title: B62_H015

city: Beijing

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

description: Gene expression after 6hr in LPS/GalN induced mouse liver

hyb_protocol: 5 ug of Cy5-labelled cRNA was fragmented at 70°C for 15 minutes in a reaction volume of 30ul containing 10x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction, 182ul of NewOA Hyb Buffer was added to the fragmentation mixture and hybridized to mouse OneArray Microarray  for 16 hours at 50°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minutes at 42°C with Wash Buffer 1 (Agilent) and 2 minute with 42°C Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: GenePix™ 4 was used for image data capture to obtain two primary DATA format GPR files, and finally the signal strength conversion of two GPR data files was performed using the control probe in Hualin chip, and the data was integrated into one GPR data file for subsequent data analysis.

source_name: Rack1F/F;Alb-cre liver, LPS/GalN induced,6h

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 15 ug RNA according to the manufacturer's instructions, followed by RNAeasy column purification. The Labeling Efficiency of OD was determined.

extract_protocol: 1. Complementary DNA synthesis: The first strand of cDNA was produced by using Reverse Transcription with T7 Oligo (dT) as the lead, and the second strand was synthesized by adding RNase and DNA Polymerase. 2. Synthesis and label of aRNA: Antisense RNA(aRNA) is synthesized by using the Promoter of gene expression, and AminoAllyl UTP (5-(3-aminoallyl)-UTP, or AA-UTP, is added during the process to form AMinoallyl-ARNA and then NHS-Cyedye is added. NHS reacts with Amino Allyl to turn AA-ARNA into Cyedye-ARNA to complete the calibration; 3. Hybridization reaction: after purification, the product is hybridized with Phalanx OneArrayTM. After cleaning and signal detection, the product is analyzed.

treatment_protocol: Fresh livers were extracted from mice after LPS/GalN treatment for 0, 1, 3, and 6 hours, respectively

tag: strain background

tag: genotype/variation

value: male

tag: age

value: LPS/GalN induced 6h

value: liver


title: pt1002310_adjNORM_CD45+_cells_scRNAseq_1 (RNA-Seq)

status: Public on Dec 31 2021

type: SRA

city: Tarrytown

first: Qingqing

last: Wang

state: NY

address: 777 Old Saw Mill River Road

country: USA

institute: Regeneron Pharmaceuticals

description:
single cell 5' RNA expression sequencing
ccRCC_4pt_scRNAseq_CD45plus_matrix.mtx
ccRCC_4pt_scRNAseq_CD45plus_barcodes.tsv
ccRCC_4pt_scRNAseq_CD45plus_genes.tsv
ccRCC_4pt_scRNAseq_CD45plus_NormalizedCounts.txt
ccRCC_4pt_scRNAseq_CD45plus_final_UMAP_coor_cell_embedding.txt
ccRCC_4pt_scRNAseq_CD45plus_final_Metadata.txt

library_source: transcriptomic

data_processing:
Cell Ranger Single-Cell Software Suite (10X Genomics, v3.0.2) was used to perform sample demultiplexing, alignment, filtering, and UMI counting.
scRNA-seq profiles were filtered using Seurat (v3.0) as instructed, with the following criteria: nFeature_RNA > 500 & nFeature_RNA < 5000 & percent.mito < 0.25 & nCount_RNA < 50000. Cells with multiple TCR alpha or beta chains were filtered as well.
Filtered data from 4 RCC patients were integrated, clustered, analyzed and visualized following the standard dataset integration and analysis workflow in Seurat 3.0
TCR-seq data were analyzed by Cell Ranger v3.0.2 and contig sequence as well as the combination of V,D,J genes extracted
Genome_build: hg38
Supplementary_files_format_and_content: genes.tsv file, 10X gene file for raw UMI counts
Supplementary_files_format_and_content: matrix.mtx file, 10X format, raw UMI counts
Supplementary_files_format_and_content: barcodes.tsv file, 10X barcodes file for raw UMI counts
Supplementary_files_format_and_content: Metadata.txt file, phenotypic metadata for cells in dataset
Supplementary_files_format_and_content: UMAP_coor_cell_embedding.txt file, UMAP coordinates of cells in dataset, from unsupervised clustering based on gene expression profiles
Supplementary_files_format_and_content: NormalizedCounts.txt file, normalized UMI counts (data integration, library-size normalization and log-transformation with Seurat)
Supplementary_files_format_and_content: cell barcode_TCR.txt file, TCR cloneType information for Tcells in the dataset
Supplementary_files_format_and_content: filtered_contig_annoatations.csv file, filtered VDJ contig information analyzed by Cell ranger v.3.0.2

molecule: polyA RNA

organism: Homo sapiens

source_name: Donor

extract_protocol:
Single cells suspended in PBS with 0.04% BSA were loaded on a Chromium Single Cell Instrument (10x Genomics).
RNA-seq and V(D)J libraries were prepared using Chromium Single Cell 5’ Library, Gel Beads & Multiplex Kit (10X Genomics). After amplification, cDNA was split into RNA-seq and V(D)J library aliquots. To enrich the V(D)J library aliquot for TCR a/b, the cDNA was split into two 20 ng aliquots and amplified in two rounds using primers designed in-house. Specifically, for first round amplification the primers used were MP147 (ACACTCTTTCCCTACACGACGC) for short R1, MP120 (GCAGACAGACTTGTCACTGGA) for human TRAC, and MP121(CTCTGCTTCTGATGGCTCAAACA) for human TRBC. For second round amplification, 20 ng aliquots from the first round were amplified using MP147, MP128 (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAGGGTCAGGGTTCTGGATA) a nested R2 plus human TRAC, and MP129 (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCAGGGTCAGGGTTCTGGATA) a nested R2 plus human TRABC. V(D)J libraries were prepared from 25 ng each hTRAC and hTRBC amplified cDNA. Paired-end sequencing was performed on Illumina NextSeq500 for RNA-seq libraries (Read 1 26-bp for UMI and cell barcode, 8-bp i7 sample index, and Read 2 55-bp transcript read) and V(D)J libraries (Read 1 150-bp, 8-bp i7 sample index, and Read 2 150-bp read). For RNA-seq libraries, Cell Ranger Single-Cell Software Suite (10X Genomics, v2.2.0) was used to perform sample demultiplexing, alignment, filtering, and UMI counting. The human GRCh38 genome assembly and RefSeq gene model for human were used for the alignment. For V(D)J libraries, Cell Ranger Single-Cell Software Suite (10x Genomics, v2.2.0) was used to perform sample de-multiplexing, de novo assembly of read pairs into contigs, align and annotate contigs against the germline segment V(D)J reference sequences from IMGT, label and locate CDR3 regions, group clonotypes.

treatment_protocol: Renal tumor and adjacent normal tissue samples were dissociated into single cells by a semi-automated mechanical and enzymatic process. Tumor tissue was cut into pieces of (~2-3 mm) in size and transferred to C Tubes (Miltenyi Biotech) containing a mix of Enzymes (Tumor Dissociation Kit, human; Miltenyi Biotech). Mechanical dissociation was performed on gentleMACS dissociator (program 37C_h_TDK_1). To allow for enzymatic digestion, the tube was incubated for 30 min at 37oC, with rotation, after the first and second mechanical dissociation step. Mononuclear cells (MNCs) from whole peripheral blood of paired subjects were isolated by density gradient centrifugation using SepMate Tubes (Stem Cell Technologies). Cells were then cryopreserved in Recovery Cell Culture Freezing Medium (ThermoFisher). Prior to single-cell sequencing cells were rapidly thawed in warm DMEM (Gibco) supplemented with 10% FBS and pelleted. Cell sorting. Tumor, adjacent normal tissue cells, and PBMCs were resuspended in FACS staining buffer (1% BSA and 1mM EDTA in DPBS; Gibco) and incubated with Human TruStain FcX (BioLegend) for 10 min on ice to block non-specific binding to Fc receptors. Cells were then washed and stained with CD45-PE-Dazzle594 (BioLegend) for 20 min on ice. Next, cells were filtered and resuspended in FACS staining buffer with addition of DNase for FACS sorting. DAPI was added to the cell suspension immediately before FACS sorting for dead cell exclusion. Live, CD45+ single cells were sorted for downstream single-cell analysis.

tag: tissue

value: Adjacent normal kidney tissue

tag: treatment

value: baseline

tag: cell type

value: adjacent normal kidney immune cells

tag: disease state

value: Early Stage ccRCC

tag: library strategy

value: RNA-seq


title: D3 WT CHIR FGF INPUT ChIP-seq biological replicate 2 (EXP6)

city: London

first: James

last: Briscoe

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: ChIP-seq

library_source: genomic

data_processing:
The nf-core/chipseq pipeline (version 1.1.0; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3529400) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --input design.csv --genome mm10 --gtf refseq_genes.gtf --single_end --narrow_peak --min_reps_consensus 2 -profile crick -r 1.1.0".
All data was processed relative to the human UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on December 11th 2017.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/chipseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using from the nf-core/chipseq pipeline command defined above.

molecule: genomic DNA

organism: Mus musculus

source_name: In vitro differentiated epiblast-like cells

growth_protocol: ES cell lines were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then either N2/B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021, or N2/B27 + 10ng/ml bFGF + 5uM LGK974 until day 3.

extract_protocol:
For each sample approximately 5*10^6 cells were resuspended in ice cold shearing buffer (1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6), 0.3% SDS + protease inhibitors) and transferred to three Diagenode TPX tubes. Chromatin was sheared using a Bioruptor plus: 25 cycles of 30s On/30s Off on high setting. Sheared lysates were diluted to 0.15% SDS  prior to immunoprecipitation.
The DNA library for sequencing was prepared from Qiagen column purified DNA. DNA fragmentation of IP and input samples was confirmed by Agilent TapeStation prior to library preparation using NEB Ultra II DNA. Libraries were sequenced as single-end, 76bp reads on the Illumina High-Seq 4000 platform (Francis Crick Institute).

treatment_protocol: Adherent cells were fixed for 45min at room temperature with 2mM Di(N-succinimidyl) glutarate, then fixed for an additional 10min at room temperature with 1% PFA. Fixation was quenched by addition of 250mM glyceine for 5 minutes.

tag: chip antibody

tag: strain

tag: genotype

value: wild-type

tag: timepoint

value: CHIR FGF


title: DMSO_24_Hours_TT_8a

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
Read alignment by Salmon (ver. 1.3.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl homosapiens annotations (GRCh38, Apr 2020) release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Genome_build: hg38 v.13
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

source_name: iPSC-CM

growth_protocol: iPSC culture, iPSC-CM differentiation, and blasticidin selection:   WTC iPSCs and derivative lines were fed daily with E8 medium (STEMCELL Technologies) and cultured under feeder-free conditions on growth factor-reduced Matrigel (BD Biosciences). iPSCs were dissociated non-enzymatically using 0.5 μM ethylenediaminetetraacetic acid (EDTA) (Thermo Fisher Scientific) and passaged with p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (10 μM; Selleckchem). iPSCs were frozen in BamBanker human iPSC Freeze Media (Thermo Fisher Scientific). Differentiation of iPSCs was induced through the Wnt modulation method with 7 μM of glycogen synthase kinase 3 b (GSK3b) inhibitor CHIR99021 (Selleckchem) and 5 μM of inhibitor of WNT production 2 (IWP2) (Sigma). Basal Media was composed of RPMI media supplemented with B27 (Thermo Fisher Scientific). As previously described, we generated a blasticidin-selectable iPSC line to purify our iPSC-CMs using 1 μM blasticidin (Thermo Fisher Scientific). Eighteen days after adding CHIR, iPSC-CMs were frozen in 90% fetal bovine serum with 10% dimethyl sulfoxide (DMSO).

extract_protocol:
RNA extraction: Left ventricular cardiac tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq stranded library preparation Illumina protocols.

treatment_protocol: TYA-018 (highly selective HDAC6 inhibitor) was administered daily by oral gavage at 15 mg/kg starting when mice were 2 months old.

value: DMSO

tag: dose

value: iPSC cardiomyocytes


title: pt1002300_tumor_CD45+_cells_scRNAseq_2 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002300_1249069_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: RCC tumor

value: tumor immune cells


title: B12_H011

type: RNA

country: China

description: Gene expression after 1hr in LPS/GalN induced mouse liver

source_name: Rack1F/F;Alb-cre liver, LPS/GalN induced,1h

tag: Sex

value: LPS/GalN induced 1h


title: B61_H014


title: pt1002300_tumor_CD45+_cells_scRNAseq_2 (RNA-Seq)


title: D3 WT CHIR FGF INPUT ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

value: In vitro differentiated epiblast-like cells


title: Ricolinostat (0.3uM)_24_Hours_TT_7b

value: Ricolinostat


title: D3 WT CHIR FGF LEF1 IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq

value: LEF1 (Millipore CS200635)


title: D3 WT CHIR FGF BCATENIN IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: Bcatenin (Invitrogen 71-2700 rabbit)


title: pt1002300_tumor_CD45+_cells_scRNAseq_1 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002300_1249069_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: Ricolinostat (1uM)_24_Hours_TT_6b


title: Ricolinostat (0.3uM)_24_Hours_TT_7a


title: pt1002300_tumor_CD45+_cells_scRNAseq_1 (RNA-Seq)


title: B31_H012

description: Gene expression after 3hr in LPS/GalN induced mouse liver

source_name: Rack1F/F;Alb-cre liver, LPS/GalN induced,3h

value: male

value: LPS/GalN induced 3h

value: liver


title: D3 WT CHIR FGF BCATENIN IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: D3 WT CHIR FGF BCATENIN IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq


title: D3 CDX CHIR FGF SOX2 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)


title: pt1002300_PBMC_CD45+_cells_scRNAseq_2 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002300_1249067_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: PBMC

value: baseline

value: blood immune cells

value: Early Stage ccRCC


title: pt1002300_PBMC_CD45+_cells_scRNAseq_2 (RNA-Seq)

value: RNA-seq


title: B11_H010


title: B02_H009

description: Gene expression after 0hr in LPS/GalN induced mouse liver

source_name: Rack1F/F;Alb-cre liver, LPS/GalN induced,0h

value: LPS/GalN induced 0h


title: A32_H006

source_name: Rack1F/F liver, LPS/GalN induced,3h


title: Ricolinostat (3uM)_24_Hours_TT_5a

value: iPSC cardiomyocytes


title: A61_H007

source_name: Rack1F/F liver, LPS/GalN induced,6h

value: LPS/GalN induced 6h


title: DMSO_24_Hours_TT_4b

value: DMSO


title: D3 CDX CHIR FGF SOX2 IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq

value: In vitro differentiated epiblast-like cells

value: CHIR FGF


title: pt1002300_PBMC_CD45+_cells_scRNAseq_1 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002300_1249067_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt


title: DMSO_24_Hours_TT_4a


title: D3 CDX CHIR FGF SOX2 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq


title: B01_H008


title: B32_H013


title: A12_H004

source_name: Rack1F/F liver, LPS/GalN induced,1h

value: LPS/GalN induced 1h


title: Ricolinostat (3uM)_24_Hours_TT_5b

value: Ricolinostat


title: A02_H002

source_name: Rack1F/F liver, LPS/GalN induced,0h

value: male


title: pt1002300_adjNORM_CD45+_cells_scRNAseq_2 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002300_1249065_2_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: Adjacent normal kidney tissue

value: adjacent normal kidney immune cells


title: D3 CDX CHIR FGF LEF1 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: LEF1 (Millipore CS200635)


title: b 2

city: Gothenburg

first: Per

last: Sunnerhagen

address: Box 462

department: Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

data_processing:
Sequencing files were imported to Geneious software version 11.1.5, (Biomatters, Auckland, New Zealand)
Mapping to reference was performed by Geneious software version 11.1.5, (Biomatters, Auckland, New Zealand)
Calcuation of expression levels and Comparison of expression levels were performed by Geneious software version 11.1.5, (Biomatters, Auckland, New Zealand)
Differentially expressed genes were selected if it presents  more than 2-fold expression increase or decrease and P-value for unchanged expression < 0.05.
Genome_build: R64
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: whole cells

growth_protocol: Yeast cells were grown at 30°C until mid-log phase (OD600 0.4 - 0.5) in synthetic complete medium (SC)

extract_protocol:
RNA extractions were performed using YeaStarTMRNA (Zymo Research, CA, USA) according to the manufacturer’s instructions.
Polyadenylated RNA was purified, and random primed cDNA libraries were constructed

treatment_protocol: To induce stress, KCl (as final concentration of 1.5M KCl) was added to a rapidly shaking culture in mid-log phase (A550nm = 0.4   0.5). Samples were taken at every 30 min

value: wild type

tag: stress

value: 1.5M KCl, 2h


title: b 15


title: A01_H001

value: liver


title: D3 CDX CHIR FGF LEF1 IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: b 1

value: 1.5M KCl, 1h


title: pt1002300_adjNORM_CD45+_cells_scRNAseq_1 (TCR-Seq)

description:
TCR-seq (included in the 5' RNA sequencing)
1002300_1249065_1_filtered_contig_annotations.csv
cellbarcode_CTstrict_cluster_info_TCR_4pt_scRNAseq.txt

value: baseline

value: Early Stage ccRCC

value: RNA-seq


title: A11_H003


title: D3 CDX CHIR FGF LEF1 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq


title: pt1002300_adjNORM_CD45+_cells_scRNAseq_1 (RNA-Seq)


title: b 05


title: A31_H005

value: LPS/GalN induced 3h


title: D3 CDX CHIR FGF INPUT ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq


title: b 0

value: 1.5M KCl, 0h


title: pt1002300_PBMC_CD45+_cells_scRNAseq_1 (RNA-Seq)

value: PBMC

value: blood immune cells


title: IFI16 shRNA replicate_2

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

description: 2000 ng shRNA; Transfection using Lipofectamine-3000

data_processing:
Raw data files were quality checked and bad quality bases were removed using cutadapt.
Cleaned fastqc files were mapped to human reference genome using HISAT2 on usegalaxy.org
BAM files were used for estimating gene counts.
Cuffdiff was used for gene differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Cuffdiff output in a tabular file. Contains p value, gene names, and log2 fold change

source_name: A549 cell line

growth_protocol: Cells were grown in DMEM media supplemented with 10% FBS and 1X antibiotic antimycotic.

extract_protocol:
Total RNA was extracted using Trizol reagent.
Libraries were prepared according to instructions accompanying the Illumina library preparation kit.

treatment_protocol: 2000 ng shRNA was transfected using lipofectamine 3000

value: Lung adenocarcinoma cells

tag: cell line

value: IFI16 shRNA


title: Givinostat (1uM)_24_Hours_TT_2a

value: Givinostat

value: iPSC cardiomyocytes


title: a 2


title: Givinostat (1uM)_24_Hours_TT_2b


title: Givinostat (3uM)_24_Hours_TT_1b


title: Givinostat (0.3uM)_24_Hours_TT_3b


title: Givinostat (3uM)_24_Hours_TT_1a


title: D3 CDX CHIR FGF INPUT ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq

value: In vitro differentiated epiblast-like cells

value: CHIR FGF


title: Givinostat (0.3uM)_24_Hours_TT_3a


title: pt1002300_adjNORM_CD45+_cells_scRNAseq_2 (RNA-Seq)

value: Adjacent normal kidney tissue

value: adjacent normal kidney immune cells


title: D3 CDX CHIR FGF INPUT ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq


title: a 15

value: wild type


title: D3 CDX CHIR FGF BCATENIN IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: Bcatenin (Invitrogen 71-2700 rabbit)


title: a 1

value: 1.5M KCl, 1h


title: IFI16 shRNA replicate_1


title: Scrambled shRNA replicate_2

value: Scrambled shRNA


title: Scrambled shRNA  replicate_1


title: D3 CDX CHIR FGF BCATENIN IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: WT TY1 rep1

city: Memphis

first: Jun

middle: J.

last: Yang

state: TN

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.2.9 with default parameters
peaks were called using MACS2 version 2.2.7.1 under --nomodel for paired-end samples
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: Jurkat cell

growth_protocol: A total amount of 2e6 Jurkat cells were treated with Complete Cell Fixative Solution for 15 minutes and Stop Solution for 5 minutes.

extract_protocol:
ChIP assays were performed on parental or RUNX1 mutation knock-in single clones of Jurkat cells using ChIP-IT High Sensitivity kit according to the manufacturer’s protocol. Briefly, a total amount of 2e6 cells were treated with Complete Cell Fixative Solution for 15 minutes and Stop Solution for 5 minutes, followed by sonication. The following antibodies are used for ChIP assays: anti-HA (ab9110, Abcam), anti-TY1 (C15200054, Diagenode), anti- RUNX1 (ab23980), Normal Rabbit IgG (2729, Cell Signaling).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

value: Wild type

value: Jurkat

value: anti-TY1 (C15200054, Diagenode)

value: untreated


title: a 0

value: 1.5M KCl, 0h


title: a 05


title: R232fs control rep2


title: WT control


title: Beta2

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

institute: Shiv Nadar Institution of Eminence

data_processing:
The raw sequencing data was trimmed using Trim Galore and mapped to GRCz11 using Bowtie2.
The sorted bam file obtained from mapping was filtered for high-quality reads (greater than or equal to 30 and Paired) and for removal of mitochrondrial reads. In addition, duplicate reads were removed using Picard MarkDuplicates.
Peak Calling was performed using Genrich.
Genome_build: Zebrafish GRCz11
Supplementary_files_format_and_content: bedGraph format, obtained from Genrich Peak Calling

organism: Danio rerio

source_name: beta cells

extract_protocol:
Enzymatic Dissociation
ATAC-Seq. was carried out using 50,000 cells collected using FACS. For ATAC-Seq. of beta-cells, primary islet for dissociation was collected from Tg(ins:BB1.0L; cryaa:RFP) line and beta-cells sorted using the red fluorescence. For hepatocytes, liver for dissociation was collected from Tg(fabp10:dsRed, ela3l:GFP) line and cells collected using the red fluorescence. Cells were processed according to the protocol outlined in Buenrostro et al., Nature Methods, 2013. In brief, cells were homogenized in a 2 ml Dounce homogenizer with 5 strokes in 1X homogenization buffer on ice. The nuclei suspension was centrifuged at 500g for 10 min at 4 °C. After removing the supernatant, transposition was carried out by incubating the nuclei in the transposition reaction mix for 30 min at 37 °C. Transposed DNA was purified using Qiagen MinElute Reaction Cleanup Kit. Barcoded libraries were generated from the isolated DNA by PCR amplification for 11 cycles. Libraries were sequenced on llumina HiSeq2500 in 2 X 75 bp paired-end mode.

value: beta cells

tag: developmental stage


title: Liver

source_name: hepatocytes

value: hepatocytes

value: Tg(fabp10:dsRed, ela3l:GFP)gz12


title: D3 BRA CHIR FGF SOX2 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)

value: T/Bra-/-


title: D3 CDX CHIR FGF BCATENIN IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

value: In vitro differentiated epiblast-like cells

value: CHIR FGF


title: WT HA rep1

value: anti-HA (ab9110, Abcam)


title: Beta1


title: R232fs TY1 rep1


title: D3 BRA CHIR FGF SOX2 IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: R232fs TY1 rep2


title: R232fs HA rep2


title: D3 BRA CHIR FGF LEF1 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

value: LEF1 (Millipore CS200635)


title: D3 BRA CHIR FGF LEF1 IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq


title: D3 BRA CHIR FGF LEF1 IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: R232fs control rep1


title: D3 BRA CHIR FGF INPUT ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq


title: G365R control rep1


title: R232fs HA rep1


title: G365R control rep2


title: G365R TY1 rep2


title: D3 BRA CHIR FGF INPUT ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: G365R TY1 rep1


title: G365R HA rep2


title: D3 BRA CHIR FGF SOX2 IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq


title: D3 BRA CHIR FGF BCATENIN IP ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

value: Bcatenin (Invitrogen 71-2700 rabbit)


title: MCF7_siNUP93_tot_rep2_S10

city: San Francisco

first: Binyamin

last: Zuckerman

state: California

institute: UCSF

description: processed data file: MCF7_fractionation_data.xlsx

data_processing:
RNA-seq reads were mapped to the human genome (hg19 assembly) with STAR (Dobin et al., 2013) and gene expression levels were quantified using RSEM (Li and Dewey, 2011) and Bowtie2.
GENCODE v26 annotations were used for further analysis. Differential expression in WCE samples was computed using DESeq2 (Love et al., 2014) with default parameters. Subcellular localization was quantified similarly using DESeq2, using gene-level RSEM output.
Genome_build: hg19
Supplementary_files_format_and_content: gene-level RSEM output

growth_protocol: Human mammary MDA-MB-231 and MCF7 cells were grown in RPMI-1640 (Gibco BRL) supplemented with 10% heat inactivated fetal calf serum (Gibco), 1mM sodium pyruvate, and a penicillin streptomycin mixture (100 U/ml; 0.1 mg/ml).

extract_protocol:
TRIREAGENT
SENSE mRNA-Seq Library prep kit (Lexogen)

treatment_protocol: cells were seeded in 6-well plates at 50% confluence, and 24 h later, they were transfected with siRNA control and siRNA NUP93 SMART pool using the Lipofectamine 2000 transfection reagent

tag: molecule subtype

value: WCE PolyA RNA


title: G365R HA rep1


title: D3 BRA CHIR FGF BCATENIN IP ChIP-seq biological replicate 2 (EXP6)

description: ChIP-seq


title: D3 BRA CHIR FGF RNA-seq biological replicate 3 (EXP5)

description: RNA-seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.16; Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”, and for paired-end data “-A AGATCGGAAGAGC” was appended to the command.
The RSEM package (version 1.3.0; Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a; Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 11th December 2017. The parameters passed to the “rsem-calculate-expression” command were “--star --star-gzipped-read-file --star-output-genome-bam --forward-prob 0”, and for paired-end data “--paired-end” was appended to the command.
Differential expression analysis was performed with the DESeq2 package (version 1.16.1; Love et al., 2014) within the R programming environment (version 3.4.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

growth_protocol: ES cell lines were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then N2/B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021 until day 3.

extract_protocol:
Total RNA was extracted from cells using a QIAGEN RNeasy kit in RLT buffer, following the manufacturer’s instructions. Extracts were digested with DNase I to eliminate genomic DNA.
The total RNA samples were quality controlled to determine RNA integrity and concentration using Agilent Tapestation prior to library preparation. Libraries were prepared using the KAPA mRNA HyperPrep kit (Roche) and sequenced as 76bp single-end, stand-specific reads on the Illumina HiSeq 4000 platform (Francis Crick Institute).


title: Y287 control rep2


title: Human Primeview_Test

city: Goyang-si

first: Ai-Young

last: Lee

state: Gyeonggi-do

address: Ilsandong-gu Siksa-dong Dongguk-ro 27

department: Dermatology

country: South Korea

institute: Dongguk University School of Medicine

description: Gene expression data from Human RNA sample

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Primeview array. Affymetrix Primeview array were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Primeview array were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneSpring GX version 14.9.1 (Agilent Technologies Inc.,). The analysis contents were performed using default settings in GeneSpring software.

label: biotin

source_name: Lesional

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Skin biopsy

value: SKIN


title: MCF7_siNUP93_tot_rep1_S4


title: MCF7_siNUP93_nuc_rep2_S12

value: nuclear PolyA RNA


title: D3 BRA CHIR FGF RNA-seq biological replicate 1 (EXP5)

description: RNA-seq


title: RNA-Seq B6.129 F1  mEpiSCs BioRep 17

city: New York

first: Daniel

last: Medina Cano

email: medinacd@mskcc.org, dmcdmc156@gmail.com

state: New York

address: 411E 67th St

department: Developmental Biology

institute: MSKCC

description:
B6.129 F1  mEpiSCs BioRep 17
RNA-seq on mEpiSCs and derivates

data_processing:
The raw reads were mapped to transcripts and quantified using Salmon (PMID: 28263959)
Deseq2, PCAexplorer and pheatmap were used for downstream analyses  (PMID: 25516281 and 31195976)
Genome_build: mm10
Supplementary_files_format_and_content: txt - normalized counts per sample
Supplementary_files_format_and_content: AllPeaks_EpiSC_VS_DE: Count matrix for ATAC-seq EpiSC VS DE, after FeatureCounts ATAC-seq analyses of EpiSC samples VS Definitive endoderm, only 4 EpiSC samples and 4 DE samples are uncluded (all from the B6 bakcground), used for figure 3
Supplementary_files_format_and_content: AllPeaks_EpiSC_VS_Biblio: Count matrix for ATAC-seq EpiSC VS FX, AFX and in vivo samples, after FeatureCounts ATAC-seq analyses of EpiSC samples developed in the present study , EpiSC cells (AF and AFX) from PMID: 33271069 and in vivo samples obtained from PMID 31844322, used for figure 1
Supplementary_files_format_and_content: RNA_Epi_VS_De.txt: Deseq2 matrix for RNA-seq EpiSC VS DE RNA-seq analyses of EpiSC samples VS Definitive endoderm, only 5 EpiSC samples and 4 DE samples are uncluded (all from the B6 bakcground), used for figure 3
Supplementary_files_format_and_content: RNA_EpiS.txt: Deseq2 matrix for RNA-seq EpiSC from different genetic backgrounds RNA-seq analyses of EpiSC samples from different backgrounds, used for figure 1

source_name: Mouse epiblast stem cells in vitro

growth_protocol: mEpiSCs were grown on feeders and in a N2B27-based media with Fgf2, ActivinA and NVP-TNKS656 as Wnt inhibitor

extract_protocol:
mEpiSCs were lifted with collagenase (to avoid feeder contamination) and resuspended to single cells with accutase. RNA was extracted using trizol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 129-500ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina). An average of 36 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 84% to 89%.

tag: passage


title: RNA-Seq B6.129 F1 mEpiSCs BioRep 9

description:
B6.129 F1 mEpiSCs BioRep 9
RNA-seq on mEpiSCs and derivates

extract_protocol:
mEpiSCs were lifted with collagenase (to avoid feeder contamination) and resuspended to single cells with accutase. RNA was extracted using trizol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 129-500ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Ki


title: RNA-Seq B6.129 F1 mEpiSCs BioRep 4

description:
B6.129 F1 mEpiSCs BioRep 4
RNA-seq on mEpiSCs and derivates


title: Human Primeview_Control

source_name: non-lesional


title: D3 BRA CHIR FGF INPUT ChIP-seq biological replicate 1 (EXP6)

description: ChIP-seq

source_name: In vitro differentiated epiblast-like cells


title: D3 BRA CHIR FGF BCATENIN IP ChIP-seq biological replicate 3 (EXP6)

description: ChIP-seq


title: Y287X TY1 rep2

value: Jurkat


title: Y287 control rep1


title: RNA-Seq PWK Definitive Endoderm BioRep695

description:
PWK Definitive Endoderm BioRep695
RNA-seq on mEpiSCs and derivates

source_name: Mouse definitive endoderm cells in vitro

growth_protocol: Definitive endoderm cells were generated from mEpiSCs in 46h. mEpiSCs were induced with chemically defined media with CHIR99201 and ActivinA for 16h. Afterwards, the media was changed to chemically defined media with ActivinA and LDN193189 for 24h more, when the cells were collected. To avoid background noise, we MACS-sorted CXCR4+ cells and used those for further analyses.

extract_protocol:
DE cells were lifted with accutase. RNA was extracted using trizol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 129-500ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina). An average of 36 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 84% to 89%.

value: PWK/PhJ


title: Y287X TY1 rep1

value: anti-TY1 (C15200054, Diagenode)

value: untreated


title: MCF7_siNUP93_nuc_rep1_S6


title: MCF7_siNUP93_cyt_rep2_S11

value: cytoplasmic PolyA RNA


title: D3 CDX CHIR FGF RNA-seq biological replicate 2 (EXP5)

description: RNA-seq


title: MCF7_siNUP93_cyt_rep1_S5


title: RNA-Seq PWK Definitive Endoderm BioRep698

description:
PWK Definitive Endoderm BioRep698
RNA-seq on mEpiSCs and derivates

extract_protocol:
DE cells were lifted with accutase. RNA was extracted using trizol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 129-500ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Ki


title: D3 CDX CHIR FGF RNA-seq biological replicate 3 (EXP5)

description: RNA-seq


title: RNA-Seq PWK Definitive Endoderm BioRep699

description:
PWK Definitive Endoderm BioRep699
RNA-seq on mEpiSCs and derivates


title: Y287X HA rep2


title: D3 CDX CHIR FGF RNA-seq biological replicate 1 (EXP5)

description: RNA-seq


title: D3 BRA CHIR FGF RNA-seq biological replicate 2 (EXP5)

description: RNA-seq


title: Y287X HA rep1


title: MCF7_siCont_tot_rep2_S7

value: siCtrl


title: RNA-Seq DBA55 mEpiSCs BioRep698

description:
DBA55 mEpiSCs BioRep698
RNA-seq on mEpiSCs and derivates


title: MCF7_siCont_tot_rep1_S1


title: D3 WT CHIR FGF RNA-seq biological replicate 2 (EXP5)

description: RNA-seq

value: wild-type


title: Y287X rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  using STAR v2.6.1c with default parameters
Raw reads count from HT-Seq were provided for each sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw reads counts for each Sample

extract_protocol:
RNA was harvested using Trizol reagent. TruSeq stranded mRNA library prep kit (Illumina) was used for whole-transcriptome library preparation, and paired-end sequencing was performed using the Illumina NovaSeq 6000 platform with a 101-bp.
RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced by NovaSeq 6000


title: MCF7_siCont_nuc_rep2_S9


title: D3 WT CHIR FGF RNA-seq biological replicate 1 (EXP5)

description: RNA-seq


title: RNA-Seq PWK mEpiSCs BioRep695

description:
PWK mEpiSCs BioRep695
RNA-seq on mEpiSCs and derivates


title: RNA-Seq PWK mEpiSCs BioRep698

description:
PWK mEpiSCs BioRep698
RNA-seq on mEpiSCs and derivates


title: R232fs rep2


title: R232fs rep1


title: Y287X rep2


title: RNA-Seq B6 Definitive Endoderm BioRep 44

description:
B6 Definitive Endoderm BioRep 44
RNA-seq on mEpiSCs and derivates


title: WT rep4

value: wild type

tag: clone


title: MCF7_siCont_cyt_rep1_S2


title: WT rep3


title: MCF7_siCont_cyt_rep2_S8


title: WTEtOH11

city: New Orleans

first: Kim

middle: B

last: Pedersen

state: LA

address: 1901 Perdido St., Rm 5206

department: Pharmacology and Exp. Therapeutics

institute: LSU Health Sciences Center, Dept. of Pharmacology

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences (GENEWIZ).
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted. (GENEWIZ)
Genome_build: Mus musculus GRCm38 reference genome
Supplementary_files_format_and_content: Text files of raw and normalized counts

source_name: Femoral shaft RNA

growth_protocol: Mice of genotypes Cat +/+ and Cat -/- were maintained on regular chow until 12 weeks of age.

extract_protocol:
Femurs were isolated, the marrow was removed by centrifugation. The femur shafts were incubated in RNAlater overnight at 4°C before storage at -80°C. RNA was isolated by a Trireagent protocol. Each sample is a pool of femoral shaft RNA from two mice.
Performed by GENEWIZ

treatment_protocol: At 12 weeks of age, mice received either binge ethanol in the form of 3, 3, 4, and 4.5 g ethanol/kg body weight by gavage from a 31.5 % (v/v) ethanol solution on four consecutive days or isovolumetric amounts of PBS. Mice were euthanized 6 hours after the last gavage.

value: Wild-type (WT) (Cat +/+)

tag: gavage treatment

value: Ethanol

tag: tissue

value: Femoral shaft


title: RNA-Seq B6 Definitive Endoderm BioRep 51

description:
B6 Definitive Endoderm BioRep 51
RNA-seq on mEpiSCs and derivates

tag: treatment


title: WTEtOH10


title: RNA-Seq B6 Definitive Endoderm BioRep 4

description:
B6 Definitive Endoderm BioRep 4
RNA-seq on mEpiSCs and derivates


title: WTctrl9

value: PBS


title: SKBR3 P2

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Aligned with STAR v.2.5.2
Quantified with RSEM 1.3.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: Breast cancer cell line

growth_protocol: Cells were seed onto 6 well plates at sub-confluent density (~500,000 cells/well).

extract_protocol:
RNA was extracted by using the RNeasy Mini Kit, followed by treatment with RNase-free, DNase to remove contaminating genomic DNA.
RNA (200 ng) RNA was reverse transcribed by using the Illumina TruSeq Stranded Total mRNA kit. Libraries were sized on an Agilent Bioanalyzer, and their concentrations were validated by qPCR.

value: breast

value: P


title: D3 WT CHIR FGF RNA-seq biological replicate 3 (EXP5)

description: RNA-seq

tag: cell type

value: In vitro differentiated epiblast-like cells

value: CHIR FGF


title: RNA-Seq PWK mEpiSCs BioRepALT

description:
PWK mEpiSCs BioRepALT
RNA-seq on mEpiSCs and derivates


title: WTEtOH12


title: WT rep2


title: SKBR3 P1


title: WTctrl8


title: RNA-Seq B6 Definitive Endoderm BioRep 2

description:
B6 Definitive Endoderm BioRep 2
RNA-seq on mEpiSCs and derivates


title: RNA-Seq B6 mEpiSCs BioRep 51

description:
B6 mEpiSCs BioRep 51
RNA-seq on mEpiSCs and derivates


title: G365R clone22 rep2


title: WTctrl7


title: MCF7_siCont_nuc_rep1_S3

description: processed data file: MCF7_fractionation_data.xlsx

value: nuclear PolyA RNA


title: SKBR3 DTP1

value: DTP


title: SKBR3 DTP2


title: RNA-Seq B6 mEpiSCs BioRep 44

description:
B6 mEpiSCs BioRep 44
RNA-seq on mEpiSCs and derivates


title: HCC1419 P2


title: G365R clone22 rep1

value: Jurkat


title: RNA-Seq B6 mEpiSCs BioRep 4

description:
B6 mEpiSCs BioRep 4
RNA-seq on mEpiSCs and derivates


title: KOEtOH4

value: Catalase knockout (KO) (Cat -/-)


title: G365R clone1 rep2


title: KOEtOH6


title: KOEtOH5


title: HCC1419 DTP2


title: G365R clone1 rep1


title: RNA-Seq B6 mEpiSCs BioRep 2

description:
B6 mEpiSCs BioRep 2
RNA-seq on mEpiSCs and derivates


title: HCC1419 P1


title: WT rep1


title: KOctrl3


title: RNA-Seq B6 mEpiSCs BioRep 1

description:
B6 mEpiSCs BioRep 1
RNA-seq on mEpiSCs and derivates


title: KOctrl2


title: EFM192A P2


title: TSC_2

city: Austin

first: Yu Jin

last: Jang

state: Texas

address: 2506 Speedway, NMS 4.246

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Illumina RTA3 software used for basecalling.
STAR was used for mapping reads of RNA-seq to human hg38 genome.
HTSeq was used for counting reads in exons for RNA-seq from gencode v35.
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq, one tab-delimited text file contains all RNA-seq data. Gene expression was shown as log2(normalized counts) for each genes.

source_name: human trophoblast stem cells

growth_protocol: Human PSCs (iPSCs and H9) were maintained on Matrigel (corning)-coated plates with mTeSR1 medium (Stemcell Technologies). When the cells reached about 70~80% confluence, they were passaged with ReLeSR (Stemcell Technologies) according to the manufacturer’s protocol, at a 1:10 ratio. TSCs were plated on 5 μg/ml Collagen IV (corning)-coated dishes with TSCM (DMEM/F12 (Gibco) medium supplemented with 1% ITS-X supplement (Gibco), 0.5% Penicillin-Streptomycin (Gibco), 0.3% BSA (Sigma-Aldrich), 0.2% FBS (GeminiBio), 0.1 mM β-mercaptoethanol (Sigma-Aldrich), 0.5 μM A83-01 (Wako Pure Chemical Corporation), 0.5 μM CHIR99021 (Selleck Chemicals), 0.5 μM SB431542 (Stemcell Technologies), 5 μM Y27632 (ROCK inhibitor, Selleck Chemicals), 0.8 mM VPA (Wako Pure Chemical Corporation), 50 ng/ml EGF (PeproTech), and 1.5 μg/ml L-ascorbic acid (Sigma-Aldrich)). When the cells were 70~80% confluent, they were detached with TrypLE (Gibco) for 10~15 mins at 37°C and then the dissociated cells were plated onto Collagen IV-coated dishes at 1:3~1:5 split ratio. The culture medium was changed every 2 days. For generating TSLCs, PSCs were detached by TrypLE and seeded on Matrigel-coated plate (3~4E4 cells/cm2) containing mTeSR1 medium supplemented with 10 μM Y27632. One day later, the cells were cultured in TSCM containing 10 ng/ml human BMP4 (Gibco) for 2 days, and then they were maintained on Matrigel-coated plates containing TSCM in the absence of BMP4. The cells were passaged every 2~3 days for additional 10~12 days (4~5 passages). All cells were incubated at 37°C in 5% CO2. For differentiation of ST, dissociated TSCs and TSLCs were cultured in a 60 mm petri dish (5x105~1x106 cells/dish) with 4 mL ST differentiation medium (DMEM/F12 medium supplemented with 1% ITS-X supplement, 0.5% Penicillin-Streptomycin, 0.3% BSA, 0.1 mM β-mercaptoethanol, 2.5 μM Y27632, 2 μM forskolin (Selleck Chemicals), and 4% SR). The ST differentiation medium was replaced on day 3. The ST derived from TSCs and TSLCs were analyzed on day 6. For differentiation of EVT, dissociated TSCs and TSLCs were plated on 1 μg/ml Collagen IV-coated 6 well plate (1~1.5x104 cells/cm2) with 2 mL of EVT differentiation medium (DMEM/F12 medium supplemented with 1% ITS-X supplement, 0.5% Penicillin-Streptomycin, 0.3% BSA, 0.1 mM β-mercaptoethanol, 100 ng/ml human neuregulin-1 (NRG1, Cell Signaling Technology), 7.5 μM A83-01, 2.5 μM Y27632, 4% SR, and 2% Matrigel). On day 3, the EVT medium was replaced with fresh medium supplemented with reduced Matrigel (0.5%) in the absence of NRG1. On day 6, the EVT medium was replaced again with the medium containing reduced Matrigel (0.5%) but omitting both NRG1 and SR. The EVT derived from TSCs and TSLCs were analyzed on day 8.

extract_protocol:
Global gene expression profiles using RNA-seq were performed in two replicates of primary hTSCs (CT27), undifferentiated hESCs (H9), undifferentiated hiPSCs, hTSLCs (TS-like cells) derived from hESCs (ES-TSLCs), hTSLCs derived from hiPSCs (iPS-TSLCs), EVT differentiated from hTSCs, EVT differentiated from ES-TSLCs (ES-EVT), EVT differentiated from iPS-TSLCs (iPS-EVT), ST differentiated from hTSCs, ST differentiated from ES-TSLCs (ES-ST), and ST differentiated from iPS-TSLCs (iPS-ST). Briefly, total RNAs were isolated using the RNeasy plus minikit (Qiagen). mRNAs were enriched from total RNAs, fragmented, and primed. First strand cDNAs were synthesized following by second strand synthesis. The ends of purified double strand cDNAs were repaired, ligated with a barcoded adaptor and index, and amplified with PCR. Purified final PCR product was sequenced using Illumina Novaseq 6000 machine.
RNA-seq library was constructed using NEBNext Ultra RNA Library prep kit (NEB, E7700L) according to manufacturer’s instruction.


title: KOctrl1


title: HCC1419 DTP1


title: TSC_1


title: IFT88_Int_4

first: Chang

last: Xie

address: 555 Mission bay blvd South, 384G

institute: University of California, San Francisco

data_processing:
Aligner: STAR_2.5.2b
Differential Expression: DESeq2 v1.16.1
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel containing gene names, normalized counts, differential expression analysis with foldchange and p value

source_name: Small Intestine

growth_protocol: mouse embryos were dissected at E11.5. tails were preserved to extract DNA for genotyping.

extract_protocol: Samples were homogenized in Trizol, then mixed with 1/5 volume chlorform and centrifuged at 12000rpm/min for 15 minutes. Water phase was taken to extract RNA using RNeasy Micro Kit

treatment_protocol: embryonic lung and small intestine were dissected and immediately lyzed in Trizol and stored at -80℃. Then samples of targeted genotypes were processed for RNA extraction.

tag: age

value: ShhCre Ift88-/lox

value: cilia-disrupted


title: EFM192A P1


title: EFM192A DTP2


title: IFT88_Int_3


title: ST_2

value: ST derived from hTSCs


title: IFT88_Int_2


title: IFT88_Int_1


title: ST_1


title: Foxp3 reporter-null rep2

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

data_processing:
alignment
read quantification per gene
normalization of gene enrichment using DESeq

source_name: Colon lamina propria

extract_protocol:
Phase separation in cells lysed in TRIzol Reagent (ThermoFisher catalog # 15596018) was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, RNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 2-10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and sequenced on Illumina HiSeq in a PE 50 run.

value: Colon lamina propria

tag: cell subset

value: Foxp3 Thy1.1+ reporter-null


title: EFM192A DTP1


title: CENPJ_Int_4

value: ShhCre Cenpj-/lox

value: centriole-disrupted


title: BT474 P2


title: Treg rep2

tag: strain

value: Foxp3-DTR-GFP+ Treg


title: iPSTSLC_1

source_name: human induced pluripotent stem cells

value: TSLCs derived from hiPSCs


title: iPSST_2

value: ST derived from iPS-TSLCs


title: CENPJ_Int_2

tag: genotype


title: Treg rep1


title: CENPJ_Int_3


title: Foxp3 reporter-null rep1


title: Tomato-pos-GFP-pos-rep2

source_name: Mesenteric lymph node

value: Mesenteric lymph node

value: Tomato-pos-GFP-pos


title: CENPJ_Int_1


title: BT474 DTP2

value: breast


title: Control_Int_4

value: ShhCre Cenpj+/lox

value: Control


title: Foxp3 reporter-null rep3


title: BT474 DTP1

value: DTP


title: Tomato-pos-GFP-pos-rep1


title: iPSST_1


title: iPSEVT_2

value: EVT derived from iPS-TSLCs


title: Control_Int_3


title: Patient-Control_scATACseq

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the hg19 reference genome using CellRanger-ATAC v. 1.2.0
Donor / Patient cell identities were inferred using SNP genotypes with pre-existing bulk data (via demuxlet)
Genome_build: hg19
Supplementary_files_format_and_content: Fragment files corresponding to each insertion pair from Tn5 barcoded by cell ID as well as cell assignments

source_name: bone marrow mononuclear cells

growth_protocol: IMDM, 2% human AB plasma, 3% human AB serum, 1x Pen/Strep, 3IU/ml heparin, 10µg/ml insulin, 200µg/ml holo-transferrin, 1 IU erythropoetin, 10ng/ml SCF, 1ng/ml IL-3.

extract_protocol:
10x lysis
10x scATAC v1 kit

tag: donor

value: healthy control + patient carrying the GATA1 p.R307C mutation

value: bone marrow mononuclear cells


title: Control_Int_2


title: Tomato-pos-Thy1-pos-rep2


title: iPSTSLC_2


title: iPSEVT_1


title: iPSC_2

value: hiPSCs


title: Tomato-pos-Thy1-pos-rep1


title: BT474 P1

value: P


title: Control_Int_1


title: Tomato-neg-GFP-pos-rep2

value: Tomato-neg-GFP-pos


title: iPSC_1


title: Tomato-neg-GFP-pos-rep1


title: EVT_2

value: EVT derived from hTSCs


title: EVT_1


title: Tomato-neg-Thy1-pos-rep2


title: ESTSLC_2

source_name: human embryonic stem cells

value: TSLCs derived from hESCs


title: Patient-Control_scRNAseq_rep1

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the hg38 reference genome using CellRanger v. 3.0.2
Donor / Patient cell identities were inferred using SNP genotypes with pre-existing bulk data (via demuxlet)
Genome_build: hg38
Supplementary_files_format_and_content: Per sample raw counts in genes

extract_protocol:
10x lysis
10x scRNA seq 3' v2 kit


title: WT_Day06_Rep1

data_processing:
Library strategy: CUT&RUN targeting GATA1
FastQ files were trimmed, aligned, and filtered using CUT&RUNTools version 20200104
Occupancy peaks were determined using macs2 as part of the CUT&RUNTools pipeline
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peak files per replicate

extract_protocol:
https://doi.org/10.17504/protocols.io.wvgfe3w
CUT&RUN targeting GATA1

value: healthy control

tag: timepoint


title: WT_Day06_Rep2


title: WT_Day12_Rep2


title: Tomato-neg-Thy1-pos-rep1


title: Patient-Control_scRNAseq_rep2


title: WT_Day12_Rep1


title: E13.5 fetal liver Fancd2-/- 3.2

city: Philadelphia

first: Peter

last: Kurre

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
Raw data in fastq files were demuliplexed, aligned and filtered by Cell Ranger 3.1.0
Genome_build: mm10
Supplementary_files_format_and_content: h5 (Feature-Barcode Matrix Format) files including feaure-cell read count matrix

source_name: E13.5 fetal liver

extract_protocol:
FL was collected, mechanically digested by pipetting, treated with 0.3% collagenase type I for 15 mins at 37°C and 220rpm, RBC lysed for 30 seconds on ice, and stained and sorted for live (PI) TER119- (FITC) cells; all wash and resuspension steps performed with ice-cold PBS + 0.04% BSA
RNA libraries were prepared for sequencing according to standard protocol in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry).

value: fetal liver

tag: Sex

value: male

tag: batch

value: pregnancy #3


title: E13.5 fetal liver Fancd2-/- 3.1

value: female


title: Patient_Day06_Rep2

value: patient carrying the GATA1 p.R307C mutation


title: Patient_Day06_Rep1


title: ESST_2

value: ST derived from ES-TSLCs


title: ESTSLC_1


title: E13.5 fetal liver Fancd2-/- 2.1

value: pregnancy #2


title: ESST_1


title: ESEVT_2

value: EVT derived from ES-TSLCs


title: IFT88_Lung_4

source_name: lung

value: ShhCre Ift88-/lox

value: cilia-disrupted


title: E13.5 fetal liver Fancd2-/- 1.1

value: pregnancy #1


title: IFT88_Lung_3


title: CENPJ_Lung_2

value: ShhCre Cenpj-/lox

value: centriole-disrupted


title: IFT88_Lung_2


title: CENPJ_Lung_1


title: CENPJ_Lung_4


title: CENPJ_Lung_3


title: ESEVT_1


title: E13.5 fetal liver WT 3.2

value: wild-type


title: BT474_NPY1R_LO_4_S8

description: BT474 NPY1R low 4

tag: cell line

value: Breast cancer cell line

value: NPY1R low


title: Control_Lung_4

value: ShhCre Cenpj+/lox

value: Control


title: ESC_2


title: E13.5 fetal liver WT 3.1

value: fetal liver

value: male


title: Control_Lung_3


title: BT474_NPY1R_LO_3_S6

description: BT474 NPY1R low 3


title: E13.5 fetal liver WT 2.1


title: IFT88_Lung_1


title: Control_Lung_2


title: BT474_NPY1R_LO_2_S4

description: BT474 NPY1R low 2


title: ESC_1


title: BT474_NPY1R_LO_1_S2

description: BT474 NPY1R low 1


title: E13.5 fetal liver WT 1.1

value: female


title: Patient_Day12_Rep2

value: patient carrying the GATA1 p.R307C mutation

value: bone marrow mononuclear cells


title: K562 ZNF417 ZNF587 control2

city: Guangzhou

first: Bo

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Approximately 6Gb and Q30>90% trimmed and filtered high-quality 150-bp paired-end reads per sample were mapped to the human genome using the TopHat v2.1.1 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1) with default parameters.
Cuffdiff (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5) was used for differential gene expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using bigwig

source_name: control KO K562

growth_protocol: K562 cells were cultured in RPMI1640 (Gibco) containing 10% FBS, 2 mM L-glutamine.

extract_protocol:
RNA was prepared from cells or embryos using the Eastep Super RNA extraction kit (Peomega).
RNA-seq libraries were prepared from total RNA from cells or embryos using TruSeq stranded mRNA sample preparation kit (Illumina)

treatment_protocol: To construct the ZNF417 and ZNF587 knockout cell lines, pX330 and GFP vector were co-transfected into K562 cells by using Nucleofector. GFP positive cells were sorted by FACS after 48 hours.

value: scrambled KO


title: Control_Lung_1


title: K562 ZNF417 ZNF587 DKO2


title: Patient_Day12_Rep1


title: BT474_NPY1R_HI_4_S9

description: BT474 NPY1R high 4

value: NPY1R high


title: K562 ZNF417 ZNF587 DKO1


title: D2 WT FGF RNA-seq biological replicate 2

first: James

institute: The Francis Crick Institute

description:
RNA-seq
D2_WT_FGF_R2

growth_protocol: WT ES cells were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days.

extract_protocol:
Total RNA was extracted from cells using a QIAGEN RNeasy kit in RLT buffer, following the manufacturer’s instructions. Extracts were digested with DNase I to eliminate genomic DNA.
The total RNA samples were quality controlled to determine RNA integrity and concentration using Agilent Tapestation prior to library preparation. Libraries were prepared using the KAPA mRNA HyperPrep kit (Roche) and sequenced as 76bp single-end, stand-specific reads on the Illumina HiSeq 4000 platform (Francis Crick Institute).

tag: time point

value: In vitro differentiated


title: D2 WT FGF RNA-seq biological replicate 3

description:
RNA-seq
D2_WT_FGF_R3


title: BT474_NPY1R_HI_3_S7

description: BT474 NPY1R high 3


title: NL4.3 integration in ZNF417 ZNF587 dKO 293T

data_processing:
Library strategy: nested PCR
The processes, except for merging of overlapping paired-end read sequences and read mapping, were achieved with in-house PERL scripts (available at https://github.com/odehir/VINSSRM).
The primer sequences for the LTR and linker are found in each 5´-end of the original paired-end read sequences (read1 and read2). Each set of overlapping paired-end read sequences was merged into one read (read3).
Then, the merged read sequences and paired-end read sequences were subjected to trimming of linker sequences and subsequent split-read mapping onto the human genome (hg38) and HIV-1 reference sequences (NL4.3).
The integration sites and breakpoints were assigned by nucleobase positions onto the human genome. The breakpoints were used to evaluate whether the integration sites are identified from clonally expanded cells. The LTR ends were assigned by nucleobase positions onto HIV-1 reference genomes. The nucleobase positions of the LTR ends are used to evaluate whether the viral end is intact or aberrant.
Genome_build: hg38
Supplementary_files_format_and_content: processed integration sites in txt format

source_name: ZNF417 ZNF587 dKO 293T

growth_protocol: HEK293T cells were cultured in DMEM High Glucose (Gibco) containing 10% FBS, 2 mM L-glutamine.

extract_protocol:
Genomic  DNA was purified from cell lysis with by phenol chloroform. DNA was sheared into 300 bp-500 bp random fragments using Covaris Adaptive Focused Acoustics (Covaris, Woburn, MA).
The sheared DNA fragments were end-repaired and a single dA was added to the 3’ ends using KAPA DNA Hyper Prep kit . A partially double stranded linker (5'GTAATACGACTCACTATAGGGCTCCGCTTAAGGGACT3’, 5'–PO4-GTCCCTTAAGCGGAG-3’-C6) with a one nucleotide 3’ T overhang was ligated to the genomic DNA fragments. The 3’ dA overhang on the genomic DNA fragments and the 3’ T overhang on the linker DNA prevented genomic-genomic DNA and linker-linker ligation, increased the efficiency of the desired ligation, and reduced the artifacts associated with cross-ligation commonly seen with restriction enzyme based linker-mediated PCR (LM-PCR). The integration junctions were selectively amplified using one primer that matched the HIV LTR sequence and the other primer that matched the single stranded portion of the linker. Nested PCR was performed with an inner primer pair; one primer matched the sequence of the LTR and the other primer matched the linker (outer: HIV-3LTR, 5’TGTGACTCTGGTAACTAGAGATCCCTC3’; Inner: HIV-3LTRnest, 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNCCCTTTTAGTCAGTGTGGAAAATC3’; outer: HIV-5LTR,TCAGGGAAGTAGCCTTGTGTGTGGT; inner: HIV-5LTRnest,  5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNGTCTTTTTTGGGACCAAATTAGCCC; outer: Linker-P1, 5’GTAATACGACTCACTATAGGGC3’; inner: PE2_Linkernest, 5'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNNAGGGCTCCGCTTAAGGGAC3’; NNNNNN stands for barcodes).

treatment_protocol: 16 μg pNL4.3-△E-RL and 4 μg pMD2.G were co-transfected into 10 cm dish 293T. Medium was changed 6–8 h after transfection, and supernatants were collected. Four 10cm dishes 293T supernatants were harvest and concentrated to 1 mL in proper culture medium. 1-2x105 control 293T cells or ZNF417 ZNF587 dKO cells were infected with 200 μL virus.

value: ZNF417 ZNF587 dKO

tag: agent


title: D2 WT FGF RNA-seq biological replicate 1

description:
RNA-seq
D2_WT_FGF_R1


title: BT474_NPY1R_HI_2_S5

description: BT474 NPY1R high 2


title: D0 WT RNA-seq biological replicate 3

description:
RNA-seq
D0_WT_R3

source_name: Undifferentiated pluripotent embryonic stem cells

value: Undifferentiated


title: BT474_NPY1R_HI_1_S3

description: BT474 NPY1R high 1


title: D0 WT RNA-seq biological replicate 2

description:
RNA-seq
D0_WT_R2


title: NL4.3 integration in control 293T

value: scramble KO


title: WT KAP1 ChIP

data_processing:
150-bp paired-end reads per ChIP-seq were mapped to the mouse (mm9) genome or human (hg38) genome using Bowtie2 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0) with default parameters.
Peaks visualized tracks were generated with bigwig files performed by bamCoverage (Galaxy toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.1.2.0.0)
The matrix between CHIP peaks and repeats was calculated using ComputeMatrix (toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.1.2.0.0).
Heatmap and profile plots then were generated by plotHeatmap or plotProfile (Galaxy toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/ deeptools_plot_heatmap/3.3.0.0.1, toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0) using calculated matrix generated by ComputeMatrix.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: mouse ES cells

growth_protocol: Zfp961-GFPflox/flox mouse Rosa26-CreERT2 ESCs were cultured in ESC medium containing DMEM (Gibco), 15% fetal bovine serum (FBS; Hyclone), 10mM NEAA, 100 μM β-mercaptoethanol, 2 mM L-glutamine, 10ng/mL LIF, 2i (3μM CHIR-99021, 1μM PD0325901, Selleck).

extract_protocol:
2-4x107 cells were cross-linked for 10 minutes at room temperature by the addition of formaldehyde solution at final concentration of 1% followed by quenching with glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was conserved in -80℃. Pellets were lysed, resuspended in 1mL of LB1 on ice for 10 min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10 min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS andprotease inhibitors) for histone marks and SDS shearing buffer (10mMTris pH8, EDTA 1mM, SDS 0.15% and protease inhibitors) for transcription factor and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 20 min), yielding genomic DNA fragments with a bulk size of 100-300bp. Coating of the beads with the specific antibody and carried out during the day at 4℃, then chromatin was added overnight at 4℃ for histone marks while antibody for transcription factor is incubated with chromatin first with 1% Triton and 150mM NaCl. Subsequently, washes were performed with 2x Low Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 150mM NaCl, 0.15% SDS), 1x High Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 0.15% SDS), 1x LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% NaDOC) and 1 with TE buffer. Final DNA was purified with QIAGEN Elute Column. Up to 10 nanograms of ChIPed DNA or input DNA (Input) were prepared for sequencing.
We performed library construction using the KAPA Hyper Prep Kit (Roche)

treatment_protocol: Zfp961-GFPflox/flox; Rosa26-CreERT2 ESCs were treated with 4-OHT or vehicle for 48 hours, then feed with ESC medium for another 72 hours before experiments.

value: derived from RosaCre ERT2 mouse embyro

value: EtOH (vector)

value: Zfp961 WT


title: KO KAP1 ChIP

value: Zfp961 KO


title: WT H3K27ac ChIP


title: KO H3K27ac ChIP


title: NGP_nutlin-3 bulk RNA-seq [NGP_nut_S2]

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

data_processing:
Raw fastq files were processed with Kallisto (v.0.43.1) (28) using Ensembl (v.91) annotation (29) .
JV1= control = SI-GA-8D = index of control
JV2= Nutlin treatment = SI-GA-8E =  index for nutlin
Genome_build: hg38

source_name: NGP cell treated with nutlin-3

growth_protocol: The neuroblastoma cell line NGP is a kind gift of prof. R. Versteeg (Amsterdam, the Netherlands). Cells were maintained in RPMI-1640 medium (Life Technologies, 52400-025) supplemented with 10 % fetal bovine serum (PAN Biotech, P30-3306), 1 % of L-glutamine (Life Technologies, 15140-148) and 1 % penicillin/streptomycin (Life Technologies, 15160-047) (referred to as complete medium) at 37 °C in a 5 % CO2 atmosphere. Short tandem repeat genotyping was used to validate cell line authenticity prior to performing the described experiments and verification of absence of mycoplasma was done on a monthly basis.

extract_protocol:
Total RNA was isolated using the miRNeasy mini kit (Qiagen, 217084) with DNA digestion on-column according to the manufacturer’s instructions. RNA concentration was measured using spectrophotometry (Nanodrop 1000, Thermo Fisher Scientific). cDNA was synthesized using the iScript Advanced cDNA synthesis kit (Bio-Rad, 1708897) using 500 ng RNA as input in a 20 µl reaction. cDNA was diluted to 2.5 ng/µl with nuclease-free water prior to RT-qPCR measurements.
The RNA of ten biological replicates of NGP cells treated with either nutlin-3 or vehicle, without serum starvation was extracted using the RNeasy mini kit. The RNA concentration was measured using spectrophotometry (Nanodrop 1000) and quality ascertained using the fragment analyzer (Advanced Analytical). 100 ng of total RNA was used as input for the TruSeq stranded mRNA library prep kit (Illumina, 20020594), according to manufacturer’s instructions.
Bulk RNA libraries were quantified using KAPA library quantification kit (Roche) and diluted to 4 nM. 1.2 pM of the RNA library was paired-end sequenced on a NextSeq 500 (Illumina) with a read length of 75 bp.

treatment_protocol: NGP cells were synchronized using serum starvation prior to nutlin-3 treatment. First, cells were seeded at low density for 48 hours in complete medium. Then, cells were refreshed with serum-free medium for 24 hours. Finally, the cells were treated with either 8 μM of nutlin-3 (Cayman Chemicals, 10004372, dissolved in ethanol) or vehicle (ethanol). Cells were trypsinized (Gibco, 25300054) 24 hours post treatment and harvested for single cell analysis, bulk RNA isolation and cell cycle analysis.

value: NGP

value: neuroblastoma cells

tag: cell cycle synchronization

value: yes

value: 8 μM of nutlin-3


title: NGP_vehicle (ethanol) bulk RNA-seq [NGP_con_S1]

source_name: NGP cell treated with vehicle (ethanol)

value: vehicle (ethanol)


title: D0 WT RNA-seq biological replicate 1

last: Briscoe

address: 1 Midland Road

description:
RNA-seq
D0_WT_R1

data_processing:
Adapter trimming was performed with cutadapt (version 1.16; Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”, and for paired-end data “-A AGATCGGAAGAGC” was appended to the command.
The RSEM package (version 1.3.0; Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a; Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 11th December 2017. The parameters passed to the “rsem-calculate-expression” command were “--star --star-gzipped-read-file --star-output-genome-bam --forward-prob 0”, and for paired-end data “--paired-end” was appended to the command.
Differential expression analysis was performed with the DESeq2 package (version 1.16.1; Love et al., 2014) within the R programming environment (version 3.4.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

value: wild-type


title: D3 SOX2 CHIR FGF DOX RNA-seq biological replicate 3

description: RNA-seq

source_name: In vitro differentiated epiblast-like cells

growth_protocol: WT and SOX2 TetON ES cells were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. 1ug/ml doxycycline was included in the culture medium of SOX2 TetON ES cells . To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then either N2/B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021 or N2/B27 + 10ng/ml bFGF + 5uM LGK974 until day 3.

value: Doxycycline maintained during differentiation


title: SE.IFNg sam20_L002

last: Krueger

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

description:
SE.IFNg
column sam20_L002 in counts.matrix

data_processing:
The normalized cDNA libraries were pooled and sequenced on Illumina Novaseq 6000 with pair-end 100 cycles in 50M reads sequencing depth.
Image analysis and bases calling were conducted in real-time by the Illumina analysis pipeline.
STAR 2.4.2a for alignment
subread 1.5.0.post3 (featureCount) for quantification of genes
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited gene expression data of each sample

source_name: Keratinocyte

growth_protocol: Primary normal human epidermal keratinocytes, adult (HEKa; Invitrogen, Carlsbad, CA) were cultured in the EpiLife medium supplemented with a defined growth supplement (Thermo Fisher Scientific, Waltham, MA). Cells were used in fewer than four passages in all experiments.

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit (Qiagen, Valencia, CA).
Libraries were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA), according to the manufacture instructions.

treatment_protocol: HEKa (2 x 10^5 cells per well) were plated in a 12 well plate and adhered overnight. After that, cells were treated with the following cytokines: IL-4/IL-13/IL-4 + IL-13/IL-22 (50 ng/ml) or IFN-γ (10 ng/ml; all from R&D systems, Minneapolis, MN) for 24 h. Then, cells were stimulated in the presence or absence  heat-killed S. aureus or S. epidermidis (both from InvivoGen, San Diego, CA) at 1 ´ 10⁸ cells per ml for 3 h (gene expression analysis except for S100A7 and CCL22) or 24 h (gene expression analysis for S100A7 and CCL22 or measurement cytokines in the culture supernatants).

value: skin, primary

value: adult

value: treated with IFNg for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: SA.IFNg sam21_L002

description:
SA.IFNg
column sam21_L002 in counts.matrix

value: treated with IFNg for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: NGP_nutlin-3 scRNA-seq [NGP_nut_S2]

data_processing:
Demultiplexing of the raw sequencing data was done by 10x Cell Ranger (v.2.0.2) software ‘cellranger mkfastq’ which wraps Illumina's bcl2fastq. The fastq files obtained after demultiplexing were used as input for ‘cellranger count’, which aligns the reads to the hg38 human reference genome using STAR using Ensembl (v.91) annotation and collapses to UMI counts. This was extended with mapping to ERCC spike-in RNA sequences, generating two separate matrices. Aggregation of samples to one dataset was done using ‘cellranger aggr’. The gene and ERCC count matrices were merged and only cells containing ERCC spikes were retained.
JV1= control = SI-GA-8D = index of control
JV2= Nutlin treatment = SI-GA-8E =  index for nutlin
Genome_build: hg38
Supplementary_files_format_and_content: count matrice

extract_protocol: Single cell RNA-seq on the Chromium system (10X Genomics) was performed for nutlin-3 (SI-GA-8E index) and vehicle (SI-GA-8D index) treated NGP cells using the GemCode Single Cell 3’ Gel Bead and Library Kit (V2 chemistry, 10X Genomics, PN-120237, PN-120236, PN-120262) according to manufacturer’s instructions with minor modifications. Cells were centrifuged at 4 °C at 400 g and resuspended in PBS + 0.04 % BSA to yield an estimated concentration of 1000 cells/µl. 3.5 µl of the cell suspension was used to obtain a cell recovery of about 2000 cells per sample. Per sample, 2.5 µl of an 1/10 dilution of ERCC spikes was added to the mastermix. After library preparation, the quality of the RNA libraries was confirmed on the Bioanalyzer.

treatment_protocol: NGP cells were synchronized using serum starvation prior to nutlin-3 treatment. First, cells were seeded at low density for 48 hours in complete medium. Then, cells were refreshed with serum-free medium for 24 hours. Finally, the cells were treated with either 8 μM of nutlin-3 (Cayman Chemicals, 10004372, dissolved in ethanol) or vehicle (ethanol). Cells were trypsinized (Gibco, 25300054) 24 hours post treatment and harvested for single cell analysis.


title: Comma-1D - scRNAseq

first: Robert

last: Sebra

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
To advance computational accuracy and remove predicted outlier data, the Seurat object representing the cells from the Comma-1D line was filtered for features that were not present in at least 15 cells (~0.3% of total cell count). To further clean the data set, data points were filtered using three parameters: high percent mitochondrial data is indicative of cell death, therefore cells with >20% were removed; a high count of unique features > 45,000 are indicative of multiplets and ribosomal RNA (rRNA) in the gel emulsion (GEM) formation and were therefore removed; a low count of unique features < 2000 is also indicative of GEMs with no cells and/or debris and these samples were also removed from the dataset. Figure 1C represents the data pre- and post-sub-setting for the above-mentioned quality standards, respectively, with 5,195 of the 5,745 sequenced cells passing these QC parameters. After passing initial QC, the data was normalized to account for variability. Cell cycle scoring was done to mitigate cell cycle heterogeneity through phase scoring of G2/M and S markers, which were then regressed out.
Counts matrix generated through Cell Ranger v3.1.0
Raw base call files demultiiplexed with Cell Ranger mfastq pipeline
Cell Range count pipeline used for alignment to Mus musculus mm10-3.0.0 reference
Feature filtering using Seurate for genes detected in less than 0.3% of the individual sample cells.
Filter cell barcodes with low Unique Molecular Identifier, sample dependent filtering
Filter cell barcodes with high total feature count, sample dependent filtering
Filter cell barcodes with high percentage mitochondrial genes, sample dependent filteirng
Supplementary_files_format_and_content: tsv files are generated by Cellranger. Each contain either detected cellular barcodes or features for expression matrices.
Supplementary_files_format_and_content: mtx files are the expression matrices generated by Cellranger.
Supplementary_files_format_and_content: rds files contain Seurat R objects

source_name: Mammary Gland

extract_protocol:
The Comma-1D cell line was thawed from frozen aliquots and cultured in CytoOne T25 flasks (USA Scientific) with culture media composing DMEM/F-12 media (Thermo Fisher), 2% FBS (Sigma-Aldrich), 1% Pen-Strep (Gibco), 10 µg/ml Insulin (Sigma-Aldrich), and 5ng/ml Endothelial Growth Factor (Thermo Fisher). Upon 80% confluency, the sample was passaged following the recommended sub culturing protocol for adherent cells.
For single-cell RNA sequencing, cells were collected at passage 5 and suspended in PBS media at 1 x 106 cells/mL. Cells was processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics) using manufacturer’s guidelines followed by sequencing on a S1 NovaSeq chip (Illumina Inc.). Qubit 3 (Fisher Scientific) and 2100 Bioanalyer (Agilent) were used for quality check of cDNA. The output BAM file from sequencing was processed through 10X Genomics Cell Ranger software v3.1.0. This outputs a read counts matrix that we used for downstream analyses using Seurat, a customizable R-Studio Package for scSeq analysis.

value: Mammary Gland


title: D3 SOX2 CHIR FGF DOX RNA-seq biological replicate 2

description: RNA-seq


title: NGP_vehicle (ethanol) scRNA-seq [NGP_con_S1]


title: TT-67

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

data_processing:
Read alignment by Salmon (ver. 1.3.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl mus musculus annotations (GRCm38, Apr 2020) release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Cardiac Tissue

growth_protocol: iPSC culture, iPSC-CM differentiation, and blasticidin selection:   WTC iPSCs and derivative lines were fed daily with E8 medium (STEMCELL Technologies) and cultured under feeder-free conditions on growth factor-reduced Matrigel (BD Biosciences). iPSCs were dissociated non-enzymatically using 0.5 μM ethylenediaminetetraacetic acid (EDTA) (Thermo Fisher Scientific) and passaged with p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (10 μM; Selleckchem). iPSCs were frozen in BamBanker human iPSC Freeze Media (Thermo Fisher Scientific). Differentiation of iPSCs was induced through the Wnt modulation method with 7 μM of glycogen synthase kinase 3 b (GSK3b) inhibitor CHIR99021 (Selleckchem) and 5 μM of inhibitor of WNT production 2 (IWP2) (Sigma). Basal Media was composed of RPMI media supplemented with B27 (Thermo Fisher Scientific). As previously described, we generated a blasticidin-selectable iPSC line to purify our iPSC-CMs using 1 μM blasticidin (Thermo Fisher Scientific). Eighteen days after adding CHIR, iPSC-CMs were frozen in 90% fetal bovine serum with 10% dimethyl sulfoxide (DMSO).

extract_protocol:
RNA extraction: Left ventricular cardiac tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cardiac Tissue


title: none.IFNg sam19_L002

description:
none.IFNg
column sam19_L002 in counts.matrix

value: treated with IFNg for 24 hrs


title: SA.IL22 sam15_L002

description:
SA.IL22
column sam15_L002 in counts.matrix

value: treated with IL-22 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: TT-68


title: D3 SOX2 CHIR FGF DOX RNA-seq biological replicate 1

description: RNA-seq


title: SE.IL22 sam14_L002

description:
SE.IL22
column sam14_L002 in counts.matrix

value: treated with IL-22 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: TT-66


title: D3 SOX2 CHIR FGF RNA-seq biological replicate 3

description: RNA-seq

value: Doxycycline withdrawn during differentiation


title: TT-65


title: Patient-GATA1_rep2

data_processing:
Raw sequencing data was processed using bcl2fastq
Paired-end reads were aligned to the hg19 reference genome using STAR
Gene count abundances were computed using the geneCounts feature in STAR
NA
Genome_build: hg19
Supplementary_files_format_and_content: Per sample raw counts in genes

source_name: bone marrow mononuclear cells from a patient carrying the GATA1 p.R307C mutation

extract_protocol:
Qiagen RLT lysis buffer
Smart-seq2

value: bone marrow mononuclear cells

tag: vector

tag: encoding

value: wildtype GATA1


title: none.IL22 sam13_L002

description:
none.IL22
column sam13_L002 in counts.matrix

value: treated with IL-22 for 24 hrs


title: Patient-GATA1_rep1


title: SA.IL4IL13 sam12_L002

description:
SA.IL4IL13
column sam12_L002 in counts.matrix

value: treated with IL-4 + IL-13 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: K562 ZNF417 ZNF587 control1

last: Yang

value: scrambled KO


title: TT-64

tag: tissue


title: SE.IL4IL13 sam11_L002

description:
SE.IL4IL13
column sam11_L002 in counts.matrix

tag: treatment

value: treated with IL-4 + IL-13 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: Patient-R307H_rep1

tag: cell type

value: GATA1 point mutant p.R307H


title: Patient-R307C_rep2

value: GATA1 point mutant p.R307C


title: D3 SOX2 CHIR FGF RNA-seq biological replicate 1

description: RNA-seq


title: TT-63


title: D3 WT CHIR FGF RNA-seq biological replicate 2

description: RNA-seq

value: wild-type


title: none.IL4IL13 sam10_L002

description:
none.IL4IL13
column sam10_L002 in counts.matrix

value: skin, primary

tag: age

value: adult

value: treated with IL-4 + IL-13 for 24 hrs


title: TT-62

value: Cardiac Tissue


title: D3 WT CHIR FGF RNA-seq biological replicate 1

description: RNA-seq


title: D3 WT CHIR FGF RNA-seq biological replicate 3

description: RNA-seq


title: Patient-HMD_rep2

value: HMD (empty vector)

value: control


title: SA.IL13 sam9_L002

description:
SA.IL13
column sam9_L002 in counts.matrix

value: treated with IL-13 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: TT-61


title: SE.IL13 sam8_L002

description:
SE.IL13
column sam8_L002 in counts.matrix

value: treated with IL-13 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: TT-59


title: Patient-HMD_rep1

value: bone marrow mononuclear cells


title: D3 SOX2 CHIR FGF RNA-seq biological replicate 2

description: RNA-seq

value: Doxycycline withdrawn during differentiation


title: D3 WT FGF RNA-seq biological replicate 3

description: RNA-seq


title: none.IL13 sam7_L002

description:
none.IL13
column sam7_L002 in counts.matrix

value: treated with IL-13 for 24 hrs


title: TT-58

value: WT

value: Vehicle


title: Patient-R307H_rep2


title: SA.IL4 sam6_L002

description:
SA.IL4
column sam6_L002 in counts.matrix

value: treated with IL-4 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: TT-57


title: Pooled Input

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1e-7.
Signal maps were extracted in bigwig format using deepTools bamCoverage function.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig = signal map in bigWIG format (UCSC)

source_name: urinary epithelial cells 5637

growth_protocol: The human bladder epithelial cell line 5637 (ATCC HTB-9) was cultured in RPMI 1640 (Invitrogen, Karlsruhe, Germany) containing 10% fetal bovine serum (Invitrogen), and incubated at 37°C in the presence of 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Uroepithelial cells grown on 6-well cell culture plates (BD Biosciences, California, USA) were infected with UPEC, HDM (MOI: 1) or UPEC + acetate for 3 h.

value: grade II bladder carcinoma cells

tag: passages

tag: chip abtibody


title: SE.IL4 sam5_L002

description:
SE.IL4
column sam5_L002 in counts.matrix

value: treated with IL-4 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: TT-56

tag: genotype


title: UPEC Ac H3k9ac

description: 4_03F8_00F3ZhengUni_UPEC-Ac_H3K9Ac_hs-dm_i95

value: UPEC + acetate for 3 h

value: H3k9ac (Active motif, 39137)


title: D3 WT CHIR FGF TCF4 IP ChIP-seq biological replicate 3

description: ChIP-seq

data_processing:
The nf-core/chipseq pipeline (version 1.1.0; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3529400) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --input design.csv --genome mm10 --gtf refseq_genes.gtf --single_end --narrow_peak --min_reps_consensus 2 -profile crick -r 1.1.0".
All data was processed relative to the human UCSC mm10 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on December 11th 2017.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Genome_build: mm10
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/chipseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using from the nf-core/chipseq pipeline command defined above.

growth_protocol: WT and SOX2 TetON ES cells were cultured in knockout DMEM, 10% serum and 1000U/ml LIF prior to differentiation. 1ug/ml doxycycline was included in the culture medium of SOX2 TetON ES cells . To induce differentiation cells were cultured in N2/B27 containing basal medium + 10ng/ml bFGF + 5uM LGK974 for 2 days, then N2B27 + 10ng/ml bFGF + 5uM LGK974 + 5mM CHIR99021 until day 3. ES cells were reverted to naive pluripotency by culturing in 2i medium (N2/B27 containing basal medium supplemented with 3uM CHIR and 500nM PD0325901).

extract_protocol:
Approximately 5*10^6 cells were transferred to a Diagenode TPX tube and resuspended in ice cold shearing buffer (1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6), 0.3% SDS + protease inhibitors). Chromatin was sheared using a Bioruptor plus: 25 cycles of 30s On/30s Off on high setting. Sheared lysates were diluted to 0.15% SDS  prior to immunoprecipitation.
The DNA library for sequencing was prepared from Qiagen column purified DNA. DNA fragmentation of IP and input samples was confirmed by Agilent TapeStation prior to library preparation using NEB Ultra II DNA. Libraries were sequenced as single-end, 76bp reads on the Illumina High-Seq 4000 platform (Francis Crick Institute).

treatment_protocol: Adherent cells were fixed  for 45min at room temperature with 2mM Di(N-succinimidyl) glutarate, then fixed for an additional 10min at room temperature with 1% PFA. Fixation was quenched by addition of 250mM glyceine for 5 minutes.

tag: chip antibody

value: TCF4 (Santa Cruz sc-8631 goat)

tag: strain

value: wild-type


title: Patient-R307C_rep1

value: GATA1 point mutant p.R307C


title: D3 WT CHIR FGF TCF4 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: SA.none sam3_L002

description:
SA.none
column sam3_L002 in counts.matrix

value: skin, primary

value: adult

value: treated with Staphylococcus aureus for 3 hrs


title: none.IL4 sam4_L002

description:
none.IL4
column sam4_L002 in counts.matrix

value: treated with IL-4 for 24 hrs


title: TT-55

value: Cardiac Tissue


title: HDM H3k9ac

description: 2_03F6_00F3ZhengUni_HDM_H3K9Ac_hs-dm_i93

value: HDM (MOI:1)


title: TT-53


title: SE.none sam2_L002

description:
SE.none
column sam2_L002 in counts.matrix

value: treated with Staphylococcus epidermidis for 3 hrs


title: none.none sam1_L002

description:
none.none
column sam1_L002 in counts.matrix

value: untreated


title: Second Heart Field (SHF)

city: Los Angeles

first: Reza

last: Ardehali

address: 675 Charles E Young Dr S

institute: UCLA

data_processing:
Standard 10X pipeline was used for data processing
Cell Ranger software package was used for de-multiplexing.
Alignment was completed using STAR software.
Analysis was performed using Loupe software package.
Genome_build: GRCh38
Supplementary_files_format_and_content: sparse matrix of all read counts for all cells

source_name: SHF

extract_protocol:
Samples were sorted and resuspended into 1xPBS+0.04%BSA and then processed using he 10X Genomics Chromium v.2 Single Cell platform according to the manufacturer's instructions.
10X Genomics Chromium v.2 Single Cell platform according to the manufacturer's instructions.


title: Ctrl H3k9ac

description: 1_03F5_00F3ZhengUni_Ctrl_H3K9Ac_hs-dm_i92

value: none (control)


title: D3 WT CHIR FGF TCF3 IP ChIP-seq biological replicate 3

city: London

description: ChIP-seq

value: TCF3 (Santa Cruz sc-8635 goat)


title: D3 WT FGF RNA-seq biological replicate 1

description: RNA-seq


title: D3 WT CHIR FGF TCF3 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: D3 WT CHIR FGF TCF4 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: First Heart Field (FHF)

source_name: FHF


title: D3 WT CHIR FGF TCF3 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: sc_RNA-seq_HS1_day_14

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17, building A11

institute: Lund University

data_processing:
bcl2fastq (Illumina) was used for base-calling.
The reads were aligned to the genome (GRCh38 and PanTro6) using STAR aligner v2.5.0a, allowing for 0.03 mismatches per base and multimapping at up to 10 loci.
The Subread package FeatureCounts was used to quantify the reads overlapping Gencode v27 gene annotations. The human Gencode annotation was lifted over to PanTro6 using UCSC LiftOver tool.
single cell fastqs:
I1 Technical: Index read
R1 Technical: 16 bp Barcode and 10bp UMI
R2 Biological
Genome_build: GRCh38 and PanTro6
Supplementary_files_format_and_content: matrix.mat: raw read counts
Supplementary_files_format_and_content: Exon.sjdb.txt: featureCounts

source_name: forebrain neural progenitors

growth_protocol: iPS cells were differentiated into forebrain neural progenitor cells using the following protocol: The iPSCs were plated at 10.000 cells/cm2 in N2 medium (1:1 DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1% N2 (Gibco), 2 mM L-glutamine (Gibco), 0.2% penicillin/streptomycin (Gibco)) with dual SMAD-inhibition (10 µM SB431542 (Axon), 100 ng/ml noggin (Miltenyi)) as well as ROCK inhibitor (10 µM Y27632) on LN111 coated Nunc delta surface multidishes (1.14 µg/cm2; Biolamina). The media was changed every 2-3 days to N2 medium with SMAD-inhibitors up until day 9 of differentiation when only N2 medium was used. On day 11 the cells were dissociated using StemPro accutase (75  µl/cm2; Gibco) and replated at 800,000 cells/cm2 on LN111-coated Nunc plates in B27 medium (Neurobasal supplemented with 1% B28 without vitamin A (Gibco), 2 mM L-glutamine and 0.2% penicillin/streptomycin) supplemented with 10 µM ROCK inhibitor, BDNF (20 ng/ml; R&D), and L-ascorbic acid (0.2mM; Sigma-Aldrich). The cells were then harvested at day 13, 14, 15, or 16.

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen) for bulk RNA-seq
Libraries for bulk RNA-seq were prepared withTruSeq RNA Library prep kit v2 (Illumina). Single cell libraries were prepared with Chromium Single Cell 3' Library & Gel Bead kit v2 (10x Genomics)

value: iPSC-derived forebrain neural progenitors


title: SE.IFNg sam20_L001

description:
SE.IFNg
column sam20_L001 in counts.matrix

value: treated with IFNg for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: TT-50

city: South San Francisco

value: Vehicle


title: TT-51


title: UPEC H3k9ac

description: 3_03F7_00F3ZhengUni_UPEC_H3K9Ac_hs-dm_i94

value: grade II bladder carcinoma cells

value: UPEC

value: H3k9ac (Active motif, 39137)


title: bulk_RNA-seq_HS2_day_14_replicate_2

description:
hg38.s2.multi.Gencode27.Exon.sjdb.v2.txt
pantro6.s2.multi.Gencode27.Exon.sjdb.v2.txt


title: none.IFNg sam19_L001

description:
none.IFNg
column sam19_L001 in counts.matrix

value: treated with IFNg for 24 hrs


title: TT-54

value: WT


title: bulk_RNA-seq_HS2_day_14_replicate_1


title: TT-48


title: D3 WT CHIR FGF SOX2 IP ChIP-seq biological replicate 1

description: ChIP-seq

value: Sox2 (R&D AF2018 goat)

value: wild-type


title: D3 WT CHIR FGF SOX2 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: SA.IL22 sam15_L001

description:
SA.IL22
column sam15_L001 in counts.matrix

value: skin, primary

value: adult

value: treated with IL-22 for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: SE.IL22 sam14_L001

description:
SE.IL22
column sam14_L001 in counts.matrix

value: treated with IL-22 for 24 hrs, treated with Staphylococcus epidermidis for 3 hrs


title: D3 WT CHIR FGF LEF1 IP ChIP-seq biological replicate 3

description: ChIP-seq

value: LEF1 (Millipore CS200635)


title: TT-52

value: Cardiac Tissue


title: SA.IFNg sam21_L001

description:
SA.IFNg
column sam21_L001 in counts.matrix

value: treated with IFNg for 24 hrs, treated with Staphylococcus aureus for 3 hrs


title: TT-47


title: bulk_RNA-seq_HS1_day_16_replicate_2

value: iPSC-derived forebrain neural progenitors


title: none.IL22 sam13_L001

description:
none.IL22
column sam13_L001 in counts.matrix

value: treated with IL-22 for 24 hrs


title: D3 WT CHIR FGF LEF1 IP ChIP-seq biological replicate 2

description: ChIP-seq


title: bulk_RNA-seq_HS1_day_16_replicate_1


title: TT-45

value: Vehicle


title: TT-46


title: bulk_RNA-seq_HS1_day_15_replicate_2


title: D3 WT CHIR FGF SOX2 IP ChIP-seq biological replicate 3

description: ChIP-seq


title: SA.IL4IL13 sam12_L001

description:
SA.IL4IL13
column sam12_L001 in counts.matrix

value: treated with IL-4 + IL-13 for 24 hrs, treated with Staphylococcus aureus for 3 hrs