title: Strand-specific RNA-seq in siH2A.Z2 treated cells- Replicate #2 [WI38]

description:
si-Z2-n2
Transfected with siRNA against H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z2vsCtrl.csv

source_name: Total RNA (ribosomal RNA depleted) from siH2A.Z2-treated proliferative WI38 hTERT RAF1-ER cells


title: H2A.Z1 ChIP-seq in U2OS Flag-Z1 cells - Replicate #1

status: Public on Feb 27 2020

type: SRA

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

library_source: genomic

data_processing:
ChIP-sequencing in U2OS cells were performed single-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (Heidelberg) with at least 400 millions reads for the 4 samples in multiplex. Drosophila Spike-in (Active Motif) was added in each ChIP-seq experiment. Alignment on a combined Drosophila dm6 and human hg38 genome was performed with BWA version 2.5.2b. Aligned data were processed with samtools: reads were selected, counted and PCR duplicates were removed. The coverage was then computed with the GenomicAlignments Bioconductor R package. For each sample, normalization was performed on BigWig file by multiplying the coverage for each base by the factor (100,000/ number of Drosophila aligned reads).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: ChIP using anti-Flag M2 antibody (Sigma) in U2OS Flag-Z1 cells

growth_protocol: U2OS cells expressing Flag-H2A.Z.1 or Flag-H2A.Z.2.

extract_protocol:
Nuclei were isolated and chromatin was sonicated and precleared. The H2A.Z histone-DNA complexes were isolated using anti-Flag M2 antibody (Sigma). Spike-in chromatin and Spike-in antibody (Active motif) were added in the ChIP experiment. After purification, 10 ng of immunoprecipitated DNA was sent to EMBL Genecore (Heidelberg, Germany) for library construction and sequencing.
Library construction (NEBNext® Ultra™ II DNA Library Prep Kit for Illumina) was performed by EMBL GeneCore. The 4 samples were barcoded and sequenced in one lane by NextSeq 500 Illumina device.

treatment_protocol: Before harvesting, cells were crosslinked for 15 min using 1% formaldehyde.

tag: cell line

value: U2OS Flag-Z1 cells

tag: chip antibody

value: anti-Flag M2 antibody (Sigma)


title: order2_N1_A27.single.cell

city: Shanghai

first: Bo O.

last: Zhou

address: 320 Yueyang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCm38 genome using HISAT (version 2-2.1.0)
gene counts were generated using HTseq (version 0.6.0) with default parameters.
All mapped reads were processed by StringTie (version 1.3.3b) to evaluate the gene expression levels (measured by FPKM, Fragment Per Kilobase per Million) with default parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: expression count of all single cells

molecule: polyA RNA

organism: Mus musculus

source_name: Skeletal Stem Cells

extract_protocol:
cells were lysed in single-cell RNA lysis buffer containing 0.45% NP-40, then subjected to reverse transcription with SuperScript Ⅱ reverse transcriptase (Invitrogen) and whole transcription amplification with KAPA HiFi HotStart ReadyMix (2X; KAPA Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: bone marrow

tag: sources

value: Tomato-

tag: genotype

value: KitMerCreMer; R26tdTomato mice


title: Strand-specific RNA-seq in siH2A.Z2 treated cells- Replicate #1 [WI38]

description:
si-Z2-n1
Transfected with siRNA against H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z2vsCtrl.csv

data_processing:
Strand-specific RNA-sequencing in proliferative cells treated with siRNAs was performed paired-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq). The 7 samples were barcoded and sequenced paired-end in one lane with ~400 millions paired end reads in total. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2b, datasets were processed (sorting and indexing) with samtools.
Raw reads were counted, per gene_id, using HT-seq Version 0.6.1 on the NCBI refseq annotation gtf file from UCSC in a strand specific mode with default parameters (20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv).
Differential analysis (siH2A.Z1 vs. siCtrl, siH2A.Z2 vs. siCtrl, siH2A.Z1 and siH2A.Z2 vs. Ctrl) was done with DESeq2 Bioconductor R package, Version 1.22.1 with default parameters. For the DE analysis in siH2A.Z1 versus siCtrl-treated WI38 cells, the GEO Sample GSM2781958 (Series GSE85083) was used as the second replicate for the siH2A.Z1 RNA-seq datasets.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: .csv files contain the output from DESeq2 and the raw counts of sequencing reads for the features from HT-seq.

molecule: total RNA

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNase (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) was performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). The 7 samples were barcoded, sequenced paired-end in one lane by NextSeq 500 Illumina device and demultiplexed.

treatment_protocol: Proliferative WI38 hTERT RAF1-ER cells were transfected by siRNAs for 3 days.

value: WI38 hTERT RAF1-ER

tag: sirna


title: Strand-specific RNA-seq in siH2A.Z1 treated cells- Replicate #1 [WI38]

description:
si-Z1-n1
Transfected with siRNA against H2A.Z1 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1vsCtrl.csv

source_name: Total RNA (ribosomal RNA depleted) from siH2A.Z1-treated proliferative WI38 hTERT RAF1-ER cells


title: Strand-specific RNA-seq in siSIRT1 treated cells- Replicate #1 [WI38]

description:
si-SIRT1-n2
Transfected with siRNA against SIRT1 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_SIRT1vsCtrl.csv

data_processing:
Strand-specific RNA-sequencing in proliferative cells treated with siRNAs was performed paired-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq). The 6 samples were barcoded and sequenced paired-end in one lane with ~400 millions paired end reads in total. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2b, datasets were processed (sorting and indexing) with samtools.
Raw reads were counted, per gene_id, using HT-seq Version 0.6.1 on the NCBI refseq annotation gtf file from UCSC in a strand specific mode with default parameters (20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv).
Differential analysis (siPHF14 vs. siCtrl, siSIRT1 vs. siCtrl) was done with DESeq2 Bioconductor R package, Version 1.22.1 with default parameters.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: .csv files contain the output from DESeq2 and the raw counts of sequencing reads for the features from HT-seq.

source_name: Total RNA (ribosomal RNA depleted) from siSIRT1-treated proliferative WI38 hTERT RAF1-ER cells

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNase (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) was performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). The 6 samples were barcoded, sequenced paired-end in one lane by NextSeq 500 Illumina device and demultiplexed.


title: Strand-specific RNA-seq in siCtrl treated cells- Replicate #2 [WI38]

description:
si-Ctrl-n2
Transfected with control siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1vsCtrl.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z2vsCtrl.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1_2vsCtrl.csv

source_name: Total RNA (ribosomal RNA depleted) from siCtrl-treated proliferative WI38 hTERT RAF1-ER cells

value: siCtrl


title: order2_N1_A25.single.cell


title: order2_N1_A26.single.cell


title: order2_N1_A22.single.cell


title: order2_N1_A23.single.cell


title: Strand-specific RNA-seq in siCtrl treated cells- Replicate #1 [WI38]

description:
si-Ctrl-n1
Transfected with control siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20170717_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1vsCtrl.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z2vsCtrl.csv
processed data file: 20181220_AssalaDESeq2_siRNASeq_Z1_2vsCtrl.csv


description:
siCtrl-n2
Transfected with control siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 20180410_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_PHF14vsCtrl.csv
processed data file: 20181219_AssalaDESeq2_siRNASeq_SIRT1vsCtrl.csv


title: Strand-specific RNA-seq in siH2A.Z1 and siH2A.Z2 treated cells- Replicate #1 [U2OS]

description:
siH2AZ-1_2-n1
Transfected with siRNAs against H2A.Z1 and H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20190507_Z12vsCtl_U2OS.csv

data_processing:
Strand-specific RNA-sequencing in proliferative cells treated with siRNAs was performed paired-end by Illumina’s NextSeq 500 technology at EMBL-GeneCore (stranded rRNA-minus RNA-seq). The 10 samples were barcoded and sequenced paired-end in one lane with ~400 millions paired end reads in total. After alignment on human genome hg38 using Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2b, datasets were processed (sorting and indexing) with samtools.
Raw reads were counted, per gene_id, using HT-seq Version 0.6.1 on the NCBI refseq annotation gtf file from UCSC in a strand specific mode with default parameters (201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv).
Differential analysis (siH2A.Z1 vs. siCtrl3 and siCtrl4, siH2A.Z2 vs. siCtrl3 and siCtrl4, siH2A.Z1 and siH2A.Z2 vs. siCtrl3 and siCtrl4) was done with DESeq2 Bioconductor R package, Version 1.22.1 with default parameters.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: .csv files contain the output from DESeq2 and the raw counts of sequencing reads for the features from HT-seq.

source_name: Total RNA (ribosomal RNA depleted) from siH2A.Z1 and siH2A.Z2-treated U2OS cells

extract_protocol:
Total RNAs were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNase (Epicentre). EMBL-GeneCore performed the ribosomal RNA depletions.
Library construction (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®) was performed by EMBL GeneCore (Heidelberg, Germany) (stranded rRNA-minus RNA-seq). The 10 samples were barcoded, sequenced paired-end in one lane by NextSeq 500 Illumina device and demultiplexed.

treatment_protocol: U2OS cells were transfected by siRNAs for 3 days.

value: siH2A.Z1 and siH2A.Z2


title: Strand-specific RNA-seq in siH2A.Z2 treated cells- Replicate #2 [U2OS]

description:
siH2AZ2-n2
Transfected with siRNA against H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z2vsCtrl3_4.csv

source_name: Total RNA (ribosomal RNA depleted) from siH2A.Z2-treated U2OS cells


title: order2_N1_A19.single.cell


title: order2_N1_A21.single.cell


title: order2_N1_A18.single.cell


title: Strand-specific RNA-seq in siH2A.Z1 treated cells- Replicate #2 [U2OS]

description:
siH2AZ1-n2
Transfected with siRNA against H2A.Z1 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z1vsCtrl3_4.csv

source_name: Total RNA (ribosomal RNA depleted) from siH2A.Z1-treated U2OS cells


title: Strand-specific RNA-seq in siH2A.Z2 treated cells- Replicate #1 [U2OS]

description:
siH2AZ2-n1
Transfected with siRNA against H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z2vsCtrl3_4.csv


title: Strand-specific RNA-seq in siCtrl 4 treated cells- Replicate #2 [U2OS]

description:
siCtrl-4-n2
Transfected with control #4 siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z1vsCtrl3_4.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z2vsCtrl3_4.csv
processed data file: 20190507_Z12vsCtl_U2OS.csv

source_name: Total RNA (ribosomal RNA depleted) from siCtrl-treated U2OS cells


title: order2_N2_A47.single.cell


title: order2_N1_A16.single.cell


title: Strand-specific RNA-seq in siCtrl 4 treated cells- Replicate #1 [U2OS]

description:
siCtrl-4-n1
Transfected with control #4 siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z1vsCtrl3_4.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z2vsCtrl3_4.csv
processed data file: 20190507_Z12vsCtl_U2OS.csv


title: order2_N1_A17.single.cell


title: Strand-specific RNA-seq in siH2A.Z1 treated cells- Replicate #1 [U2OS]

description:
siH2AZ1-n1
Transfected with siRNA against H2A.Z1 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z1vsCtrl3_4.csv


title: Strand-specific RNA-seq in siCtrl 3 treated cells- Replicate #2 [U2OS]

description:
siCtrl-3-n2
Transfected with control #3 siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z1vsCtrl3_4.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z2vsCtrl3_4.csv
processed data file: 20190507_Z12vsCtl_U2OS.csv


title: order2_N1_A24.single.cell


title: order2_N1_A14.single.cell


title: order2_N1_A15.single.cell


title: Strand-specific RNA-seq in siCtrl 3 treated cells- Replicate #1 [U2OS]

description:
siCtrl-3-n1
Transfected with control #3 siRNA for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z1vsCtrl3_4.csv
processed data file: 201901_AssalaDESeq2_siRNASeq_U2OS_Z2vsCtrl3_4.csv
processed data file: 20190507_Z12vsCtl_U2OS.csv


title: order2_N2_A43.single.cell


title: Strand-specific RNA-seq in siH2A.Z1 and siH2A.Z2 treated cells- Replicate #2 [U2OS]

description:
siH2AZ-1_2-n2
Transfected with siRNAs against H2A.Z1 and H2A.Z2 for 3 days.
Ribosomal RNA depleted.
Strand-specific RNA-seq.
processed data file: 201901_AssalaDESeq2_siRNASeq_CountAllConditions.csv
processed data file: 20190507_Z12vsCtl_U2OS.csv


title: order2_N1_A12.single.cell


title: order2_N1_A13.single.cell


title: ChIP-seq_H3K27ac_CR3flp_rep2

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

country: USA

institute: NIEHS

data_processing:
Reads were filtered based on a mean base quality score >20.
For ChIP-seq analysis, reads were mapped to hg19 genome using Bowtie 0.12.8. Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package. Paired-end reads were converted to a single fragment for metaplot analyses and visualization on the UCSC Genome Browser. After normalization within each data set, bigWig files were generated to visualize the genomic coverage. Peak calling was performed with HOMER v4.1 at default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: Cells were grown on 15 cm plats in high glucose DMEM medium with 10% FBS

extract_protocol:
Cells were treated with a hypotonic buffer, and lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Covaris. DNA was precipitated with antibody against each target protein.
Libraries were prepared according to BIOO SCIENTIFIC instruction.

tag: genotype/variation

value: T47D wt/R330fsl cells

tag: passages

tag: antibody

value: anti-H3K27ac (abcam, ab4729)


title: ChIP-seq_H3K27ac_T47Dflp_rep1

value: T47D Flp control cells


title: ChIP-seq_H3K27ac_T47Dflp_rep2


title: ChIP-seq_H3K27ac_CF3flp_rep1


title: order2_N1_A11.single.cell


title: order2_N1_A20.single.cell


title: order2_N1_A10.single.cell


title: order2_N1_A9.single.cell


title: order2_N1_A8.single.cell


title: ChIP-seq_H3K27me3_CR3flp_rep2

value: anti-H3K27me3 (abcam, ab192985)


title: order2_N1_A7.single.cell


title: ChIP-seq_H3K27me3_T47Dflp_rep2


title: order2_N1_A6.single.cell


title: order2_N1_A5.single.cell


title: ChIP-seq_H3K4me1_CR3flp_rep2

value: anti-H3K4me1 (abcam, ab8895)


title: ChIP-seq_H3K27me3_T47Dflp_rep1


title: order2_N1_A4.single.cell


title: order2_N1_A3.single.cell


title: ChIP-seq_H3K4me1_T47Dflp_rep1


title: order2_N1_A2.single.cell


title: ChIP-seq_H3K4me1_CR3flp_rep1


title: order2_N1_A1.single.cell


title: ChIP-seq_H3K4me1_T47Dflp_rep2


title: order1_P3_A40.single.cell

value: Tomato+


title: order1_P3_A38.single.cell


title: order1_P3_A37.single.cell


title: order1_P3_A39.single.cell


title: order1_P3_A36.single.cell


title: ChIP-seq_H3K27me3_CR3flp_rep1


title: non-MG cells, replication 2

type: RNA

city: Tokushima

first: Kensei

last: Nishida

state: Tokushima

address: 3-18-15 Kuramoto-cho

country: Japan

institute: Tokushima University Graduate school

description: control

hyb_protocol: Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol. The fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4858A) for 17 hours at 65C in a rotating Agilent hybridization oven.

scan_protocol: Microarrays were scanned using Agilent’s DNA Microarray Scanner (P/N G2600D).

data_processing: Data extracted using Agilent's Feature Extraction software. Raw data output was imported into Genespring GX14.9 (Agilent) and normalized each chip to the 75th percentile of all measurements (per chip normalization).

source_name: colon cancer cell line

label_protocol: Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis’ Protocol. These protocols are available for download from Agilent's DNA Microarray Manuals website. For microarray analysis, total RNA (400 ng) was used for amplification and labeling of complementary RNA (cRNA) using a Low RNA Input Liner Amplification Kit PLUS and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent).

extract_protocol: The total RNA was extracted using miRNeasy kit (Qiagen) according to the manufacturer’s protocol.

value: HCT116  cells

tag: group

value: low migratory cells


title: MG cells, replication 1

description: control

value: high migratory cells


title: non-MG cells, replication 1

description: control


title: order1_P3_A35.single.cell


title: order1_P3_A33.single.cell


title: order1_P3_A32.single.cell


title: order1_P3_A31.single.cell


title: order1_P3_A30.single.cell


title: order1_P3_A29.single.cell


title: BS_NFIA_KO1

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC. Pairend reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a)
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and normalized using DESeq2 (v1.20.0).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

source_name: Brainstem

extract_protocol:
The olfactory bulb, hippocampus, cortex, and brainstem from 20-week old NFIAfl/fl; Aldh1l1-CreER; Aldh1l1-GFP and NFIAfl/fl; Aldh1l1-GFP mice was dissected, dissociated, and FAC sorted into QIAGEN RLT lysis buffer (Cat# 74004) with 1% ß-Mercaptoethanol. RNA was isolated using the RNeasy Micro Kit (74004, QIAGEN).
Illumina sequencing libraries were constructed from 5ng of total RNA using the Trio RNA-Seq System (0507-96, NuGEN).

value: Brainstem

tag: age

value: NFIAfl/fl; Aldh1l1-CreER; Aldh1l1-GFP


title: CX_NFIA_KO3

source_name: Cortex

value: Cortex


title: BS_Control2

description: Control

value: NFIAfl/fl; Aldh1l1-GFP


title: BS_NFIA_KO3


title: CX_NFIA_KO2


title: BS_Control1

description: Control


title: BS_Control3

description: Control


title: BS_NFIA_KO2


title: order1_P3_A28.single.cell

value: bone marrow

value: KitMerCreMer; R26tdTomato mice


title: CX_Control3

description: Control


title: CX_NFIA_KO1


title: CX_Control1

description: Control


title: CX_Control2

description: Control


title: HC_NFIA_KO3

source_name: Hippocampus

value: Hippocampus


title: MG cells, replication 2

description: control


title: order1_P3_A25.single.cell


title: order1_P3_A27.single.cell


title: order1_P3_A24.single.cell


title: order1_P3_A34.single.cell


title: HC_NFIA_KO1


title: HC_Control3

description: Control


title: HC_NFIA_KO2


title: order1_P3_A23.single.cell


title: order1_P3_A22.single.cell


title: HC_Control2

description: Control


title: order1_P3_A21.single.cell


title: order1_P3_A20.single.cell


title: order1_P3_A26.single.cell


title: HC_Control1

description: Control


title: order1_P3_A19.single.cell


title: order1_P3_A15.single.cell


title: order1_P3_A17.single.cell


title: order1_P3_A18.single.cell


title: order1_P3_A16.single.cell


title: order1_P3_A11.single.cell


title: order1_P3_A13.single.cell


title: OB_Control2

description: Control

source_name: Olfactory bulb

value: Olfactory bulb


title: OB_Control1

description: Control


title: OB_Control3

description: Control


title: OB_NFIA_KO1


title: cDNA_S1: MDR1-sufficient and MDR1-deficient Day 8 P14 CD8+ T cells

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

description: cDNA library was generated with 50,000 reads per cell for cDNA

data_processing:
Demultiplexing, alignment, and barcoded data matrices: Cell ranger
Data analysis:SCANPY framework
Differential gene expression:  DESeq2 with the ZINBWAVE R
Genome_build: mm10

source_name: Sorted Day 8 Post-LCMV-Arm Infection P14 cells

growth_protocol: Thy1.1+Thy1.2+ MDR1-sufficient and Thy1.1+Thy1.2- MDR1-deficient  P14 CD8+ T cells were extracted and sorted from ten congenically-transferred and LCMV-infected wild type B6 mice at day 8 post-infection.

extract_protocol:
Samples were pooled equally and adjusted to a final concentration between 700-1200 cells/mL; 35,000 total cells were loaded into one lane of the single cell A chip kit (P/N 1000009). Single-cell gel beads in emulsion (GEM) were generated using the 10X Chromium Controller (10X Genomics). Single-cell GEM and sequencing libraries were generated using the Single-Cell 3’ Library and Gel Bead Kit V2 (P/N 120267) according to manufacturer recommendations.
Libraries were loaded (1.8 pM) on the Illumina NextSeq500 and sequenced with Read 1 25-bp, index i7 8-bp, and Read 2 98-bp.

treatment_protocol: P14 cells with or without MDR1 were barcoded with TotalSeq-A anti-mouse hashtag antibodies (BioLegend), to enable sample multiplexing, and then counted on the CountessÔ II FL automated cell counter (Thermo Fisher Scientific) using Trypan blue to determine viability and cell number (Stoeckius et al., 2018)

value: C57BL/6 and C57BL/6 Abcb1a/1b-/-

value: CD8+ T cells


title: order1_P3_A12.single.cell


title: 266_8: Mdr1ko+elacridar_replicate 3

data_processing:
Alignment: Salmon
Differential gene expression: DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Gene abundance in raw countsand  TPMs

source_name: Day 6 in vitro-generated CD8 T cells in 10 U/mL rhIL-2

growth_protocol: three biologically independent replicates of B6 wild type or Abcb1a/1b-/- CD8+ T cells activated and expanded for 6-days in 10 U/mL rhIL-2-containing media

extract_protocol:
total RNA (RIN > 9 by Bioanalyzer; Agilent Technologies) was isolated using RNeasy columns with on-column DNase treatment (QIAGEN) and processed with the NEBNext Ultra II ribosomal (r)RNA-depletion module Human/Mouse/Rat (New England BioLabs Inc.) using 400 ng total RNA as input
rRNA-depleted RNA was processed using the NEBNext Ultra II directional RNA kit for Illumina (New England BioLabs Inc.) to generate strand-specific libraries. Final libraries were amplified by PCR (10-cycles), size selected using beads to enrich for fragments > 400 bp and purified using Ampure XP beads (Beckman Coulter).  Final libraries were validated on the Agilent 2100 Bioanalyzer DNA chips and quantified on the Qubit (Thermo Fisher Scientific). Libraries were pooled at equimolar ratios and loaded onto the Illumina NextSeq500 flow cell and sequenced using 40 bp paired-end chemistry

treatment_protocol: cells grown with or without elacridar

value: CD8 T cells


title: order1_P3_A9.single.cell


title: 266_7: WT+elacridar_replicate 3


title: order1_P3_A10.single.cell


title: order1_P3_A7.single.cell


title: order1_P3_A8.single.cell


title: OB_NFIA_KO3


title: order1_P3_A14.single.cell


title: 266_4: Mdr1ko+elacridar_replicate 2


title: 266_6: Mdr1ko_replicate 3


title: 266_5: WT_replicate 3


title: 266_3: WT+elacridar_replicate 2


title: OB_NFIA_KO2


title: order1_P3_A6.single.cell


title: order1_P3_A5.single.cell


title: 266_2: Mdr1ko_replicate 2


title: 266_1: WT_replicate 2


title: order1_P3_A4.single.cell


title: 261_4: Mdr1ko_replicate 1


title: order1_P3_A3.single.cell


title: 261_3: WT_replicate 1


title: order1_P2_A5.single.cell


title: 261_1: WT+elacridar_replicate 1


title: order1_P3_A2.single.cell


title: 261_2: Mdr1ko+elacridar_replicate 1


title: order1_P2_A4.single.cell


title: order1_P2_A3.single.cell


title: Sorted  lung ILC2, KO 1

city: Los Angeles

first: Lauriane

last: Galle

state: California

address: 1450 Biggy Street NRT 5509

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v3.5.3) with default parameter settings
Gencode M16 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wild-type and Atg5-/- mice were stimulated intranasally for 3 consecutive days with rm IL-33 (0.5µg), On day 4 lung ILC2s were isolated and then RNA was extracted.

value: lung

tag: cell type

value: sorted ILC2s

value: 8 weeks


title: Sorted  lung ILC2, KO 2


title: order1_P2_A2.single.cell

value: Tomato+


title: Sorted  lung ILC2, WT 3

value: wild-type


title: order1_P2_A1.single.cell


title: order1_P1_A94.single.cell


title: Sorted  lung ILC2, WT 2


title: order1_P1_A93.single.cell


title: order1_P1_A92.single.cell


title: order1_P1_A91.single.cell


title: order1_P1_A90.single.cell


title: Sorted  lung ILC2, WT 1


title: order1_P3_A1.single.cell


title: order1_P1_A89.single.cell


title: Sorted  lung ILC2, KO 3


title: order1_P1_A88.single.cell


title: order1_P1_A86.single.cell


title: ZR751_DMSO_Rep2

city: Berlin

first: Bernard

last: Haendler

address: Muellerstr. 178

country: Germany

institute: Bayer AG

data_processing:
Illumina bcl2fastq v2.17 was used to convert bcl to fastqs.
RNA-seq reads were aligned to GRCh38 using STAR aligner.
RSEM was used to quantify reads in genes.
Expected counts were further analyzed in R, DESeq2 was used for differential gene expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes expected counts (obtained with RSEM) for all samples

source_name: ZR-7-51 (breast)

growth_protocol: PANC-1 was cultured in DMEM supplemented with 10% FCS; BT-474, MiaPaCa2 and SW1463 were cultured in DMEM / Ham's F12 +10% FCS; G-401 was cultured in McCoy's 5A +10% FCS; 22RV1, JMSU-1, DLD-1, LoVo, ZR-75-1 were cultured i.n RPMI 1640+10% FCS. MCF7, VCaP and LNCaP cells were cultured in starvation medium. Cell lines were cultured at 37C in 5% CO2.

extract_protocol:
RNA was isolated using RNeasy-Plus Mini kit (Qiagen)
Libraries were prepared using Illumina TruSeq Stranded mRNA Kit and sequenced on Illumina HiSeq2500 HTv4 (single-end, dual-indexing, 50 Cycles).

treatment_protocol: ZR-75-1, BT474, PANC-1, MiaPaCa-2, 22RV1, JMSU-1, DLD-1, SW1463, LoVo, G401 cells were treated with 5µM BAY-155 or DMSO for 48h prior RNA extraction. MCF7, VCaP and LNCaP cells were treated with DMSO or BAY-155 in starvation medium for 48h. After that they were stimulated with steroid hormones (0.1 nM or 1 nM of E2 (ß-Estradiol) or R1881, respectively) for 12h.

tag: agent 1

value: DMSO


title: ZR751_DMSO_Rep3


title: order1_P1_A87.single.cell

source_name: Skeletal Stem Cells


title: ZR751_DMSO_Rep1


title: order1_P1_A85.single.cell


title: ZR751_BAY155_Rep3


title: order1_P1_A83.single.cell


title: Dami-GFP [NC]

city: Guangzhou

first: Fei

last: Li

address: Xingang West Road

department: School of Life Science

institute: Sun Yat-sen university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)；Nt (NCBI non-redundant nucleotide sequences)；Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: Quantification of gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: Dami_AMKL cells

growth_protocol: AMKL cell Dami stably expressing GFP, c-Mpl-del-GFP or c-Mpl-p were established by transduction with GFP, c-Mpl-del-GFP or c-Mpl-p lentiviruses and cultured in 10%FBS IMDM medium

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, Part#15596206) according to the manufacturer’s instructions.
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（RNase H-）. 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.

treatment_protocol: Dami-GFP (NC) and Dami-DEL (Mpl-del) were treated with or without 10 μM Ara-c in the presence of 20ng/mL TPO for 48h. Dami-P (Mpl-p) were cultured with 20ng/mL TPO for 48h.

tag: cell ine

value: Dami

value: acute megakaryoblasttic leukemia (AMKL) cells

tag: disease state

value: AML (M7)

tag: tissue source

value: blood

value: GFP control


title: Dami-DEL +Ara-c [del-Ara]

value: c-Mpl-del

tag: treatment

value: 10 μM Ara-c


title: B3_4h_IL21

city: Groningen

first: Raul

last: Aguirre-Gamboa

address: Antonius Deusinglaan 1

department: Department of Genetics

country: Netherlands

institute: University of Groningen, University Medical Center Groningen

data_processing:
fastQ files were then trimmed for: low quality reads, adaptors and poly-A tails
Trimmed fastQ files were aligned to build human_g1k_v37 ensemble Release 75 reference genome, using hisat.
Aligned reads were sorted using SAMTools
Gene level quantification was performed using HTSeq-count
Genome_build: ensemble Release 75
Supplementary_files_format_and_content: Tab delimited file that contains the raw count table

source_name: IEIL cell line derived from Intestinal biopsies

growth_protocol: IE-CTLs were co-cultured with irradiated allogenic peripheral blood mononuclear cells (from 2 donors) and EBV (Epstein Barr virus) transformed B cells in RPMI 1640 (GIBCO) medium supplemented with 1ug/ml PHA-L (Merck Millipore), 10% human serum albumin (Sigma-Aldrich) and 100 U/ml IL-2 (Biolegend).

extract_protocol:
RNA from unstimulated or stimulated IE-CTLs was isolated with the RNeasy plus mini kit (Qiagen). RNA concentration and quality were measured using the Nanodrop 1000 Spectrophotometer (Thermo Scientific) and the high-sensitivity RNA analysis kit (Experion, software version 3.0, Bio-Rad).
RNA-seq libraries were prepared from 1ug of total RNA using the Quant seq 3’ kit (Lexogen).  The libraries were sequenced on the Nextseq500 (Illumina) yielding at least fifteen million sequence reads per sample.

treatment_protocol: After 12 days of culture, the cells were washed, starved for IL-2 for 48 hrs, and subsequently stimulated for 30 minutes, 3, 4 or 24 hrs with IL-15 (20 ng/ml, Biolegend, cat 570304), IL-21 (3 ng/ml, Biolegend, cat 571204) or IFN (300 ng/ml, Pbl Assay science, cat 11410-2). Unstimulated IE-CTLs were included as control

tag: type

value: Celiac

tag: donor

tag: stimulation

tag: time point


title: B4_unsti

value: unsti


title: Dami-P [Mpl-p]

value: c-Mpl-p overexpressed


title: order1_P1_A82.single.cell

tag: strain

tag: tissue

value: bone marrow

tag: sources

tag: genotype

value: KitMerCreMer; R26tdTomato mice


title: HTO_S2: MDR1-sufficient and MDR1-deficient Day 8 P14 CD8+ T cells

description: HTO library was generated with 2000 reads per cell for HTO

value: C57BL/6 and C57BL/6 Abcb1a/1b-/-

value: CD8+ T cells


title: Dami-DEL [Mpl-del]

tag: genotype/variation


title: order1_P1_A81.single.cell

value: Tomato+


title: Dami-GFP +Ara-c [NC-Ara]


title: ZR751_BAY155_Rep2

tag: cell line


title: order1_P1_A84.single.cell


title: B4_4h_IL21


title: order1_P1_A80.single.cell


title: ZR751_BAY155_Rep1


title: B4_4h_IL15


title: order1_P1_A79.single.cell


title: order1_P1_A78.single.cell


title: VCaP_R1881_Rep3

source_name: VCaP (prostate)

value: VCaP


title: order1_P1_A77.single.cell


title: B4_4h_IFNb

value: IFNb


title: VCaP_R1881_Rep2


title: order1_P1_A76.single.cell


title: order1_P1_A75.single.cell


title: VCaP_R1881_Rep1


title: B4_3h_IL21


title: order1_P1_A74.single.cell


title: order1_P1_A66.single.cell


title: VCaP_DMSO_Rep3

value: DMSO


title: order1_P1_A70.single.cell


title: order1_P1_A72.single.cell


title: order1_P1_A73.single.cell


title: B4_3h_IL15


title: VCaP_DMSO_Rep2


title: VCaP_DMSO_Rep1


title: order1_P1_A71.single.cell


title: B4_30_min_IL21


title: order1_P1_A69.single.cell


title: order1_P1_A68.single.cell


title: order1_P1_A65.single.cell


title: order1_P1_A67.single.cell


title: B4_30_min_IFNb


title: VCaP_BAY155_R1881_Rep3

tag: agent 2


title: order1_P1_A63.single.cell


title: order1_P1_A64.single.cell


title: order1_P1_A62.single.cell


title: B4_24h_IL21


title: order1_P1_A61.single.cell


title: VCaP_BAY155_R1881_Rep2


title: SW1463_DMSO_Rep3

source_name: SW1463 (colorectal)


title: order1_P1_A60.single.cell


title: VCaP_BAY155_R1881_Rep1


title: order1_P1_A59.single.cell


title: B4_30_min_IL15


title: SW1463_DMSO_Rep1


title: SW1463_DMSO_Rep2


title: SW1463_BAY155_Rep3


title: B4_24h_IL15


title: B3_4h_IL15


title: B3_4h_IFNb


title: B3_unsti


title: B3_3h_IL21


title: SW1463_BAY155_Rep2


title: SW1463_BAY155_Rep1


title: B3_3h_IL15


title: B3_3h_IFNb


title: PANC1_DMSO_Rep3

source_name: PANC-1 (pancreas)


title: order1_P1_A53.single.cell


title: B4_24h_IFNb


title: order1_P1_A47.single.cell


title: order1_P1_A58.single.cell


title: order1_P1_A55.single.cell


title: order1_P1_A56.single.cell


title: order1_P1_A54.single.cell


title: order1_P1_A49.single.cell


title: order1_P1_A48.single.cell


title: order1_P1_A57.single.cell


title: order1_P1_A51.single.cell


title: PANC1_DMSO_Rep2


title: order1_P1_A46.single.cell


title: order1_P1_A50.single.cell


title: order1_P1_A45.single.cell


title: order1_P1_A52.single.cell


title: B4_3h_IFNb


title: B3_30_min_IL21


title: PANC1_BAY155_Rep3


title: order1_P1_A43.single.cell


title: B3_30_min_IL15


title: B3_30_min_IFNb


title: order1_P1_A42.single.cell


title: PANC1_BAY155_Rep2


title: B3_24h_IL21


title: order1_P1_A38.single.cell


title: PANC1_BAY155_Rep1


title: order1_P1_A39.single.cell


title: MiaPaCa2_DMSO_Rep2

source_name: MiaPaCa2 (pancreas)


title: order1_P1_A35.single.cell


title: order1_P1_A34.single.cell


title: MiaPaCa2_DMSO_Rep3


title: order1_P1_A31.single.cell


title: B2_unsti


title: order1_P1_A32.single.cell


title: order1_P1_A36.single.cell


title: order1_P1_A44.single.cell


title: B3_24h_IFNb


title: PANC1_DMSO_Rep1


title: MiaPaCa2_DMSO_Rep1


title: MiaPaCa2_BAY155_Rep3


title: order1_P1_A30.single.cell


title: order1_P1_A41.single.cell


title: B2_4h_IL21


title: order1_P1_A29.single.cell


title: order1_P1_A40.single.cell


title: order1_P1_A28.single.cell


title: MiaPaCa2_BAY155_Rep2


title: order1_P1_A33.single.cell


title: order1_P1_A37.single.cell


title: B2_4h_IFNb


title: MiaPaCa2_BAY155_Rep1


title: order1_P1_A26.single.cell


title: B3_24h_IL15


title: MCF7_E2_Rep3

source_name: MCF7 (breast)


title: order1_P1_A25.single.cell


title: order1_P1_A24.single.cell


title: B2_3h_IL21


title: B2_3h_IL15


title: MCF7_E2_Rep2


title: order1_P1_A21.single.cell


title: order1_P1_A20.single.cell


title: order1_P1_A22.single.cell


title: order1_P1_A19.single.cell


title: MCF7_E2_Rep1


title: order1_P1_A23.single.cell


title: order1_P1_A17.single.cell


title: B2_4h_IL15


title: order1_P1_A27.single.cell


title: MCF7_DMSO_Rep1


title: order1_P1_A15.single.cell


title: MCF7_BAY155_E2_Rep3


title: B2_30_min_IFNb


title: order1_P1_A14.single.cell


title: B2_30_min_IL21


title: B2_24h_IL21


title: B2_3h_IFNb


title: MCF7_DMSO_Rep2


title: B2_24h_IL15


title: order1_P1_A11.single.cell


title: MCF7_BAY155_E2_Rep2


title: B2_24h_IFNb


title: order1_P1_A8.single.cell


title: order1_P1_A10.single.cell


title: order1_P1_A13.single.cell


title: order1_P1_A7.single.cell


title: order1_P1_A6.single.cell


title: LoVo_DMSO_Rep3

source_name: LoVo (colorectal)

value: LoVo


title: B1_unsti


title: order1_P1_A18.single.cell


title: order1_P1_A5.single.cell


title: order1_P1_A16.single.cell


title: B2_30_min_IL15


title: order1_P1_A4.single.cell


title: B1_4h_IL21


title: LoVo_DMSO_Rep1


title: B1_4h_IL15


title: order1_P1_A3.single.cell


title: order1_P1_A2.single.cell


title: LoVo_BAY155_Rep3


title: order1_P1_A1.single.cell


title: order1_P1_A9.single.cell


title: MCF7_BAY155_E2_Rep1


title: order1_N2_A60.single.cell

value: Tomato-


title: LoVo_DMSO_Rep2


title: B1_4h_IFNb


title: B1_3h_IL21


title: order1_N2_A58.single.cell


title: order1_N2_A57.single.cell


title: B1_3h_IL15


title: order1_N2_A59.single.cell


title: order1_N2_A56.single.cell


title: LNCaP_R1881_Rep3

source_name: LNCaP (prostate)

value: LNCaP


title: LNCaP_R1881_Rep2


title: B1_3h_IFNb


title: B1_30_min_IL21


title: order1_N2_A54.single.cell


title: order1_N2_A53.single.cell


title: LoVo_BAY155_Rep1


title: order1_N2_A52.single.cell


title: LNCaP_R1881_Rep1


title: order1_N2_A51.single.cell


title: B1_30_min_IL15


title: LNCaP_DMSO_Rep3


title: order1_N2_A50.single.cell


title: order1_N2_A49.single.cell


title: order1_N2_A48.single.cell


title: LoVo_BAY155_Rep2


title: LNCaP_DMSO_Rep2


title: order1_N2_A47.single.cell


title: B1_24h_IL21


title: B1_30_min_IFNb


title: order1_N2_A55.single.cell


title: order1_N2_A46.single.cell


title: B1_24h_IL15


title: order1_N2_A44.single.cell


title: B1_24h_IFNb


title: LNCaP_DMSO_Rep1


title: order1_N2_A43.single.cell


title: order1_N2_A40.single.cell


title: A4_unsti

value: Control


title: order1_N2_A42.single.cell


title: order1_N2_A41.single.cell


title: order1_N2_A39.single.cell


title: A4_4h_IL21


title: order1_N2_A38.single.cell


title: LNCaP_BAY155_R1881_Rep2


title: LNCaP_BAY155_R1881_Rep1


title: JMSU1_DMSO_Rep3

source_name: JMSU-1 (bladder)


title: order1_N2_A36.single.cell


title: order1_N2_A37.single.cell


title: JMSU1_DMSO_Rep2


title: A4_4h_IL15


title: A4_4h_IFNb


title: order1_N2_A34.single.cell


title: JMSU1_DMSO_Rep1


title: order1_N2_A35.single.cell


title: order1_N2_A45.single.cell


title: A4_3h_IL21


title: LNCaP_BAY155_R1881_Rep3


title: JMSU1_BAY155_Rep3


title: order1_N2_A33.single.cell


title: order1_N2_A32.single.cell


title: order1_N2_A31.single.cell


title: order1_N2_A30.single.cell


title: A4_3h_IL15


title: A4_3h_IFNb


title: order1_N2_A29.single.cell


title: JMSU1_BAY155_Rep1


title: G401_DMSO_Rep3

source_name: G401 (kidney)


title: order1_N2_A25.single.cell


title: order1_N2_A26.single.cell


title: order1_N2_A27.single.cell


title: order1_N2_A24.single.cell


title: A4_30_min_IL15


title: order1_N2_A23.single.cell


title: A4_30_min_IFNb


title: G401_DMSO_Rep2


title: G401_DMSO_Rep1


title: G401_BAY155_Rep3


title: A4_24h_IL21


title: JMSU1_BAY155_Rep2


title: A4_24h_IL15


title: order1_N2_A21.single.cell


title: order1_N2_A19.single.cell


title: order1_N2_A18.single.cell


title: order1_N2_A20.single.cell


title: G401_BAY155_Rep2


title: order1_N2_A17.single.cell


title: order1_N2_A15.single.cell


title: DLD1_DMSO_Rep3

source_name: DLD-1 (colorectal)


title: A4_24h_IFNb


title: order1_N2_A28.single.cell


title: order1_N2_A16.single.cell


title: G401_BAY155_Rep1


title: A4_30_min_IL21


title: order1_N2_A13.single.cell


title: order1_N2_A12.single.cell


title: A3_unsti


title: order1_N2_A22.single.cell


title: A3_4h_IL21


title: order1_N2_A14.single.cell


title: A3_4h_IL15


title: order1_N2_A11.single.cell


title: DLD1_DMSO_Rep2


title: order1_N2_A9.single.cell


title: A3_3h_IL21


title: A3_3h_IL15


title: A3_3h_IFNb


title: order1_N2_A8.single.cell


title: A3_4h_IFNb


title: DLD1_DMSO_Rep1


title: order1_N2_A10.single.cell


title: order1_N2_A7.single.cell


title: DLD1_BAY155_Rep3


title: order1_N2_A6.single.cell


title: order1_P1_A12.single.cell


title: DLD1_BAY155_Rep2


title: DLD1_BAY155_Rep1


title: A3_30_min_IL21


title: BT474_DMSO_Rep2

source_name: BT-474 (breast)


title: BT474_DMSO_Rep1


title: A3_30_min_IL15


title: order1_N2_A2.single.cell


title: TSA-early-2-cell_rep2

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

institute: Tongji University

description: in situ Hi-C for nuclear transfer embryonic early 2-cell with TSA treated replicate 2

data_processing:
Paired-end sequencing reads were trimmed for adaptor and low-quality reads using cutadapt(v1.16)
Then, the Hi-C labrary reads were processed using HiC-Pro (v2.9.0) as described.
The Hi-C and ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2.
The RNA-seq reads were aligned to the mm10 using Hisat2.
All valid pairs of contacts were generated after filter and remove duplicates in HiC-Pro.
BigWig of ChIP-seq data were generated using deepTools.
Raw counts of genes were generated using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Valid pairs; BigWig; Raw counts;

growth_protocol: mESCs:R1 ES cells were purchased from American Type Culture Collection (ATCC) and cultured on mitomycin C-treated MEFs in ES medium containing DMEM (Merck Millipore) supplemented with 15% (v/v) fetal bovine serum (HyClone), 1 mM l-glutamine (Merck Millipore), 0.1 mM mercaptoethanol (Merck Millipore), 1% nonessential amino acid stock (Merck Millipore), penicillin/streptomycin (100×, Merck Millipore), nucleosides (100×, Merck Millipore) and 1,000 U/ml LIF (Merck Millipore). These cells tested negative for mycoplasma contamination.

extract_protocol:
①SCNT procedure:Eight- to ten-week-old B6D2F1 (C57BL/6×DBA/2) female mice were superovulated by injection with 5 IU of pregnant mare serum gonadotropin (PMSG), followed by injection of 7 IU of human chorionic gonadotropin (hCG, San-Sheng Pharmaceutical) 48 h later. Mouse MII oocytes were retrieved from the dissected oviducts at 13 h post-hCG injection and incubated in Chatot-Ziomek-Bavister medium (CZB) at 37°C and 5% CO2 until use. CCs were removed by incubating the cumulus-oocyte complex in hyaluronidase from bovine testes (0.5 mg/ml, Sigma) at 37°C for 3-5 min. Fully dissociated cumulus cells were collected and washed in Hepes-CZB and then stored at 4°C until nuclear transfer manipulation. Mouse MII oocytes were enucleated in Hepes-CZB containing 5 μg/ml cytochalasin B (Sigma) at 37°C. The inner diameter of the transfer needles used for CC nucleus was 5-6 μm. The somatic cell was administered 1-2 piezo pulses (intensity 1 or 2) while at the tip of the transfer needle to break the plasma membrane. Then, the cell was immediately injected into an enucleated oocyte in Hepes-CZB containing 5 μg/ml cytochalasin B. The plasma membrane of the enucleated oocyte was broken with a single piezo pulse, the cumulus cell was injected, and the membrane was sealed by aspiration of a small amount of cytoplasm. Reconstructed embryos were cultured in CZB at 37°C and 5% CO2 for one hour and activated for 5 hours using strontium chloride in calcium-free CZB in the presence of 5 μg/ml cytochalasin B to prevent the extrusion of a pseudopolar body. The reconstructed embryos were then transplanted into G1 medium and cultured to the blastocyst stage. ②Sample harvest:embryos at each of the following stages were collected: 0.5 h and 1 h postinjection; 1 h, 6 h and 12 h postactivation; 2-cell, 4-cell, and 8-cell; morula; ICM and TE of day 3.5 blastocysts. An ES cell line (R1, male) and cumulus cells were also harvested for the Hi-C experiment. For the one-cell and cleavage-stage embryos, the zona pellucidae of the embryos were removed with 0.5% pronase E (Sigma), and the embryos were then incubated in calcium-free CZB for 5 min. Polar bodies were removed by gently pipetting using a firepolished glass needle with an inner diameter of 120 μm. For morula, ICM and TE isolation, the zona pellucidae of blastocysts were removed with 0.5% pronase E. The embryos were then incubated in calcium-free CZB for 20 min, and the tight junctions of morula, TE and ICM cells were separated by gently pipetting using a pipette with an inner diameter of 40–60 μm.
①Hi-C libaries:The generation of Hi-C libraries with a low number of cells was optimized according to a previous protocol. For Hi-C library generation and sequencing, 100 ~ 500 cells were used per reaction, and at least two replicates were analyzed for each stage. All isolated cells were washed three times with a 0.5% bovine serum albumin in phosphate-buffered saline (BSA-PBS, Sigma) solution to avoid potential contamination. DNA was sheared to 300 ~ 500 bp with the Covaris S220 instrument. Biotin-labeled DNA was then pulled down with 10 μl of Dynabeads MyOne Streptavidin T1 (Life Technologies, SA-T1). The sequencing library was prepared using beads with the KAPA hyper kit. In total, 14 ~ 16 cycles of PCR amplification were performed. DNA was removed from the SA-T1 beads by heating at 98°C for 10 min with an additional 15 μl of elution buffer. Finally, size selection was performed using AMPure XP beads. Fragments ranging in size from 200 bp to 500 bp were selected. All libraries were sequenced on the Illumina HiSeq X Ten or Nova platform. ②ULI-NChIP libaries:The ULI-NChIP libraries for CCs were generated according to a previous protocol45. At least 500 cells were used per reaction, and two replicates were performed. All isolated cells were washed three times with a 0.5% BSA-PBS solution to avoid potential contamination. One microgram of the histone H3K9me3 antibody (39161, Active Motif) was used for each immunoprecipitation reaction. Paired-end 150-bp sequencing was performed on the Illumina HiSeq X Ten platform. ③RNA-seq:ICM cells and TE cells were harvested as described above. For RNA-seq library construction and sequencing, 5 ~ 10 cells were used per reaction. All isolated cells were washed three times with 0.5% BSA-PBS solution to avoid potential contamination. A single-cell RNA-seq library was generated as described previously46. The RNA-seq libraries were generated using the KAPA Hyper Prep Kit according to the manufacturer’s instructions. Single-end 50-bp sequencing was performed on the Illumina HiSeq 2500 platform.

treatment_protocol: ①Kdm4d injection group:Kdm4d overexpression in SCNT embryos were performed as described below. In brief, in vitro transcription of Kdm4d was performed with the mMESSAGE mMACHINE T7 Ultra Kit (Life Technologies, Grand Island, NY, USA) according to the manufacturer’s instructions. The storage concentration of mRNA was 1100ng/μl. Enucleated MII oocytes were injected with approximately 10pl of mRNA using a Piezo-driven micromanipulator. ②TSA treatment group:for TSA-treated group, extra 50nM Trichostatin A (Sigma, T8552) were added to the activation and culture mediums for 9 hours after somatic cells injection.

value: embryo

tag: development stage

value: Preimplantation embryo

tag: strategy

value: in situ Hi-C


title: CC_H3K9me3_rep1

description: H3K9me3 ChIP-seq for mouse cumulus cells replicate 1

value: cumulus cell

value: Terminal differentiation

value: H3K9me3 ChIP-seq


title: order1_N2_A4.single.cell

value: bone marrow

value: KitMerCreMer; R26tdTomato mice


title: CC_H3K9me3_rep2

description: H3K9me3 ChIP-seq for mouse cumulus cells replicate 2


title: order1_N2_A5.single.cell


title: order1_N2_A3.single.cell


title: TSA-early-2-cell_rep1

description: in situ Hi-C for nuclear transfer embryonic early 2-cell with TSA treated replicate 1


title: BT474_BAY155_Rep2

tag: agent 1


title: CC_input_rep1

description: input DNA for mouse cumulus cells replicate 1

value: input DNA


title: BT474_DMSO_Rep3


title: A3_30_min_IFNb


title: A2_unsti

value: unsti


title: order1_N2_A1.single.cell


title: CC_input_rep2

description: input DNA for mouse cumulus cells replicate 2


title: BT474_BAY155_Rep3


title: Kdm4d-early-2-cell_rep2

description: in situ Hi-C for nuclear transfer embryonic early 2-cell injected Kdm4d replicate 2


title: A2_4h_IL21


title: ICM_rep1

description: in situ Hi-C for nuclear transfer embryonic Inner cell mass replicate 1


title: Morula_rep1

description: in situ Hi-C for nuclear transfer embryonic morula cells replicate 1


title: Morula_rep2

description: in situ Hi-C for nuclear transfer embryonic morula cells replicate 2


title: A3_24h_IL21


title: A3_24h_IL15


title: ICM_rep2

description: in situ Hi-C for nuclear transfer embryonic Inner cell mass replicate 2


title: BT474_BAY155_Rep1


title: A2_4h_IL15


title: A2_4h_IFNb


title: A2_3h_IL21


title: TE_rep2

description: in situ Hi-C for nuclear transfer embryonic trophectoderm cells replicate 2


title: 22RV1_BAY155_Rep1

source_name: 22RV1 (prostate)


title: 8-cell_rep3

description: in situ Hi-C for nuclear transfer embryonic 8-cell replicate 3


title: 4-cell_rep2

description: in situ Hi-C for nuclear transfer embryonic 4-cell replicate 2


title: 8-cell_rep1

description: in situ Hi-C for nuclear transfer embryonic 8-cell replicate 1


title: 8-cell_rep2

description: in situ Hi-C for nuclear transfer embryonic 8-cell replicate 2


title: Kdm4d-early-2-cell_rep1

description: in situ Hi-C for nuclear transfer embryonic early 2-cell injected Kdm4d replicate 1


title: A3_24h_IFNb


title: A2_3h_IFNb


title: TE_rep1

description: in situ Hi-C for nuclear transfer embryonic trophectoderm cells replicate 1


title: TE_rep3

description: in situ Hi-C for nuclear transfer embryonic trophectoderm cells replicate 3


title: 22RV1_DMSO_Rep3


title: 22RV1_DMSO_Rep2


title: A2_30_min_IL15


title: Morula_rep3

description: in situ Hi-C for nuclear transfer embryonic morula cells replicate 3


title: 22RV1_DMSO_Rep1


title: 22RV1_BAY155_Rep3


title: Early-2-cell_rep1

description: in situ Hi-C for nuclear transfer embryonic early 2-cell replicate 1


title: 22RV1_BAY155_Rep2


title: Early-2-cell_rep2

description: in situ Hi-C for nuclear transfer embryonic early 2-cell replicate 2


title: Late-2-cell_rep2

description: in situ Hi-C for nuclear transfer embryonic late 2-cell replicate 2


title: A2_3h_IL15


title: media straurosporine biol. rep.1

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description:
smallRNA
nucleotide (nt) size < 200 nt

data_processing:
Adapter Trimming was performed on fastq files using trimmomatic 0.36 with standard commands (ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Trimmed Fastq files were aligned to the reference genome (Gencode M11) using STAR_2.5.2b with the following commands: STAR --runThreadN 10 --genomeDir /home/npath/Annotations/Gencode_M11/STARgenome_Gencode_vM11_050bp --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn XXX_trimmed.fq.gz --readFilesCommand zcat --outFileNamePrefix XXX --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignEndsType EndToEnd --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --quantMode GeneCounts
miRNA counts were generated using featurecounts featureCounts v1.6.2 with the MirBASE 21 mouse dataset as reference ; Command:featureCounts -a/MirBASE/mmu.gtf -G GRCm38.primary_assembly.genome.fa -o counts_mature_miRNA.txt -F GTF -g Name -t miRNA -T 10 --largestOverlap
Differential miRNA expression was analysed using DESeq2 1.20. The two samples of batch rep.4 showed strong batch effects and were removed from downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: miR.Counts.csv comma delineated file with miRNA counts

source_name: neonatal brain

growth_protocol: Two million primary cortical neurons E17.5 were grown fro three days in standard cell culture conditions in Neurobasal Medium (Gibco #21103-049).

extract_protocol:
Primary cultures of purified cortical neurons were generated as described previously [Lehmann et al. 2012]. Neonatal neurons were isolated from mice cortex of embryonic day E17.5. Brains were separated from blood vessels, meningea and cerebellum into a 15 ml Falcon tube filled with HBSS buffer (Gibco #14170-088). After two washing steps 500 µl of Trypsin (2.5%) was added following an incubation step of 20 minutes at 37°C. Trypsination was stopped with four ml of heat-inactivated FCS, cells were washed twice with HBSS and incubated with 100 µl DNAse (1mg/ml) for one minute. Subsequently, cells were washed twice with Neurobasal Medium (Gibco #21103-049) supplemented with 1% L-Glutamin (Gibco #25030-024), 1% penicillin/streptomycin (Gibco #15140-122) and 10% B27 supplement (Gibco #17504-044). Neurons were transferred into a new 50 ml Falcon tube, resuspended in 10 ml Neurobasal Medium and centrifuged at 300rpm at 4°C for five minutes. Supernatants were separated carefully and transferred into a 50 ml Falcon tube. Neurons were resuspended in Neurobasal Medium and seeded into 6-well plates. Next, day half of the media was replaced by new media and cells were incubated for additional 48 hours before the start of the experiment. smallRNA enrichment was performed as previously described [Glynn et al. 2013]. Briefly, 700 µl of Trizol™ (Thermo Fisher Scientific #15596026) were added to media or neurons samples. Samples were vortexed for at least ten seconds and allowed to rest at room temperature for additional five minutes. Then, 140 µl of chloroform was added and samples were shaken for additional 15 seconds and centrifuged at 14.000rpm (Eppendorf #5417R) at 4°C for 15 minutes. The aqueous phase was transferred to a new tube without touching the interphase. smallRNA enrichment was performed with the mirVana™ (Thermo Fisher Scientific #AM1560) isolation kit according to the manufacturer’s protocol.
Library preparation and RNAseq were carried out according to the TruSeq Small RNA Library Preparation Kit Reference Guide (Illumina, Inc., San Diego, CA, USA), the Illumina HiSeq 1000 System User Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA).  In brief, 10 ng of small RNA enriched (mirVana Kit) total RNA was used for ligation of the RNA 3’ and the RNA 5’ adapters, followed by reverse transcription to create single stranded cDNA. The cDNA was then PCR amplified for 12 cycles using a common and an index primer. Instead of a gel purification of the small-RNA libraries, a magnetic bead clean up (Agencourt AMPure XP, Beckman Coulter, Brea, Ca, USA) with a final elution volume of 10 µl elution buffer was performed. Purity and integrity was assessed on the Agilent 2100 Bioanalyzer with the High Sensitivity DNA Assay (Agilent, Palo Alto, CA, USA). The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on an HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide.

treatment_protocol: Media were replaced to 1 µM staurosporine (Merck #S6942) or solvent control containing media and primary neurons were incubated for eight hours. Conditioned media was separated from cells and the material was stored at -80° before starting smallRNA enrichment protocol.

tag: cells

value: primary cortical neurons

tag: strains

tag: age

value: neonatal E17.5


title: media DMSO control biol. rep.1

description:
smallRNA
nucleotide (nt) size < 200 nt


title: media straurosporine  biol. rep.3

description:
smallRNA
nucleotide (nt) size < 200 nt


title: media DMSO control  biol. rep.3

description:
smallRNA
nucleotide (nt) size < 200 nt


title: neurons straurosporine biol. rep.3

description:
smallRNA
nucleotide (nt) size < 200 nt


title: 1hpi_rep1

description: in situ Hi-C for nuclear transfer embryonic 1-hour post injecting cells replicate 1


title: A2_24h_IFNb

tag: type

value: IFNb


title: A2_30_min_IL21

tag: donor


title: media straurosporine biol. rep.2

description:
smallRNA
nucleotide (nt) size < 200 nt


title: media DMSO control biol. rep.2

description:
smallRNA
nucleotide (nt) size < 200 nt


title: 1hpa_rep1

description: in situ Hi-C for nuclear transfer embryonic 1-hour post activating cells replicate 1


title: A2_30_min_IFNb

tag: stimulation


title: 1hpi_rep2

description: in situ Hi-C for nuclear transfer embryonic 1-hour post injecting cells replicate 2


title: 0.5hpi_rep2

description: in situ Hi-C for nuclear transfer embryonic 30-min post injecting cells replicate 2


title: 0.5hpi_rep1

description: in situ Hi-C for nuclear transfer embryonic 30-min post injecting cells replicate 1


title: A2_24h_IL21

tag: time point


title: 6hpa_rep1

description: in situ Hi-C for nuclear transfer embryonic 6-hour post activating cells replicate 1

tag: strain


title: 12hpa_rep1

description: in situ Hi-C for nuclear transfer embryonic 12-hour post activating cells replicate 1

tag: tissue


title: 12hpa_rep3

description: in situ Hi-C for nuclear transfer embryonic 12-hour post activating cells replicate 3


title: 6hpa_rep2

description: in situ Hi-C for nuclear transfer embryonic 6-hour post activating cells replicate 2


title: Bcell_S2P_WT1_20452

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
Trimmed reads larger than 18nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata --tryhard -m 1)
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities

source_name: primary activated splenic B lymphocytes

growth_protocol: Primary immature B cells were isolated from spleens of Supt5hFl/-Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ mice and cultured in complete RPMI medium wit IL4/LPS stimulation.

extract_protocol:
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, samples were end-repaired with the Epicenter End-Repair Kit. After A-tailing the samples with Klenow (exo-) enzyme, NEXTflex adapters were ligated to the samples and then purified with AMPure XP beads. PCR amplification of the libraries was performed with the Phusion-HF enzyme and the NEXTflex primer mix.

treatment_protocol: Primary acttivated B cells were activated for 28h prior to the addition of 2 uM 4-HT for 32h (total of 60 h B cell activation with 32h 4-HT treatment) and then harvested for all downstream applications.

tag: antibody

value: RNA Pol II (Ser2-phospho)

tag: cell type

value: Rosa26ERT2-cre/+ primary B cells

tag: treatment

value: 4-hydroxy tamoxifen (4-HT)


title: 1hpa_rep2

description: in situ Hi-C for nuclear transfer embryonic 1-hour post activating cells replicate 2


title: A1_4h_IL15

value: Control


title: Bcell_S5P_WT1_20451

value: RNA Pol II (Ser5-phospho)


title: 12hpa_rep2

description: in situ Hi-C for nuclear transfer embryonic 12-hour post activating cells replicate 2

value: embryo

value: Preimplantation embryo


title: CC_rep4

description: in situ Hi-C for mouse cumulus cells replicate 4

value: cumulus cell

value: in situ Hi-C


title: Bcell_4H8_Spt5dep1_20454

value: RNA Pol II (4H8)

value: Supt5hFl/- Rosa26ERT2-cre/+ primary mature B cells


title: A2_24h_IL15


title: Bcell_4H8_WT1_20450


title: A1_4h_IFNb


title: neurons DMSO control biol. rep.3

description:
smallRNA
nucleotide (nt) size < 200 nt


title: neurons straurosporine biol. rep.2

description:
smallRNA
nucleotide (nt) size < 200 nt


title: A1_unsti


title: neurons straurosporine biol. rep.1

description:
smallRNA
nucleotide (nt) size < 200 nt


title: A1_3h_IL21


title: A1_4h_IL21


title: neurons DMSO control biol. rep.2

description:
smallRNA
nucleotide (nt) size < 200 nt


title: CC_rep2

description: in situ Hi-C for mouse cumulus cells replicate 2

value: Terminal differentiation


title: CC_rep3

description: in situ Hi-C for mouse cumulus cells replicate 3


title: A1_30_min_IL21


title: mESC500_rep1

description: in situ Hi-C for 500 mouse embryonic stem cells replicate 1

value: cell line

value: Pluripotent stem cell


title: mESC500_rep2

description: in situ Hi-C for 500 mouse embryonic stem cells replicate 2


title: CC_rep1

description: in situ Hi-C for mouse cumulus cells replicate 1


title: A1_30_min_IL15


title: neurons DMSO control biol. rep.1

description:
smallRNA
nucleotide (nt) size < 200 nt

value: primary cortical neurons


title: KO1

city: Columbus

first: Mireia

last: Guerau

state: OH

address: 453 W 10th Ave

department: HRS-Medical Laboratory Science

institute: The Ohio State University

description: processed data header: 19-0748-1_Th17_36plus51

data_processing:
fastq files were aligned to the GRCm38.p3 assembly of the Mus musculus reference from NCBI using version 2.6.0c of the RNA-Seq aligner STAR
Features were identified from the GFF file that came with the assembly from Gencode (Release M19)
Feature coverage counts were calculated using featureCounts
Differentially expressed features were calculated using DESeq2
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: Coverage files and Excel file including raw counts and DESeq produced normalized values

source_name: Th17 cell polarized from naive CD4 T-cells isolated from spleen and lymph nodes

growth_protocol: 2.5x10^6 naive CD4 T cells from murine spleens and lymph nodes are cultured 24 well tissue culture plates for 72 hours in activating, coated anti-CD3/CD28 conditions with rh-TGFβ and m-IL6 (5% CO2, 37°C incubator).

extract_protocol:
RNA was isolated using Direct-zol RNA miniprep kit from Zymo research as per manufacturer's instructions.
RNA-seq libraries were prepared using Illumina’s TruSeq Stranded protocol. rRNAremoval was done using Ribo-zero Human/Mouse/Rat Gold kit

treatment_protocol: T cells activated with anti-CD3/CD28 for 72hr and polarizing cytokines rh-TGFβ and m-IL-6

tag: background strain

tag: genotype

value: rh-TGFbeta + m-IL6 polarization + alphaCD3/CD28 treatment for 72hr


title: A1_30_min_IFNb

value: IFNb


title: A1_24h_IL21


title: media straurosporine biol. rep.4

description:
smallRNA
nucleotide (nt) size < 200 nt

value: neonatal E17.5


title: A1_3h_IL15


title: media DMSO control biol. rep.4

description:
smallRNA
nucleotide (nt) size < 200 nt


title: A1_24h_IL15

source_name: IEL cell line derived from Intestinal biopsies


title: WT1

description: processed data header: 19-0745-1_Th17_30


title: A1_3h_IFNb

source_name: IEIL cell line derived from Intestinal biopsies


title: mESC200_rep1

description: in situ Hi-C for 200 mouse embryonic stem cells

tag: development stage


title: L104_Kidney_mRNA-seq

city: Kyoto

first: Kazuhiro

last: Yagita

address: Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Trimmotatic (Version 0.38) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome mm10 with STAR (2.5.4b) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools (1.9) (Li et al. 2009).
The University of California, Santa Cruz (UCSC) known canonical gene set (32,989 genes) was used for annotation, and the reads mapped to the exons were quantified using Homer (Heinz et al. 2010).
The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
Fragments Per Kilobase per Million mapped reads (FPKM) were calculated using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and tab-delimited text files include and FPKM values for each Sample.

source_name: Kidney

growth_protocol: Male C57BL/6J mice exposed to the three light conditions for 65 weeks (aged 77 weeks) or 85 weeks (aged 97 weeks):  LD-condition (light–dark condition with an 8:00–20:00 light period) and ADV-condition (8-h phase advance once every 4 days)

extract_protocol:
Tissue samples were homogenized in Invitrogen TRIzol reagent. RNA was extracted by using QIAGEN RNeasy columns as per manufacturer’s protocol.
Poly(A)-enriched stranded RNA sequencing was carried out by Takara Bio, Japan, on Illumina HiSeq 2500 with 100-bp paired-end reads and by Macrogen Japan on Illumina NovaSeq 6000 with 101-bp paired-end reads.

value: Kidney

tag: Sex

value: male

tag: chronic jet lag (cjl) conditions

value: LD

tag: period of cjl


title: KO3

description: processed data header: 19-0750-1_Th17_53plus51


title: KO2

description: processed data header: 19-0749-1_Th17_39plus51


title: mESC100_rep1

description: in situ Hi-C for 100 mouse embryonic stem cells

tag: strategy


title: 4-cell_rep1

description: in situ Hi-C for nuclear transfer embryonic 4-cell replicate 1


title: WT2

description: processed data header: 19-0746-1_Th17_42


title: A1_24h_IFNb

value: Control


title: Late-2-cell_rep1

description: in situ Hi-C for nuclear transfer embryonic late 2-cell replicate 1

value: embryo


title: L86_Kidney_mRNA-seq


title: L63_Kidney_mRNA-seq


title: WT3

description: processed data header: 19-0747-1_Th17_52


title: L65_Kidney_mRNA-seq


title: KO1act

source_name: CD4 T-cells isolated from spleen and lymph nodes

growth_protocol: 5x10^6 whole CD4 T cells from murine spleens and lymph nodes are cultured 24 well tissue culture plates for 48 hours in activating, coated anti-CD3/CD28 conditions without any added cytokines (5% CO2, 37°C incubator).

treatment_protocol: T cells activated with anti-CD3/CD28 for 48hr

value: alphaCD3/CD28 treatment for 48hr


title: WT4act


title: KO5act


title: KO4act_R2


title: A91_Kidney_mRNA-seq

value: ADV


title: WT2act


title: blood_patient57

city: Grålum

first: camilla

middle: furlund

last: nystrand

address: Kalnesveien 320

country: Norway

institute: Østfold hospital trust

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix.

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization.

label: biotin

source_name: healthy control_male_group3

label_protocol: Total RNA (150 ng) from each sample was prepared using the Ambion WT Expression Kit (Ambion Inc., Austin, Texas, USA) according to manufacturer’s instructions.

growth_protocol: Pheripheral blood cells

extract_protocol: RNA extraction was performed with PAXgene Blood RNA kit according to manufactors instruction, and RNA quality assesed with Bioanalyzer

treatment_protocol: Blood samples were collected with PAXgene Blood RNA tubes

tag: subject id

tag: subject status

value: healthy control

tag: gender

tag: age

tag: hh group

tag: mutation

value: pheripheral blood


title: A75_Kidney_mRNA-seq

tag: tissue

tag: strain


title: A115_Kidney_mRNA-seq


title: A94_Kidney_mRNA-seq


title: blood_patient55

source_name: healthy control_female_group3

value: female


title: blood_patient47


title: WT1act


title: blood_patient53


title: blood_patient51


title: POOL REFERENCE B: Sample - Reference 27

city: Botucatu

first: Tainara

middle: Francini

last: Felix

state: SP

address: Av. Prof. Mário Rubens Guimarães Montenegro, s/n, s/n

department: Surgery and Orthopedics

country: Brazil

institute: UNESP

description: Sample - Reference 27

data_processing:
Global data normalization was performed using Expression Suite software (Thermo Fisher, Waltham, MA, USA), and miRNA expression profiles were determined using RQ Manager v.1.2 software (Thermo Fisher, Waltham, MA, USA).
Fold Change – FC ≥ 1,5 and p< 0.05

source_name: Healthy Control

extract_protocol: Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation (Thermo Fisher Scientific, Waltham, MA, USA) according to Goswami RS, Atenafu EG, Xuan Y, Waldron L, Reis PP, Sun T, et al. MicroRNA signature obtained from the comparison of aggressive with indolent non-Hodgkin lymphomas: potential prognostic value in mantle-cell lymphoma. J Clin Oncol [Internet]. 2013;31(23):2903–11.

treatment_protocol: Samples obtained from FFPE tissue blocks  were needle microdissected using the stereomicroscope Leica EZ4 (Leica Microsystems, Wetzlar, Germany) before RNA extraction, in order to isolate the target tumor or normal cell populations.

value: Esophageal biopsy (normal)

tag: age (years)

value: F

tag: follow-up (years)


title: blood_patient37

source_name: hemochromatosis patient_male_group1

value: hemochromatosis patient

value: C282Y homozygotes


title: blood_patient40


title: POOL REFERENCE B: Sample - Reference 25

description: Sample - Reference 25

value: M


title: POOL REFERENCE B: Sample - Reference 26

description: Sample - Reference 26


title: POOL REFERENCE B: Sample - Reference 24

description: Sample - Reference 24


title: blood_patient36

source_name: hemochromatosis patient_female_group1


title: POOL REFERENCE B: Sample - Reference 23

description: Sample - Reference 23


title: blood_patient34


title: 200611820005_R05C01

type: genomic

city: Exeter

first: Stefania

last: Policicchio

state: Devon

address: RILD building, BARRACK ROAD, Albion Place

country: United Kingdom

institute: University of Exeter, Medical School

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit  (Zymo Research) according to the manufacturer’s standard protocol.bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: Samples were assessed using the Illumina Infinium Human Methylation850K BeadChip (Illumina) and arrays were imaged using a Illumina iScan System (Illumina).

data_processing: llumina Genome Studio software was used to extract the raw signal intensities of each probe (without background correction or normalization).   Probes containing a SNP with minor allele frequency (MAF) >5% within 10bp of the single base extension site based on   Illumina’s database and probes identified by Chen et al.* were removed. Data was then  pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: Cy3 and Cy5

source_name: postmortem brain

label_protocol: Samples were processed according to the Illumina Infinium Human Methylation850K BeadChip (Illumina) standard protocol.

extract_protocol: Genomic DNA was isolated from post mortem human brain using a standard phenol-chloroform extraction method, and tested for degradation and purity before analysis.

tag: groupid

value: Female


title: 200616470047_R02C01

value: Male


title: POOL REFERENCE B: Sample - Reference 20

description: Sample - Reference 20


title: PAWSCY_SNP

city: Tampa

first: Andrew

middle: Scott

last: Brohl

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were scanned using an Affymetrix M10 scanner

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (4.0.0.1567). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using chomosome analysis suite v3.3.0.139.
analysis results generated by the chromosome analysis suite (cychp)

source_name: tumor

label_protocol: As per manufacturer

growth_protocol: not applicable

extract_protocol: allprep DNA/RNA kit (Qiagen)

tag: disease state

value: undifferentiated embryonic sarcoma of the liver (UESL)

value: UESL tumor

value: 1825 days


title: PAVZCN_SNP

value: 3652 days


title: 200616470047_R07C01


title: POOL REFERENCE B: Sample - Reference 21

description: Sample - Reference 21


title: POOL REFERENCE B: Sample - Reference 22

description: Sample - Reference 22


title: 200611820014_R08C01


title: POOL REFERENCE B: Sample - Reference 19

description: Sample - Reference 19


title: 200603290023_R07C01


title: PAWSXX_SNP

value: 272 days


title: PATJSC_SNP

value: 3112 days


title: PAWYLP_SNP

value: 3065 days


title: PAUPDM_SNP

value: 2520 days


title: PATXJY_SNP

value: 1956 days


title: POOL REFERENCE B: Sample - Reference 18

description: Sample - Reference 18


title: PATWXD_SNP

value: 4236 days


title: PATWFW_SNP

value: 4294 days


title: blood_patient31

value: female

value: pheripheral blood


title: blood_patient25

value: hemochromatosis patient

value: male

value: C282Y homozygotes


title: POOL REFERENCE B: Sample - Reference 16

description: Sample - Reference 16

value: Esophageal biopsy (normal)

value: M


title: POOL REFERENCE B: Sample - Reference 17

description: Sample - Reference 17


title: PAPWGG_SNP

value: undifferentiated embryonic sarcoma of the liver (UESL)

value: UESL tumor

value: 3542 days

value: Female


title: POOL REFERENCE A: Sample - Reference 15

description: Sample - Reference 15


title: blood_patient27


title: 200603290023_R04C01


title: PARCGJ_SNP

value: 1590 days

value: Male


title: PAUPRI_SNP

value: 3867 days


title: blood_patient26


title: POOL REFERENCE A: Sample - Reference 14

description: Sample - Reference 14


title: PAUGAD_SNP

value: 4257 days


title: POOL REFERENCE A: Sample - Reference 13

description: Sample - Reference 13

value: F


title: blood_patient17


title: blood_patient15

source_name: hemochromatosis patient_female_group2

value: H63D homozygotes and/or H63D/C282Y heterozygotes


title: blood_patient16

source_name: hemochromatosis patient_male_group2


title: POOL REFERENCE A: Sample - Reference 12

description: Sample - Reference 12


title: blood_patient11


title: blood_patient12


title: POOL REFERENCE A: Sample - Reference 9

description: Sample - Reference 9


title: 200603220015_R03C01


title: POOL REFERENCE A: Sample - Reference 10

description: Sample - Reference 10


title: blood_patient10


title: 200616470004_R03C01


title: TE_RNA_rep3

city: Shanghai

description:
RNA-seq for nuclear transfer embryonic trophectoderm cells replicate 3
RNA.featureCount.txt

value: embryo

tag: development stage

value: Preimplantation embryo

value: RNA-seq


title: POOL REFERENCE A: Sample - Reference 8

description: Sample - Reference 8

tag: Sex


title: blood_patient5

value: hemochromatosis patient

value: male

value: pheripheral blood


title: blood_patient19

value: female

value: C282Y homozygotes


title: blood_patient8


title: POOL REFERENCE A: Sample - Reference 7

description: Sample - Reference 7

value: Esophageal biopsy (normal)

value: M


title: TE_RNA_rep2

description:
RNA-seq for nuclear transfer embryonic trophectoderm cells replicate 2
RNA.featureCount.txt


title: POOL REFERENCE A: Sample - Reference 6

description: Sample - Reference 6


title: TE_RNA_rep1

description:
RNA-seq for nuclear transfer embryonic trophectoderm cells replicate 1
RNA.featureCount.txt


title: POOL REFERENCE A: Sample - Reference 5

description: Sample - Reference 5


title: ICM_RNA_rep3

description:
RNA-seq for nuclear transfer embryonic Inner cell mass replicate 3
RNA.featureCount.txt


title: ICM_RNA_rep4

description:
RNA-seq for nuclear transfer embryonic Inner cell mass replicate 4
RNA.featureCount.txt


title: POOL REFERENCE A: Sample - Reference 4

description: Sample - Reference 4


title: Aβ42l+FMN_RNASeq 4, biological rep3

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
The raw reads from each sample were mapped to the CEN.PK 113-7D reference genome using TopHat (v 2.0.12), with 84.0—87.6% of the reads successfully mapped.
Cufflinks version 2.2.1 was used to calculate FPKM values, and the feature Counts module of the Subread package (v 1.4.6) was used to determine raw read counts.
Genome_build: CEN.PK 113-7D

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: shake flask 30 ˚C, 200rpm

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.
RNA was prepared for sequencing using the Illumina TruSeq samples preparation kit v2, with poly-A enrichment. The fragments were clustered on cBot and sequenced on a single lane on a HiSeq 4000 with paired ends (2 × 150 bp), according to the manufacturer’s instructions. The number of read pairs obtained for each sample ranged from 12.0–16.0 million.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.

value: integration of two copies of promoter+ABeta42+terminator sequences

tag: supplementation

value: FMN


title: 200611820005_R07C01

value: Male


title: blood_patient4


title: ICM_RNA_rep1

description:
RNA-seq for nuclear transfer embryonic Inner cell mass replicate 1
RNA.featureCount.txt


title: blood_patient28


title: Aβ42l+FMN_RNASeq 3, biological rep3


title: 200611820005_R02C01


title: POOL REFERENCE A: Sample - Reference 3

description: Sample - Reference 3


title: POOL REFERENCE A: Sample - Reference 2

description: Sample - Reference 2


title: 200616470070_R03C01


title: 200616470070_R08C01


title: Aβ42l+FMN_RNASeq 2, biological rep3


title: POOL REFERENCE A: Sample - Reference 1

description: Sample - Reference 1


title: ICM_RNA_rep2

description:
RNA-seq for nuclear transfer embryonic Inner cell mass replicate 2
RNA.featureCount.txt


title: POOL B2: Sample - Lesion from Patient 13

description: Sample - Lesion from Patient 13

source_name: Sodium hydroxide (NaOH)

value: Esophageal biopsy (lesion)


title: Aβ42l+FMN_RNASeq 1, biological rep3


title: 200603290076_R08C01


title: POOL REFERENCE A: Sample - Reference 11

description: Sample - Reference 11


title: Aβ42+FMN_RNASeq 4, biological rep2


title: 200616470004_R05C01

value: Female


title: old_aorta5

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - fastp 0.20.0, --in1 ../SAMPLE_R1.fastq.gz --out1 clt_SAMPLE_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j SAMPLE_fastp.json
Genome Alignment - STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir GENOME --readFilesIn SAMPLE --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 - subread-1.6.4, featurecounts, -s 2 -t exon -g gene_name
Genome_build: GRCm38 + gencode M22
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: male C57BL/6 mouse at the age of 92.5 weeks

extract_protocol:
Total RNA were extracted from aortas (free from periadventitial adipose tissue) using miRNeasy RNA extraction kit and subjected to RNA-seq.
Illumina TruSeq Stranded mRNA

treatment_protocol: Young and old mice were sacrificed at the same time for tissue isolation. After removal of periadventitial adipose tissue, purified aortas were subjected to total RNA extraction.

value: aorta

value: 92.5 weeks


title: old_aorta3


title: old_aorta4


title: POOL B2: Sample - Lesion from Patient 12

description: Sample - Lesion from Patient 12


title: POOL B2: Sample - Lesion from Patient 8

description: Sample - Lesion from Patient 8

value: F


title: Aβ42+FMN_RNASeq 3, biological rep2


title: old_aorta2


title: old_aorta1


title: 200616470004_R02C01


title: Aβ42+FMN_RNASeq 2, biological rep2


title: young_aorta5

source_name: male C57BL/6 mouse at the age of 14.5 weeks

value: 14.5 weeks


title: POOL B2: Sample - Lesion from Patient 7

description: Sample - Lesion from Patient 7


title: POOL B1: Sample - Lesion from Patient 10

description: Sample - Lesion from Patient 10


title: 200603220015_R02C01


title: young_aorta4


title: 200611820039_R01C01


title: 200616470070_R06C01


title: Aβ42+FMN_RNASeq 4, biological rep1


title: young_aorta3


title: POOL B1: Sample - Lesion from Patient 6

description: Sample - Lesion from Patient 6


title: Aβ42+FMN_RNASeq 3, biological rep1


title: 200616470047_R03C01


title: young_aorta2


title: Aβ42+FMN_RNASeq 2, biological rep1


title: POOL B1: Sample - Lesion from Patient 7

description: Sample - Lesion from Patient 7


title: POOL B1: Sample - Lesion from Patient 1

description: Sample - Lesion from Patient 1


title: young_aorta1


title: Aβ42+FMN_RNASeq 1, biological rep1


title: POOL A2: Sample - Lesion from Patient 14

description: Sample - Lesion from Patient 14


title: 200616470006_R07C01


title: 200616470006_R05C01


title: Aβ42+FMN_RNASeq 1, biological rep2


title: A115_Liver_mRNA-seq

source_name: Liver

value: Liver

tag: chronic jet lag (cjl) conditions

value: ADV

tag: period of cjl


title: POOL A2: Sample - Lesion from Patient 15

description: Sample - Lesion from Patient 15


title: POOL A2: Sample - Lesion from Patient 11

description: Sample - Lesion from Patient 11


title: Aβ42_RNASeq 3, biological rep3


title: A94_Liver_mRNA-seq

value: male


title: A91_Liver_mRNA-seq


title: Aβ42_RNASeq 2, biological rep3


title: POOL A2: Sample - Lesion from Patient 9

description: Sample - Lesion from Patient 9


title: 200611820039_R08C01


title: 200603220015_R05C01


title: A75_Liver_mRNA-seq


title: Aβ42_RNASeq 1, biological rep3


title: L104_Liver_mRNA-seq

value: LD


title: Aβ42_RNASeq 4, biological rep2


title: 200616470004_R01C01


title: 200611820005_R04C01


title: 200616470006_R01C01


title: L86_Liver_mRNA-seq


title: 200611820008_R02C01


title: 200603220015_R07C01


title: Aβ42_RNASeq 4, biological rep3


title: 200603220015_R01C01


title: 200616470047_R06C01


title: POOL A1: Sample - Lesion from Patient 7

description: Sample - Lesion from Patient 7


title: POOL A1: Sample - Lesion from Patient 1

description: Sample - Lesion from Patient 1


title: 200611820039_R07C01


title: Aβ42_RNASeq 2, biological rep2


title: POOL A2: Sample - Lesion from Patient 2

description: Sample - Lesion from Patient 2

source_name: sulphonic and  hydrofluoric acid (home made aluminum brightener product)


title: POOL A2: Sample - Lesion from Patient 3

description: Sample - Lesion from Patient 3


title: POOL A1: Sample - Lesion from Patient 6

description: Sample - Lesion from Patient 6


title: Aβ42_RNASeq 1, biological rep2


title: MiV_HET_FBN1

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

data_processing:
Fastq files were trimmed to remove adapter and low quality sequences using Trimmomatic
Trimmed reads were mapped to the reference mouse genome mm10 using Hisat2
After trimming reads were quantified using Kallisto to produce TPM and counts
Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text file includes TPM for individual WT and FBN1-HET samples.

source_name: mitral valve tissue

extract_protocol:
Mitral valve tissue was harvested and pooled from 8 hearts of each genotype in separate WT and FBN1Het samples.  RNA was isolated using NucleoSpin RNA/Protein extraction kit (Machery-Nagel) and amplified using the Ovation RNAseq system v2 (NuGEN). cDNA was generated using the Nextera XT DNA sample preparation kit.
RNA libraries were prepared for sequencing using Illumina HiSeq 2500 system

tag: genotype

value: 5 Months

value: Pooled Male and Female

value: mitral valve tissue


title: Aβ42_RNASeq 3, biological rep2


title: POOL A1: Sample - Lesion from Patient 5

description: Sample - Lesion from Patient 5

value: M


title: 200616470004_R06C01


title: L63_Liver_mRNA-seq


title: 200616470047_R05C01


title: 200611820008_R04C01


title: MiV_WT_FBN1

value: WT


title: Aβ42_RNASeq 3, biological rep1

value: integration of two copies of promoter+ABeta42+terminator sequences


title: 200603290076_R06C01

value: Male


title: Bcell_ATACSeq_Spt5dep2_48857

data_processing:
The illumina reads were adapter trimmed on their 3’ ends with cutadapt (version 1.15;  --match-read-wildcards -O 1 -f fastq -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC for read1 and cutadapt --match-read-wildcards -O 1 -f fastq -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for read2).
The paired end trimmed reads larger then 18nt were aligned with bowtie2 (version 2.1.0;  --sensitive   -p 10 -X 5000 -N 0   --trim5 0 --trim3 0) to the mouse mm9 genome.
The aligned reads were sorted by position with samtools (version 0.1.19).
Strand specific and undirected occupancy profiles were generated with deeptools bamCoverage v2.2.2.
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities

source_name: primary activated splenic B lymphocytes

growth_protocol: Primary mature B cells were isolated from spleens of Supt5hFl/-Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ mice and cultured in complete RPMI medium wit IL4/LPS stimulation.

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor modifocations in the tagmentation step where we used a homemade Tn5 enzyme and assembeld the Tn5-adapter tagmentation mix ourselves. However, the adapter sequences and primers used for library amplification are the same as in the Buenrostro et al. protocol.
transposed DNA was amplified with RT-qPCR monitoring to avoid oveamplification and the libraries were purified with AMPure XP beads.

treatment_protocol: Primary acttivated B cells were activated for 28h prior to the addition of 2 mM 4-HT for 32h (total of 60h B cell activation with 32h 4-HT treatment) and then harvested for all downstream applications.

tag: cell type

value: Supt5hFl/- Rosa26ERT2-cre/+ primary mature B cells

tag: treatment

value: 4-hydroxy tamoxifen (4-HT)


title: 200616470006_R02C01

tag: age

tag: gender

value: Female


title: POOL A1: Sample - Lesion from Patient 4

description: Sample - Lesion from Patient 4

value: Esophageal biopsy (lesion)


title: Aβ42_RNASeq 2, biological rep1


title: Aβ42_RNASeq 1, biological rep1


title: Bcell_ATACSeq_Spt5dep1_48856


title: Bcell_ATACSeq_WT2_48855

value: Rosa26ERT2-cre/+ primary B cells


title: 200611820057_R08C01


title: Control+FMN_RNASeq 4, biological rep3

value: integration of two copies of promoter+terminator sequences

value: FMN


title: 200603220015_R06C01


title: Bcell_ATACSeq_WT1_48854


title: Bcell_PROCap_WT2_39537

data_processing:
Library strategy: PRO-cap
The illumina reads were adapter trimmed on their 3’ ends with cutadapt(version 1.15;  --match-read-wildcards -f fastq -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
Afterwards 5 nucleotides from their 5’ end were removed with fastx_trimmer (fastx_toolkit version 0.0.13;  -Q33 -t 5 ).
The trimmed reads larger then 18nt were aligned with bowtie (version 1.0.0;  -S  -p 10   --trim5 0 --trim3 0   -v 2 --best --strata --tryhard   -m 1  --phred33-quals   --chunkmbs 256) to the mouse mm9 genome.
The aligned reads were sorted by position with samtools (version 0.1.19).
Strand specific and undirected occupancy profiles were generated with deeptools bamCoverage v2.2.2.
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities

growth_protocol: Primary mature B cells were isolated from spleens of Supt5hFl/- Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ mice, and cultured in complete RPMI medium with IL4/LPS stimulation.

extract_protocol:
Following cell membrane lysis with hypotonic buffer, nuclei were isolated via sucrose gradient density centrifugation. PRO-cap was performed as described (Kwak et al., 2013 and Mahat et al., 2016). Briefly, 20 million nuclei were used per reaction, and the run-on was performed for 5 minutes with biotin-NTPs  followed by extraction of RNA with Trizol reagent (Thermo Fisher, 15596026) and subsequent enrichment of biotin-labeled RNA with anti-BrU beads.
After 3' end repair, Illumina-compatible 3' end RNA adapters were ligated. All free 5' end were dephosphorylated and capped 5'ends were enzymatically treated to remove the cap to ligate the Illumina-compatile 5' end RNA adapters. After Streptavidin enrichment of biotin labeld RNA, the library was reverse transcribed and amplified.

treatment_protocol: Primary acttivated B cells were activated for 28h prior to the addition of 2 mM 4-HT for 32h (total of 60 h B cell activation with 32h 4-HT treatment) and then harvested for all downstream applications.


title: Control+FMN_RNASeq 2, biological rep3


title: 200603290023_R03C01


title: 200616470070_R07C01


title: Control+FMN_RNASeq 1, biological rep3


title: Control+FMN_RNASeq 4, biological rep2


title: 200616470047_R01C01


title: Bcell_S5P_WT2_40929

tag: antibody

value: RNA Pol II (Ser5-phospho)


title: Control+FMN_RNASeq 3, biological rep2


title: Bcell_S2P_WT2_40926

value: RNA Pol II (Ser2-phospho)


title: Bcell_PROCap_WT1_39536


title: L65_Liver_mRNA-seq

tag: tissue

value: Liver

value: male

value: LD


title: Control+FMN_RNASeq 3, biological rep3

tag: strain


title: Aβ42_RNASeq 4, biological rep1


title: RVA4: Vemurafenib_Acalabrutinib_3

city: East Lansing

first: Sean

middle: Alexander

last: Misek

state: MI

address: 1355 Bogue Street

institute: Michigan State University

data_processing:
Basecalls performed with Illumina Real Time Analysis, RTA
Demultiplexing and FastQ conversion with Illumina Bcl2fastq
Quality Control with FastQC v0.11.5
Read Trimming with Trimmomatic v0.33
Read Mapping with HISAT2 v2.1.0
Read Counting/Analysis with HTSeq v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw HTSeq counts for each sample

source_name: Human Melanoma Cells

growth_protocol: M229R cells were grown in DMEM + 1% Anti/Anti + 10% FBS which was supplemented with 2 µM vemurafenib.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit, prepared libraries were QCd and quantified using a Qubit and Labchip Bioanalyzer.

treatment_protocol: M229R cells were treated with either vemurafenib (2 µM), ibrutinib (5 µM), acalabrutinib (5 µM), or the combination of ibrutinib/acalabrutinib and vemurafenib for 24 h prior to RNA extraction.

value: Human Melanoma Cells

tag: cell line


title: 200611820039_R03C01


title: Control+FMN_RNASeq 1, biological rep2


title: RVA3: Vemurafenib_Acalabrutinib_2


title: Bcell_4H8_WT2_40924

value: RNA Pol II (4H8)


title: RVA2: Vemurafenib_Acalabrutinib_1


title: Control+FMN_RNASeq 4, biological rep1


title: 200603290076_R02C01