 10% FBS (culture medium) onto the 12 well plate.

extract_protocol:
After 24 h culture, total RNA was extracted from the bacteria treated THP-1 cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol, the RNA purity was determined by a Nanodrop 2000 (Thermo Fisher).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The final concentration of 2 ng/ml LPS isolated from B. fungorum, S. marcescens, and P. myrsinacearum were added to each well.

value: myeloid cell line

value: Medium control


title: thp_3


title: dendritic_cells_siCTL_repC (RNA-seq)

description: Dendritic cells transfected with siRNA control (ThermoFisher Silencer Select Negative Control #1) and differentiated from monocytes for 6 days (donor C)

source_name: Dendritic cells transfected with siRNA control (siCTL) (donor C)


title: sm_3

value: S. marcescens LPS


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d8

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g4

description: HsMm.csv

source_name: Single cell from U87-3T3 cell mixture


title: thp_1


title: sm_1


title: sm_2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g5

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g3

description: HsMm.csv


title: pe_2

value: P. myrsinacearum LPS


title: pe_3


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g2

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d5

description: umi0.csv, umi1.csv, counts.csv

source_name: Single cell from cultured HEK293 cells


title: pe_1


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g12

description: HsMm.csv


title: bf_3

value: B. fungorum LPS


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d2

description: umi0.csv, umi1.csv, counts.csv


title: bf_1


title: bf_2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g10

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1g1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f9

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d10

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d11

description: umi0.csv, umi1.csv, counts.csv


title: Control_epidermidis_R6

city: Kiel

first: Lucas

last: Moitinho-Silva

address: Rosalind-Franklin-Straße 12

department: nstitute of Clinical Molecular Biology (IKMB)

country: Germany

institute: University of Kiel

data_processing:
Raw sequences were processed using the nf-core/rnaseq pipeline v3.0, which includes adapter quality trimming with Trim Galore (https://github.com/FelixKrueger/TrimGalore), removal of ribosomal RNA with SortMeRNA, alignment with STAR and transcript quantification with Salmon.
Raw counts were generated by nf-core/rnaseq v.3 pipeline, used STAR alignment and Salmon quantification.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Table with raw gene counts for every gene and every sample.

source_name: Keratinocytes

growth_protocol: Normal human epidermal keratinocytes (NHEKs) (Promocell, Heidelberg, Germany, Lot number 407Z001) were cultured in Keratinocyte Growth Medium (KGM; Lonza Biosciences, Walkersville, USA) + supplements + CaCl2 + penicillin/streptomycin at 37°C and 5% CO2. Cells were used at passages 4-6. Keratinocytes were seeded into 6-well plates and grown until confluency. Staphylococcus epidermidis (ATCC 14990) were cultured in Tryptic Soy Broth (TSB; Thermo Fischer, Waltham, USA) medium at 37°C.

extract_protocol:
Plates were washed twice before RNA isolation using Trizol (Thermo Fischer, Waltham, USA) as per manufacturer’s instruction.
Sequencing libraries were prepared using TruSeq Stranded mRNA kit (Illumina Inc., San Diego, USA). Sequencing was performed on the Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, USA) with 2 x 50 base pairs length.

treatment_protocol: For co-cultivation with keratinocytes, bacteria were centrifuged, resuspended in KGM + CaCl2, and added to the keratinocytes at an optic density (OD) of 0.1 in KGM + CaCl2. Plates were centrifuged at 350 x g for 5 min to allow bacteria to settle on the bottom. After 3 h incubation, plates were washed, and KGM + CaCl2 with gentamycin was added for a further incubation of 23 h at 37°C and 5% CO2.

value: skin

value: Cultured with Staphylococcus epidermidis


title: Control_epidermidis_R5

value: Normal human epidermal keratinocytes (NHEKs)


title: Control_epidermidis_R1


title: Control_Control_R6

value: Untreated


title: Control_epidermidis_R3


title: Control_epidermidis_R2


title: Control_Control_R4


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f7

description: HsMm.csv

value: U87 and 3T3


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d1

description: umi0.csv, umi1.csv, counts.csv


title: Control_Control_R2


title: Control_Control_R5


title: Control_epidermidis_R4


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c9

description: umi0.csv, umi1.csv, counts.csv


title: Control_Control_R1


title: Control_Control_R3


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2d12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f6

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c8

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f8

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f3

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f12

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c6

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c3

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c4

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c2

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f5

description: HsMm.csv


title: siLATS1/2 Wnt3a M01 R2 [M010_siLATS_Wnt3a_2]

city: Basel

first: Gerhard

last: Christofori

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: BSSE_QGF_118943_H7M5KDRXX_1_M010_siLATS1_2_Wnt3a_2_GGTCACGA_GTATTATG_S34_L001_R1

data_processing:
We obtained single-end RNA-seq reads (81-mers) and mapped them to the human genome assembly,  version  hg19  (GRCh37.75),  with  RNA-STAR,  with default parameters except for allowing only unique hits to the genome (outFilterMultimapNmax  =  1)  and  filtering  reads  without  evidence  in  spliced  junction  table (outFilterType = "BySJout"). Expression levels per gene (counts over exons) for the RefSeq mRNA  coordinates  from  UCSC  (genome.ucsc.edu,  downloaded  in  December  2015)  were quantified  using  qCount  function  from  the  Bioconductor  R  package  QuasR  (version  1.12.0).
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text file with gene expression counts

source_name: melanoma cells

growth_protocol: Cells were  cultured  in  RPMI1640  (Sigma) supplemented  with  10%  heat-inactivated  fetal  bovine  serum  (Sigma),  5mM  L-glutamine 407 (Sigma),  1mM  sodium  pyruvate  (Thermo  Fisher  Scientific),  100U  penicillin  and  0.1mg/ml streptomycin  (Sigma).  Cells were  kept  in  a  humidified  incubator  at  37°C  and  5%  CO2.

extract_protocol:
Samples were prepared as technical duplicates and  total  RNA  was  isolated  using  the  miRNeasy  Mini  Kit  (Qiagen)  with  on-column  DNA digestion using RNase-Free  DNase  Set  (Qiagen)  according  to  the  manufacturer’s instructions.
RNA sequencing libraries were prepared from total RNA using poly(A) enrichment using 200 ng input RNA with TruSeq stranded mRNA Sample prep (Illumina). QC was performed on a fragment analyzer using DNF-473-33-SS NGS Fragment 1-6000bp kit (Agilent). Libraries were sequenced with an Illumina NovaSeq 6000 system with Single Read conditions (Read 1: 101/Index 1 : 8/Index 2: 8).

treatment_protocol: M000921  and  M010817  cells  were  reverse  transfected  with  siRNA  targeting  LATS1  (Dharmacon ON-TARGETplus SMARTpool) and LATS2 (Dharmacon ON-TARGETplus SMARTpool) or non-targeting control (Dharmacon ON-TARGETplus). Transfected cells were treated with human TGFb1 (R&D Systems) and/or murine Wnt-3a (Peprotech) for two days starting one day post-transfection.

value: M010817 patient-derived melanoma cell line (RRID:CVCL_S674)

value: Knockdown of LATS1 and LATS2 + Wnt-3a treatment for 2 days

tag: sample group

value: perturbation


title: siCtrl M01 R2 [M010_siCtrl_2]

description: BSSE_QGF_118935_H7M5KDRXX_1_M010_siCtrl_2_TGGCCGGT_TAGAGCGC_S26_L001_R1

value: siCtrl

value: control


title: siLATS1/2 Wnt3a M01 R1 [M010_siLATS_Wnt3a_1]

description: BSSE_QGF_118942_H7M5KDRXX_1_M010_siLATS1_2_Wnt3a_1_AACTGTAG_ACGCCGCA_S33_L001_R1


title: siLATS1/2 TGFb1 M01 R1 [siLATS_TGFb1_1]

description: BSSE_QGF_118938_H7M5KDRXX_1_M010_siLATS1_2_TGFb1_1_TGCGAGAC_CATTGTTG_S29_L001_R1

value: Knockdown of LATS1 and LATS2 + TGFb1 treatment for 2 days


title: siLATS1/2 M01 R2 [siLATS_2]

description: BSSE_QGF_118937_H7M5KDRXX_1_M010_siLATS1_2_2_GACGTCTT_GGTTCACC_S28_L001_R1

value: Knockdown of LATS1 and LATS2 for 2 days


title: siCtrl M01 R1 [M010_siCtrl_1]

description: BSSE_QGF_118934_H7M5KDRXX_1_M010_siCtrl_1_CAATTAAC_CGAGATAT_S25_L001_R1


title: siLATS1/2 M01 R1 [siLATS_1]

description: BSSE_QGF_118936_H7M5KDRXX_1_M010_siLATS1_2_1_AGTACTCC_AACCTGTT_S27_L001_R1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f10

description: HsMm.csv


title: siCtrl Wnt3a M01 R2 [M010_siCtrl_Wnt3a_2]

description: BSSE_QGF_118933_H7M5KDRXX_1_M010_siCtrl_Wnt3a_2_GTCTACAC_GCCAAGGT_S24_L001_R1

value: siCtrl + 2 days Wnt-3a treatment


title: siLATS1/2 TGFb1 Wnt3a M01 R1 [M010_siLATS_TGFb1_Wnt3a_1]

description: BSSE_QGF_118944_H7M5KDRXX_1_M010_siLATS1_2_TGFb1_Wnt3a_1_CTGCTTCC_GATAGATC_S35_L001_R1

value: Knockdown of LATS1 and LATS2 + TGFb1 and Wnt-3a treatment for 2 days


title: siLATS1/2 TGFb1 Wnt3a M01 R2 [M010_siLATS_TGFb1_Wnt3a_2]

description: BSSE_QGF_118945_H7M5KDRXX_1_M010_siLATS1_2_TGFb1_Wnt3a_2_TCATCCTT_AGCGAGCT_S36_L001_R1


title: siLATS1/2 TGFb1 M01 R2 [siLATS_TGFb1_2]

description: BSSE_QGF_118939_H7M5KDRXX_1_M010_siLATS1_2_TGFb1_2_CATAGAGT_TGCCACCA_S30_L001_R1


title: siCtrl Wnt3a M01 R1 [M010_siCtrl_Wnt3a_1]

description: BSSE_QGF_118932_H7M5KDRXX_1_M010_siCtrl_Wnt3a_1_ACTCGTGT_ATTGGAAC_S23_L001_R1


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c12

description: umi0.csv, umi1.csv, counts.csv


title: siCtrl TGFb1 M01 R2 [M010_siCtrl_TGFb1_2]

description: BSSE_QGF_118931_H7M5KDRXX_1_M010_siCtrl_TGFb1_2_ATTGTGAA_TGCATTGC_S22_L001_R1

value: siCtrl + 2 days TGFb1 treatment


title: siCtrl TGFb1 M01 R1 [M010_siCtrl_TGFb1_1]

description: BSSE_QGF_118930_H7M5KDRXX_1_M010_siCtrl_TGFb1_1_GCCACAGG_CATGCCAT_S21_L001_R1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f1

description: HsMm.csv


title: TGFb1 Wnt3a M01 R2 [M010_TGFb1_Wnt3a_2]

description: BSSE_QGF_118941_H7M5KDRXX_1_M010_TGFb1_Wnt3a_2_GTGAATAT_TCTCATTC_S32_L001_R1

value: siCtrl + 2 days TGFb1 and Wnt-3a treatment


title: TGFb1 Wnt3a M01 R1 [M010_TGFb1_Wnt3a_1]

description: BSSE_QGF_118940_H7M5KDRXX_1_M010_TGFb1_Wnt3a_1_ACAGGCGC_CTCTGCCT_S31_L001_R1


title: C15_3

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

country: China

institute: Chinese Academy of Sciences

data_processing:
SOAPnuke v1.4.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.4.0 with parameters -I 15-q 0.2 -n 0.1 and trimmomatic v0.36 with parameters -ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Assembled the transcriptomes using Trinity v2.0.6.
The counted and normalized expression of RNA were calculated using RSEM v1.2.8 with default parameters.
Supplementary_files_format_and_content: text files include FPKM values for each sample.

organism: Netzelia tuberspinifera

source_name: Netzelia tuberspinifera

growth_protocol: The individuals or cells of N. tuberspinifera were cleaned with sterile water, and then inoculated into a cell culture plastics (24 orifices) containing culture medium.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells of  N. tuberspinifera adapted at 35,25 and 15 °C for 24 h.

value: N. tuberspinifera from China

tag: temperature

value: adapted at 15 C for 24 h


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1f2

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c11

description: umi0.csv, umi1.csv, counts.csv


title: Vehicle Control M01 R2 [M010_Vehicle_Control_2]

description: BSSE_QGF_118929_H7M5KDRXX_1_M010_Vehicle_Control_1__CCTTCACC_GACGCTCC_S20_L001_R1

value: Lipofectamin only


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e9

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e8

description: HsMm.csv


title: C15_1


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2c1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e7

description: HsMm.csv


title: B25_3

value: adapted at 25 C for 24 h


title: B25_1


title: siLATS1/2 TGFb1 Wnt3a M0009 R1 [M0009_siLATS_TGFb1_Wnt3a_1]

description: BSSE_QGF_118926_H7M5KDRXX_1_M0009_siLATS1_2_TGFb1_Wnt3a_1_ACACTAAG_ATCCATAT_S17_L001_R1

value: M000921 patient-derived melanoma cell line (RRID:CVCL_S808)


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e6

description: HsMm.csv

value: U87 and 3T3


title: siLATS1/2 Wnt3a M0009 R2 [M0009_siLATS_Wnt3a_2]

description: BSSE_QGF_118925_H7M5KDRXX_1_M0009_siLATS1_2_Wnt3a_2_CCATTCGA_GTTGTCCG_S16_L001_R1


title: B25_2


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b7

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b9

description: umi0.csv, umi1.csv, counts.csv


title: A35_3

value: adapted at 35 C for 24 h


title: siLATS1/2 Wnt3a M0009 R1 [M0009_siLATS_Wnt3a_1]

description: BSSE_QGF_118924_H7M5KDRXX_1_M0009_siLATS1_2_Wnt3a_1_TTGCCTAG_ACCACTTA_S15_L001_R1

value: Knockdown of LATS1 and LATS2 + Wnt-3a treatment for 2 days


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b6

description: umi0.csv, umi1.csv, counts.csv


title: A35_2


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b5

description: umi0.csv, umi1.csv, counts.csv


title: siLATS1/2 TGFb1 Wnt3a M0009 R2 [M0009_siLATS_TGFb1_Wnt3a_2]

description: BSSE_QGF_118927_H7M5KDRXX_1_M0009_siLATS1_2_TGFb1_Wnt3a_2_GTGTCGGA_GCTTGCGC_S18_L001_R1

value: perturbation


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b8

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e5

description: HsMm.csv


title: TGFb1 Wnt3a M0009 R2 [M0009_TGFb1_Wnt3a_2]

description: BSSE_QGF_118923_H7M5KDRXX_1_M0009_TGFb1_Wnt3a_2_TAAGGTCA_TGTCGTAG_S14_L001_R1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e2

description: HsMm.csv


title: TGFb1 Wnt3a M0009 R1 [M0009_TGFb1_Wnt3a_1]

description: BSSE_QGF_118922_H7M5KDRXX_1_M0009_TGFb1_Wnt3a_1_CGGAACTG_CACTACGA_S13_L001_R1


title: A35_1


title: siLATS1/2 TGFb1 M0009 R2 [M0009_siLATS_TGFb1_2]

description: BSSE_QGF_118921_H7M5KDRXX_1_M0009_siLATS1_2_TGFb1_2_AGCTCGCT_GCAGAATC_S12_L001_R1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e3

description: HsMm.csv


title: Vehicle Control M01 R1 [M010_Vehicle_Control_1]

description: BSSE_QGF_118928_H7M5KDRXX_1_M010_Vehicle_Control_1__TTCCTGTT_AGTATCTT_S19_L001_R1

value: M010817 patient-derived melanoma cell line (RRID:CVCL_S674)


title: C15_2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e4

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e11

description: HsMm.csv


title: siLATS1/2 TGFb1 M0009 R1 [M0009_siLATS_TGFb1_1]

description: BSSE_QGF_118920_H7M5KDRXX_1_M0009_siLATS1_2_TGFb1_1_GATCTATC_ATGAGGCT_S11_L001_R1


title: snATACseq_Sox10_Cre_bact_BtR_60dpf_rep_1

city: Los Angeles

first: Gage

last: Crump

state: CA

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

description: To increase the sequencing depth of this library, we sequenced it twice and subjected all the sequence files as input to the cellranger-atac v1.2.0 (10X Genomics) pipeline.

data_processing:
For scRNAseq libraries, Cellranger v3.0.0 (10X Genomics) was used for demultiplexing, alignment, and raw count matrix generation. The alignment was performed against zebrafish genome index (built with GRCz11.fa and GRCz11.98.gtf). For snATACseq libraries, Cellranger ATAC v1.2.0 (10X Genomics) was used for alignment against zebrafish genome index (built with GRCz11.fa, JASPAR2020, and GRCz11.98.gtf), peak calling, and peak-by-cell count matrix generation with default parameters. QC step for the library was performed along with the Cellranger or Cellranger ATAC alignment process.
We performed a second round of peak calling for our snATACseq data using package Snaptools and SnapATAC. We first removed cell debris, low-quality cells, and cell duplicates, by setting cutoffs based on percentage of reads in peaks (> 30 for 60 dpf, > 45 for 210 dpf, and > 50 for the rest) and fragment number within peaks (5,000 – 30,000 for 5 dpf, 1,000 – 11,000 for 14 dpf, and 1,000 – 20,000 for the rest).  To  recover every aligned fragment, we binned the genome into 5 kb sections and constructed the bin-by-cell matrices (bmats) for each library by Snaptools from the positional-sorted bam files generated by cellranger-atac. The cells were filtered, dimensionally reduced by diffusion map, and clustered with inputs of the first 34 dimensions followed the SnapATAC vignette. The specific peaks were called for each cluster by the wrapped MACS2 function in SnapATAC with parameter gsize = 1.5e9, shift = 100, ext = 200, and qval = 5e-2. The finalized and refined peak profile was derived by collapsing and merging all 175 individual peak files to about 450K peaks.
The count matrices of both scRNAseq and snATACseq data were analyzed by R package Seurat and Signac. The count matrices of each sample were aggregated if there is any replicate. For scRNAseq data, the matrices are normalized (NormalizeData) and scaled for the top 2,000 variable genes (FindVariableFeatures and ScaleData). The scaled matrices were dimensional reduced to 50 principal components (60 components for 150 dpf), which then subjected to neighbor finding (FindNeighbors, k = 20) and clustering (FindClusters, resolution = 0.8). The data were visualized through UMAP with 50 principal components as input. For snATACseq data, the matrices are dimensionally reduced 30 latent semantic indices (LSIs) through RunTFIDF and RunSVD functions. The neighbor finding, clustering, and visualization are performed with the second to the thirtieth LSIs as input (algoritm = 3 for FindClusters).
Genome_build: GRCz11
Supplementary_files_format_and_content: Each sample comes with four processed data files: a tab-delimited cell barcode file (tsv), a tab-delimited feature file with genes for scRNAseq or peaks for snATACseq (tsv), a sparse matrix of count table (mtx), and a cluster table (tsv). The previous three files are suffice for creating a single cell count matrix. The cluster table can be further added to recreat the corresponding cluster information as published.

organism: Danio rerio

source_name: Cranial neural crest derived cells

growth_protocol: The Institutional Animal Care and Use Committee of the University of Southern California approved all animal experiments (Protocol 20771). Zebrafish embryos (Danio rerio) were raised in embryo media at 28.5°C. For adults, in the institute vivarium according to Protocol 20771.

extract_protocol:
Dissected heads from converted Sox10:cre; bactin:loxP-eGFP-loxP-DsRed fish were incubated in fresh Ringer’s solution 5-10 min, followed by mechanical and enzymatic dissociation by pipetting every 5 minutes in protease solution (0.25% trypsin (Life Technologies, 15090-046)), 1 mM EDTA, and 400 mg/ml Collagenase D (Sigma, 11088882001 in PBS) and incubated at 28.5°C for 20-30 minutes or until full dissociation. Reaction was stopped by 6X stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS). Cells were pelleted (2000 rpm, 5 minute, 4 °C) and resuspended in suspension media (1% FBS, 0.8 mM CaCl2, 50 U/ml penicillin, and 0.05 mg/ml streptomycin (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)) twice. Final volumes of 500 µl resuspended cells were placed on ice and sorted by fluorescence activated cell sorting (FACS) to isolate live cells that excluded the cytoplasmic stain Zombie green (BioLegend, 423111) or the nuclear stain DAPI. Live cells were sorted into PBS solution containing 0.04% BSA and loaded to 10X Genomics microfluidic chips. The version 2 of Chromium Single Cell 3' Reagent Kits was used for RNA extraction. For snATACseq library construction, we used the same cell dissociation and sorting protocol as for scRNAseq, with isolation of live cells that excluded the cytoplasmic stain Zombie green (product information). Nuclei isolation was performed per manufacturer’s instructions (10X Genomic, protocol CG000169). Cells were incubated with lysis buffer on ice for 90 second, followed by integrity check of nuclei under fluorescence microscope with DAPI before library synthesis.
For scRNAseq, the cell lysis, polyA pull down, tagging with cell barcode, and RNA:DNA hybrid synthesis were performed in the GEMs per manufacturer's instruction. GEMs containing barcoded single-cell cDNA  were lysis for further fragmentation and ligation of illumina P5 and P7 ends. Libraries were sequenced to depths of at least 1,000,000 reads per cell for each library. For snATACseq, the open chromatins of the isolated nuclei were targeted and tagged by transposase, barcoded and ligated with Illumina P5 sequence in the individually-encapsulated GEMs per manufacturer's instruction. Barcoded single-nucleus genomic DNA were released from GEMs and pulled down for further ligation of library-specific index and Illumina P7 sequence. Libraries were sequenced to depths of at least 75,000 read pairs per nucleus for each library.

value: Cranial neural crest derived cells

tag: developmental stage

value: 60 dpf

tag: facs markers

value: Zombie- / dsRed+


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b2

description: umi0.csv, umi1.csv, counts.csv


title: snATACseq_Sox10_Cre_bact_BtR_210dpf_rep_1

value: 210 dpf


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b4

description: umi0.csv, umi1.csv, counts.csv


title: siLATS1/2 M0009 R2 [M0009_siLATS_2]

description: BSSE_QGF_118919_H7M5KDRXX_1_M0009_siLATS1_2_2_CATAATAC_TTCTAACG_S10_L001_R1

value: Knockdown of LATS1 and LATS2 for 2 days


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b12

description: umi0.csv, umi1.csv, counts.csv


title: snATACseq_Sox10_Cre_bact_BtR_14dpf_rep_2

value: 14 dpf


title: siLATS1/2 M0009 R1 [M0009_siLATS_1]

description: BSSE_QGF_118918_H7M5KDRXX_1_M0009_siLATS1_2_1_TGCGGCGT_CCTCGGTA_S9_L001_R1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d9

description: HsMm.csv


title: snATACseq_Sox10_Cre_bact_BtR_14dpf_rep_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e1

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e12

description: HsMm.csv


title: snATACseq_Sox10_Cre_bact_BtR_3dpf_rep_2

value: 3 dpf


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b10

description: umi0.csv, umi1.csv, counts.csv


title: snATACseq_Sox10_Cre_bact_BtR_5dpf_rep_1

value: 5 dpf


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d8

description: HsMm.csv


title: siCtrl M0009 R1 [M0009_siCtrl_1]

description: BSSE_QGF_118916_H7M5KDRXX_1_M0009_siCtrl_1_AGGCAGAG_AGAATGCC_S7_L001_R1

value: siCtrl

value: control


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2b1

description: umi0.csv, umi1.csv, counts.csv


title: siCtrl Wnt3a M0009 R2 [M0009_siCtrl_Wnt3a_2]

description: BSSE_QGF_118915_H7M5KDRXX_1_M0009_siCtrl_Wnt3a_2_TGGTGGCA_TCCTGTAA_S6_L001_R1

value: siCtrl + 2 days Wnt-3a treatment


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1e10

description: HsMm.csv


title: siCtrl M0009 R2 [M0009_siCtrl_2]

description: BSSE_QGF_118917_H7M5KDRXX_1_M0009_siCtrl_2_GAATGAGA_GAGGCATT_S8_L001_R1

value: M000921 patient-derived melanoma cell line (RRID:CVCL_S808)


title: siCtrl Wnt3a M0009 R1 [M0009_siCtrl_Wnt3a_1]

description: BSSE_QGF_118914_H7M5KDRXX_1_M0009_siCtrl_Wnt3a_1_CAACAATG_CTTCACGG_S5_L001_R1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d6

description: HsMm.csv

value: U87 and 3T3


title: siCtrl TGFb1 M0009 R2 [M0009_siCtrl_TGFb1_2]

description: BSSE_QGF_118913_H7M5KDRXX_1_M0009_siCtrl_TGFb1_2_GGTGAACC_GCGTTGGA_S4_L001_R1

value: siCtrl + 2 days TGFb1 treatment


title: snATACseq_Sox10_Cre_bact_BtR_2dpf_rep_2

value: 2 dpf


title: snATACseq_Sox10_Cre_bact_BtR_2dpf_rep_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d5

description: HsMm.csv


title: snATACseq_Sox10_Cre_bact_BtR_3dpf_rep_1


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d4

description: HsMm.csv


title: siCtrl TGFb1 M0009 R1 [M0009_siCtrl_TGFb1_1]

description: BSSE_QGF_118912_H7M5KDRXX_1_M0009_siCtrl_TGFb1_1_AACAGGTT_ATACCAAG_S3_L001_R1

value: perturbation


title: Vehicle Control M0009 R2 [M0009_Vehicle_Control_2]

description: BSSE_QGF_118911_H7M5KDRXX_1_M0009_Vehicle_Control_1__GCGCTCTA_GCTCCGAC_S2_L001_R1

value: Lipofectamin only


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d3

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a5

description: umi0.csv, umi1.csv, counts.csv


title: snATACseq_Sox10_Cre_bact_BtR_1.5dpf_rep_1

value: Cranial neural crest derived cells

value: 1.5 dpf


title: Vehicle Control M0009 R1 [M0009_Vehicle_Control_1]

description: BSSE_QGF_118910_H7M5KDRXX_1_M0009_Vehicle_Control_1__ATATCTCG_ATCTTAGT_S1_L001_R1


title: scRNAseq_Sox10_Cre_bact_BtR_150dpf_rep_1

value: 150 dpf

value: Zombie- / dsRed+


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d2

description: HsMm.csv


title: scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_2

value: 60 dpf


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d12

description: HsMm.csv


title: Synovial tissue - none

city: Schlieren

first: Caroline

last: Ospelt

address: Wagistrasse 14

department: Department of Rheumatology

institute: University Hospital Zurich

data_processing:
Raw sequencing data was processed with cellranger count (v6.0.0, 10x Genomics) with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx

source_name: Synovial tissue

extract_protocol:
Synovial biopsies were mechanically minced and enzymatically digested with 100 ug/ml Liberase TL and 100 ug/ml DNAseI in pre-warmed RPMI 1640 containing 2 mM glutamine and 25 mM HEPES  for 30 min at 37°C. The digestion was stopped by adding 20 v/v % with RPMI containing 20% FCS and the dissociated tissue was filtered through a 40 um cell strainer. Red blood cells were lysed with RBC lysis buffer. Cell viability was analysed with a LUNA-FL dual fluorescence cell counter.
cDNA libraries were prepared for sequencing following the 10x Genomics protocol (Chromium Single Cell 3ʹ Reagent Kits (v3 chemistry)


title: Synovial tissue - GCs

value: glucocorticoids


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a3

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a2

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a8

description: umi0.csv, umi1.csv, counts.csv


title: scRNAseq_Sox10_Cre_bact_BtR_14dpf_rep_ceratohyal

description: This dataset was used to identify the non gill derivatives.

value: 14 dpf


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a12

description: umi0.csv, umi1.csv, counts.csv


title: scRNAseq_Sox10_Cre_bact_BtR_60dpf_rep_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d10

description: HsMm.csv


title: scRNAseq_Sox10_Cre_bact_BtR_14dpf_rep_2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1d1

description: HsMm.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a10

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate2 HEK293_SC_P2a1

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c9

description: HsMm.csv


title: scRNAseq_Sox10_Cre_bact_BtR_14dpf_rep_1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c8

description: HsMm.csv


title: scRNAseq_Sox10_Cre_bact_BtR_5dpf_rep_1

value: 5 dpf


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h8

description: umi0.csv, umi1.csv, counts.csv


title: scRNAseq_Sox10_Cre_bact_BtR_3dpf_rep_2

value: 3 dpf


title: BCN-scRNA

city: Shanghai

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

description: paracancerous tissue from BC4

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: paracancerous tissue

extract_protocol:
Tumor tissues were ressected by transurethral resection and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: Male

tag: age

tag: tumor stage


title: scRNAseq_Sox10_Cre_bact_BtR_5dpf_rep_2


title: scRNAseq_Sox10_Cre_bact_BtR_3dpf_rep_3


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c6

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c5

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c4

description: HsMm.csv


title: scRNAseq_Sox10_Cre_bact_BtR_2dpf_rep_1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c3

description: HsMm.csv


title: kah_delZnf_3

city: Gothenburg

first: Ruth

last: Palmer

address: Medicinaregatan 9A, Shalgrenska Academy

department: Medical Biochemistry & Cell Biology

country: Sweden

institute: Gothenburg University

description: mutant

data_processing:
mapping: hisat2, v2.0.5, --dta --phred33
quantification: FeatureCounts, v1.5.0-p3, Default
Differential Analysis: DESeq2, v1.20.0, padj<=0.05
Genome_build: ensembl_drosophila_melanogaster_bdgp6_gca_000001215_4
Supplementary_files_format_and_content: Excel, FPKM & log2FC

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Drosophila melanogaster strains were maintained on a standard fly food.

extract_protocol:
Embryos were collected at 25°C (5-16 h after egg laying) and dechorionated in 2% sodium hypochlorite  solution for 4 min. After subsequent washing with embryo wash (0.8% NaCl and 0.05% Triton X-100) and H20, embryos were stored at -80°C. Once embryo collection for 3 biological replicates per genotype was obtained, RNA-extraction was carried out according to the manufacturer’s protocol (Promega ReliaPrepTM RNA Tissue Miniprep System, REF-Z6111). Total RNA was measured using NanoDrop OneC (Thermo Scientific) for its concentration and RNA-integrity was checked on the gel electrophoresis. 9-15 µg of total RNA/biological replicate was shipped to Novogene Co. Ltd (UK) for sequencing.
cDNA

value: Embryo

value: 5-16 hour

tag: group

value: Mutant

value: kah-deltaznf


title: kah_delZnf_2

description: mutant


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c2

description: HsMm.csv

value: U87 and 3T3


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h4

description: umi0.csv, umi1.csv, counts.csv


title: kah_delZnf_1

description: mutant


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c12

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h3

description: umi0.csv, umi1.csv, counts.csv


title: kah_delATG_3

description: mutant

value: kah-deltaATG


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h9

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h2

description: umi0.csv, umi1.csv, counts.csv


title: kah_delATG_1

description: mutant


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c10

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b9

description: HsMm.csv


title: w1118_3

description: Wild type

value: Control

value: Wild type


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h10

description: umi0.csv, umi1.csv, counts.csv


title: w1118_2

description: Wild type


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1c1

description: HsMm.csv


title: w1118_1

description: Wild type


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b7

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1h1

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g9

description: umi0.csv, umi1.csv, counts.csv


title: MyoD-f-f-cre_RNAseq_Rep3

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

data_processing:
RNA-seq reads were aligned to the mm9 genome with TopHat (v2.1.0) using default settings. Duplicates were removed, and aligned reads were calculated for each protein-coding gene using HTSeq, followed by FPKM transformation by normalizing gene exon length and sequencing depth.
ChIP-Seq reads were mapped to mm9  genome with Bowtie2. Aligned reads were filtered for a minimum MAPQ of 20, and duplicates were removed using SAMtools. Signal tracks and peaks were generated by using the –SPMR option in MACS2. Then, the UCSC Genome Browser utility bedGraphToBigWig was used with default parameters to transform the bedgraph files to bigwig files.
ChIA-PET2 was used to trim the bridge linkers of BL-Hi-C data and HiC-Pro to align reads, filter artifact fragments, and remove duplicates; Juicer was applied to the resulting uniquely mapped contacts to generate individual or merged Hi-C files that could be deposited as contact matrices with multiple resolutions.
Loops were called by HiCCUPS at 3kb, 5 kb and 10 kb resolutions with modified parameters for pooled Hi-C matrices of each  condition.
Genome_build: mm9
Supplementary_files_format_and_content: .hic files were genrated by Juicer which compress Hi-C matrix under mutiscale resolutions;.h5 files were generated by HiCExplorer which can be visualized by  pyGenomeTracks;.bedpe files were loops called by HiCCUPS;.bigwig files were generated using MACS2;.excel  file includes gene count for each sample

source_name: RNA-Seq of MyoD-KO differentiating myocytes at 24h

extract_protocol:
Primary myoblasts were isolated from the hindlimb skeletal muscle of WT and KO mice at 2~3 weeks, minced and digested in a mixture of type II collagenase and Dispase B (Roche Applied Science). Cells were filtered from debris, centrifuged and cultured in growth medium (F-10 Ham’s medium supplemented with 20% FBS, 10 ng/ml basic fibroblast growth factor, 1% penicillin– streptomycin and 1% glutamine) on collagen-coated cell culture plates at 37 °C in 5% CO2. At 60-70% confluence, cells can be switched to differentiation medium (DMEM with 2% horse serum). Primary myoblasts were isolated from the hindlimb skeletal muscle of floxed MyoD mice at 2~3 weeks, minced and digested in a mixture of type II collagenase and Dispase B (Roche Applied Science). Cells were filtered from debris, centrifuged and cultured in growth medium (F-10 Ham’s medium supplemented with 20% FBS, 10 ng/ml basic fibroblast growth factor, 1% penicillin– streptomycin and 1% glutamine) on collagen-coated cell culture plates at 37 °C in 5% CO2. Cells were transfected Ad-ctrl and Ad-Cre, after 48 h, sorting  for GFP positive cells. Then, seed cells in plate, at 60-70% confluence, cells can be switched to differentiation medium (DMEM with 2% horse serum).
Hi-C were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). Briefly, cells were cross-linked with formaldehyde and nucleuses were isolated by lysis buffers. The chromain was then randomly fragmented by 4-bp enzymes (HaeIII) and then two proximal fragments were connected by 20 bp biotinylated bridge linker in nucleus. A whole genome chromatin was extracted and sheared into 400 bp. Then the biotinylated junctions were captured by M-280 streptavidin magnetic beads. After amplification, the DNA were ready for library construction. RNA for RNA-seq was harvested using Trizol reagent.
Hi-C libaries were performed on 0.5 million cells per sample according to the BL-Hi-C protocol (PMID: 29158486). RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: passage

value: Differentiating myocytes for 24h

value: skeletal muscle

value: MyoD-KO


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b6

description: HsMm.csv

tag: cell line


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g8

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b5

description: HsMm.csv


title: MyoD-f-f-cre_RNAseq_Rep1

tag: tissue


title: MyoD-f-f-NC_RNAseq_Rep3

source_name: RNA-Seq of MyoD-flox/flox differentiating myocytes at 24h

tag: genotype

value: MyoD-flox/flox


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b4

description: HsMm.csv


title: MyoD-f-f-cre_RNAseq_Rep2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g6

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g7

description: umi0.csv, umi1.csv, counts.csv


title: MyoD-f-f-NC_RNAseq_Rep2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g5

description: umi0.csv, umi1.csv, counts.csv


title: kah_delATG_2

description: mutant


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b2

description: HsMm.csv


title: MyoD-f-f-NC_RNAseq_Rep1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g4

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b12

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b8

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 11.2

city: Oslo

first: Kari

last: Guderud

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

data_processing:
Primary base calling and quality scoring was performed using BSMAP v.2.90 (-p4, -D C-CGG, -v2, -n1, -q28)
getting methylation ratios in methratio.py with samtools
Getting CGs: grep -c "CG" sorted_*.txt
Methratio format to RnBeads format were transformed with a custom R-script
Call methylation differences: RnBeads v.1.10.8  No SNPs, cov treshold=10, min.group.size=5, no sex chromosomes)
Genome_build: hg19
Supplementary_files_format_and_content: .bed file, ready for RnBeads analysis

source_name: CD4+ naïve t cell

extract_protocol:
RNA/DNA/Protein Purification Kit (Norgen Biotek Corp)
Diagenode RRBS, In house mRRBS

tag: library prep kit

value: Diagenode mRRBS

tag: disease state

value: Newly diagnosed Rheumatoid Arthritis

tag: replicate

tag: molecule

value: MSP1 fragmented DNA


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b11

description: HsMm.csv

data_processing:
After demultiplexing, UMIs from the barcode read (8nt) were concatenated onto the 5’ part of corresponding mappable reads using a custom Python script.
The concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --quantMode TranscriptomeSAM so that output alignments are translated into transcript coordinates for downstream analysis, and --clip5pNbases 8 so that the UMI sequences are not mapped. All other options for STAR are set as default.
Specifically, for mix-species experiments, the concatenated mappable reads were aligned and mapped using the STAR 2.5.1a with option --outFilterMultimapNmax 1 so that only reads that uniquely mapped are considered.
The mapped transcripts per gene and mapped reads per gene were quantified using a custom Python script. When measuring mapped transcripts per gene, we use hamming distance threshold 1, which means only if the hamming distance between two UMIs is greater than 1, then they are considered from different transcripts.
Genome_build: UCSC hg38 for HEK293 RNA-Seq and scRNA-Seq, and U87 scRNA-Seq.
Genome_build: Concatenated UCSC hg38 and mm10 for U87-3T3 cell mixture scRNA-Seq profiles.
Supplementary_files_format_and_content: comma separated file including umi matrix, counts matrix and cross-species matrix.

extract_protocol:
published scPLATE-Seq protocol
published scPLATE-Seq protocol


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 11.1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b10

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 10.2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g2

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g12

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b1

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 10.1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a9

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 9.2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g10

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a8

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 9.1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1b3

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g1

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a6

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f8

description: umi0.csv, umi1.csv, counts.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 8.1


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a5

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 7.1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f6

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a4

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 5.2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f7

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f5

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a2

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 5.1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f4

description: umi0.csv, umi1.csv, counts.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 3.2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a12

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1g11

description: umi0.csv, umi1.csv, counts.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 3.1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f3

description: umi0.csv, umi1.csv, counts.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 2.2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a7

description: HsMm.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a10

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 2.1


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 7.2


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a1

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 1.2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f10

description: umi0.csv, umi1.csv, counts.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4nai 1.1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f1

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f12

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e9

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a3

description: HsMm.csv


title: Newly diagnosed Rheumatoid Arthritis patient CD4mem 7.2

source_name: CD4+ memory t cell


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e7

description: umi0.csv, umi1.csv, counts.csv


title: U87-3T3 scRNA-Seq with 15xSMRT, 12xNextera and SPRI Plate1 U87_3T3_SC_C1_P1a11

description: HsMm.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1f2

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e6

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e5

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e8

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e3

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e2

description: umi0.csv, umi1.csv, counts.csv


title: KP_Cis_rep3

description: Biological replicate_control

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.Normalized log10 ratio (Cy5/Cy3) representing test/reference were imported into R. The Limma package in R was used for background correction using the normexp method and parameter estimation method set to mle and normalization was completed with two steps, first using limma normalizeWithinArrays with loess method follow by limma normalizeBetweenArrays with Aquantile method.

source_name: RNA from dissected tumors

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).

growth_protocol: KrasG12D;p53fl/fl mice were given intranasal Adenoviral Cre which activates LSL-Kras and deletes a floxed p53 allele in lung cells, leading to tumor development in 2-3 months.

extract_protocol: Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol and including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.

treatment_protocol: Mice were treated with 7mg/kg Cisplatin or vehicle control (PBS) once a week for three weeks before tumors were dissected from lungs.

source_name: Universal Mouse Reference (UMR) from Stratagene

tag: sample type

value: pooled mouse reference


title: KP_Cis_rep4

description: Biological replicate_control


title: KP_Cis_rep5

description: Biological replicate_control


title: Human jejunum – Reperfusion 120 min 6

city: Maastricht

first: Marco

last: Manca

state: Limburg

address: P. Debyelaan 25

department: CARIM

country: Netherlands

institute: University of Maastricht

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised robust spline normalization in lumi (BioConductor, R)

source_name: Human jejunum – Reperfusion 120min

label_protocol: Per sample, 200 ng RNA was used for anti-sense RNA synthesis, amplification, purification, and labelling with the Illumina TotalPrep 96 RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) according to the manufacturer's protocol

extract_protocol: RNA was isolated from snap-frozen tissue samples using AllPrep DNA/RNA/Protein kit (Qiagen, Hilden, Germany). Disruption and homogenization of the tissue was performed using an Ultra Turrax Homogenizer (IKA Labortechnik, Staufen, Germany) in lysis buffer containing β-mercaptoethanol (Promega, Madison, WI). RNeasy spin columns were used to bind RNA. Columns were washed and RNA was eluted in RNase-free water. RNA samples were treated with DNAse (Promega) to ensure removal of contaminating genomic DNA.

tag: treatment

value: 45-60 min ischaemia 120 min reperfusion

tag: patient

value: jejunum


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e12

city: Tucson

first: Hongxu

last: Ding

address: The University of Arizona

institute: University of Arizona

description: umi0.csv, umi1.csv, counts.csv


title: KP_Cis_rep1

city: San Francisco

first: David

last: Simpson

address: 1550 4th Street

institute: UCSF

description: Biological replicate_control


title: KP_Cis_rep2

description: Biological replicate_control


title: Human jejunum – Reperfusion 120 min 1


title: Human jejunum – Reperfusion 120 min 7


title: MyoD-f_f-cre_BL-HiC_Rep4

description:
processed data file:
MyoD-f-f-cre.hic
MyoD-f-f-cre_5k.h5
MyoD-f-f-NC_loops.bedpe

source_name: BL-Hi-C of MyoD-KO differentiating myocytes at 24h

tag: cell type


title: Human jejunum – Reperfusion 120 min 5


title: Human jejunum – Reperfusion 30 min 7

source_name: Human jejunum – Reperfusion 30min

value: 45-60 min ischaemia 30 min reperfusion


title: Human jejunum – Reperfusion 120 min 3


title: KP_PBS_rep5

description: Biological replicate_control


title: Human jejunum – Reperfusion 30 min 6


title: MyoD-f_f-cre_BL-HiC_Rep3


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e11

description: umi0.csv, umi1.csv, counts.csv

source_name: Single cell from cultured HEK293 cells


title: Human jejunum – Reperfusion 30 min 4


title: KP_PBS_rep1

description: Biological replicate_control


title: KP_PBS_rep4

description: Biological replicate_control


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e4

description: umi0.csv, umi1.csv, counts.csv


title: Human jejunum – Reperfusion 120 min 2


title: Human jejunum – Reperfusion 120 min 4


title: MyoD-f_f-cre_BL-HiC_Rep2


title: KP_PBS_rep3

description: Biological replicate_control


title: KP_PBS_rep2

description: Biological replicate_control


title: MyoD-f_f-cre_BL-HiC_Rep1


title: MyoD-f_f-NC_BL-HiC_Rep4

description:
processed data file:
MyoD-f-f-NC.hic
MyoD-f-f-NC_5k.h5
MyoD-f-f-NC_loops.bedpe

source_name: BL-Hi-C of MyoD-flox/flox differentiating myocytes at 24h


title: Human jejunum – Reperfusion 30 min 3


title: Human jejunum – Reperfusion 30 min 2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d7

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e10

description: umi0.csv, umi1.csv, counts.csv


title: MyoD-f_f-NC_BL-HiC_Rep2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d4

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d2

description: umi0.csv, umi1.csv, counts.csv


title: Human jejunum – Ischaemia 6

source_name: Human jejunum – Ischaemia

value: 45-60 min ischaemia


title: SH26-1259-Resist

city: New York

first: Han

last: Han

address: 550 First Avenue

institute: NYU Langone Medical Health

data_processing:
STAR analysis for alignment
RSEM analysis for the level of expression
Genome_build: mm10
Supplementary_files_format_and_content: Count and TPM

source_name: Lung Tumor Nodules

extract_protocol:
Lung tumor nodules were snap frozen and RNAs were extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Long term treatment with vehicle, monocertinib (TAK-788), T-DM1 and the combination.

tag: strain

value: Lung Tumor Nodules

value: HER2 Exon20YVMA

value: Acquired resistance to mobocertinib monotherapy


title: SH26-1291-Resist


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d12

description: umi0.csv, umi1.csv, counts.csv


title: Human jejunum – Ischaemia 7


title: Human jejunum – Reperfusion 30 min 5


title: Human jejunum – Ischaemia 5


title: MyoD-f_f-NC_BL-HiC_Rep1


title: Human jejunum – Ischaemia 2


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d11

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1e1

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d9

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1226-Combo

value: Treated with combination


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d8

description: umi0.csv, umi1.csv, counts.csv


title: MyoD-f_f-NC_BL-HiC_Rep3


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d6

description: umi0.csv, umi1.csv, counts.csv


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d10

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1182-Combo


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d5

description: umi0.csv, umi1.csv, counts.csv


title: Human jejunum – control 5

source_name: Human jejunum – control

value: Control


title: SH26-1127-TDM1

value: Treated with T-DM1


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d3

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1275-Resist


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c7

description: umi0.csv, umi1.csv, counts.csv


title: BC7-scRNA

source_name: bladder cancer

tag: subject status

value: patient with bladder cancer

tag: Sex

value: Male

value: pTa


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c6

description: umi0.csv, umi1.csv, counts.csv


title: SH26-1270-TAK

value: Treated with mobocertinib (TAK-788)


title: Human jejunum – Ischaemia 3


title: leaf, S3

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

data_processing:
Bcl2fastq Conversion software (v2.20) was used for basecalling.
The raw data was trimmed with strict standards as followsd:(1) Trimmed Reads with adapter seq;(2) Trimmed low quality bases(Reads would be discarded if percent of N base is greater than 10% or percent of low quality bases is greater than 50%).
We mapped the clean data against the reference genome of Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/). HISAT2 (https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download) is used as an alignment software for RNA-seq. Based on mapped data, we carried out library insert size check, sequencing randomness check, gene expression quantification analysis, alternative splicing analysis, novel genes detection and genes structure optimization.
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Differential expression analysis of two sample groups was performed using the DEseq2. Fold Change(FC)≥2 and FDR<0.01 were used as the screening criteria to identify differentially expressed genes.
Genome_build: Darmor-bzh (http://www.genoscope.cns.fr/brassicanapus/data/)
Supplementary_files_format_and_content: Tab-delimited text files include count number and fragments per kilobase of transcript per million fragments mapped (FPKM) values for each sample.

organism: Brassica napus

source_name: leaf

growth_protocol: The plants of different lines of  the BC1F3 generation of 'White Flower' x 'Zhongshuang11' were cultivated in a greenhouse.

extract_protocol:
The leaf samples were collected and put into liquid nitrogen. Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA). The total RNA quantity and purity were analyed by using of Bioanalyzer 2100 (Agilent, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, the cDNA libraries were sequenced on Illumina Novaseq6000 platform with flow cell type PE150, generating high-quality raw data in FASTQ format. Raw data for each sequencing sample included two FASTQ files contain all cDNA fragments were measured at both ends of reads.
RNA-seq. Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, the cDNA libraries were sequenced on Illumina Novaseq6000 platform with flow cell type PE150. Raw Data for each sequencing sample included two FASTQ files contain all cDNA fragments were measured at both ends of reads.

treatment_protocol: The seedlings growing in the greenhouse were inoculated with powdery mildew. The symptom on each individual seedling were observed to determine the resistant and susceptible plants in the segregating population.

value: leaf

tag: inoculation

value: powdery mildew

tag: development stage

value: ten-days after inoculation

tag: phenotype

value: susceptible


title: Human jejunum – control 7

value: jejunum


title: SH26-1239-Combo


title: Human jejunum – control 1


title: Human jejunum – Ischaemia 1


title: BC6-scRNA

tag: age

tag: tumor stage


title: Human jejunum – control 3

tag: tissue


title: Human jejunum – control 6


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1d1

description: umi0.csv, umi1.csv, counts.csv

tag: cell line


title: Human jejunum – Ischaemia 4


title: Human jejunum – control 4


title: HEK293 scRNA-Seq Plate1 HEK293_SC_P1c3

description: umi0.csv, umi1.csv, counts.csv