title: P53

data_processing:
ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).
FastQC initially processed raw sequence reads for quality control, and then adapter sequences and poor quality reads were removed.
Quality filtered reads were then mapped to reference genome using BWA and only uniquely mapped reads were kept,
Filtered bam files were used for peak calling by MACS2 and an initial threshold q-value of 0.01 as cutoff.
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: cancer associated fibroblast

growth_protocol: CAFs were cultured in DMEM media supplemented with 10% FBS at 37°C under 5% CO2.

extract_protocol:
Cells were collected and lysed to obtain purified nucleus; The Tn5 enzyme transposable reaction was carried out and the open regions of chromatin were fragmented; the fragmented DNA was purified; the purified DNA was amplified. The amplified DNA was sized to remove non-target fragments.
ATAC libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina kit.Purified fragmented DNA were amplified by PCR reaction,and the libraries were first purified by MinElute PCR purification column(Qiagen)and then further size-selected by VAHTS DNA Clean Beads to obtain libraries with a size distribution between 100 and 1500 bp.

treatment_protocol: For cancer assocciated fibroblasts, enzalutamide (1M) and TGF-β1 (5 ng/ml) was added into different conditions, treatment was performed in two biological replicates.

value: cancer associated fibroblast

value: stroma

tag: library type

value: Genomic DNA

value: DMSO

value: isolated from PtenPC-/-; Trp53PC-/- mice


title: CCAF_Flag

status: Public on Jun 22 2023

type: SRA

city: Shanghai

first: Hanling

last: Wang

address: Shanghai

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

library_source: genomic

data_processing:
Paired-end fastq files were trimmed and uniquely aligned to the GRCm38/mm10 mouse genome assembly using BWA.
After alignment, reads mapped to the same genomic positions were filtered by PICARD-MarkDuplicates (Galaxy Version 2.18.2.2)
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified DNA was prepared for sequencing as per the manufacturer’s instructions (Illumina). Libraries were quantified and sequenced on the Illumina NovaSeq 6000 Sequencer.

treatment_protocol: For cancer assocciated fibroblasts, enzalutamide (1 μM) and TGF-β1 (5 ng/ml) was added into different conditions, treatment was performed in two biological replicates.

tag: cell line

tag: cell type

tag: treatment

tag: chip antibody


title: input


title: p53enz

value: enzalutamide 1 μM


title: p53tgfb

value: TGF-β1 5 ng/ml


title: Ca

value: isolated from PtenPC-/-; Trp53PC-/- ADT mice


title: p53enztgfb

value: enzalutamide 1 μM, TGF-β1 5 ng/ml


title: CCAF_AR


title: ca-1

description:
Cafs_gene_exp.txt
ca-1_TPM

library_source: transcriptomic

data_processing:
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligaion and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher  Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).
HISAT2 was used to align the clean reads to the mouse reference genome mm10 with default parameters.
HTSeq was subsequently employed to convert aligned short reads into read counts for each gene
Differential expression was assessed by DESeq2 using read counts as input.
Assembly: hg19, mm10
Supplementary files format and content: tab-delimited text files include RPKM or TPM values for each Sample

molecule: total RNA

growth_protocol: LNCap were cultured in RPM1640 media supplemented with 10% FBS at 37°C under 5% CO2. Cancer associated fibroblasts were cultured in DMEM media supplemented with 10% FBS at 37°C under 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was subjected to Hiseq RNA-Seq, performed by RiboBio Co., Ltd.
RNA libraries for RNA-seq were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA)

treatment_protocol: For LNCap, enzalutamide (1μM) was added into different conditions, treatment was performed in two biological replicates. For cancer assocciated fibroblasts, enzalutamide (1 μM) and TGF-β1 (5 ng/ml) was added into different conditions, treatment was performed in two biological replicates.

tag: genotype

value: WT

tag: time

value: Day 0


title: ca-2

description:
Cafs_gene_exp.txt
ca-2_TPM


title: CCAF_k27

value: H3K27ac (Abcam, #ab4729)


title: sox4CAF_k27

value: isolated from PtenPC-/-; Trp53PC-/- mice, sox4 overexpressed


title: sox4


title: sox4_flag


title: CRPCCAF_AR


title: sox4-1

description:
Cafs_gene_exp.txt
sox4-1_TPM


title: CDP_Flt3L_6h_3

city: Saint Louis

first: Sunkyung

last: KIM

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

country: USA

institute: Washington University in Saint Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Mouse Ensembl GRCm38.76 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with merged differential expression results

source_name: Bone marrow

growth_protocol: BM cells were isolated from 8 week old WT mice and CD3-, CD19-, CD105-, NK1.1-, TER-119-, Ly-6G- and B220-expressing lineage-committed cells were depleted. The CDP (lineage– cKitint Flt3+ M-CSFR+ MHCII–, CD11c–) were sort-purified and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) supplemented with 10% FBS, 1% Penicilin Streptomycin solution, 1% Sodium Pyruvate, 1% MEM non-essention amino acid, 1% L-glutamine solution, and 55 mL β-mercaptoethanol (complete IMDM) cultured in the presence of Flt3L or Flt3L with murine recombinant IL-6 for 6 h.

extract_protocol:
RNA was isolated from 50,000 CDPs after 6 h stimulation using NucleoSpin RNA XS Kit (Macherey-Nagel).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: The sort-purified CDPs (50,000 cells) were (1) untreated, (2) Flt3L (conditioned medium 5%), or (3) Flt3L (conditioned medium 5%) and IL-6 (25 ng/ml) for 6 h.

tag: tissue

value: Bone marrow

value: Common dendritic cell progenitor

value: Flt3L conditioned media (5%)


title: p53TGF-2

description:
Cafs_gene_exp.txt
p53TGF-2_TPM

value: Day 7


title: p53ENZTGF-1

description:
Cafs_gene_exp.txt
p53ENZTGF-1_TPM

value: cancer associated fibroblast


title: p53ENZTGF-2

description:
Cafs_gene_exp.txt
p53ENZTGF-2_TPM

value: stroma


title: p53ENZ-1

description:
Cafs_gene_exp.txt
p53ENZ-1_TPM


title: p53TGF-1

description:
Cafs_gene_exp.txt
p53TGF-1_TPM


title: p53-2

description:
Cafs_gene_exp.txt
p53-2_TPM


title: p53-1

description:
Cafs_gene_exp.txt
p53-1_TPM


title: iPSC WT vc-chir-pd-y-bix GFP+ line #1

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt vc-chir-pd-y-bix gfpp rp1

data_processing:
Aligned to genome/transcriptome using STAR (2.7.10a)
Genes and TEs counted using te_counts (https://github.com/oaxiom/te_counter)
Normalised using EDASeq (v2.30.0)
Differential expression using DESeq2 (v1.36.0) q-value <0.01 fold-change >2
All other analysis was performed using glbase3 (Hutchins et al., 2014).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalised tag counts for each sample
Supplementary files format and content: tab-delimited text files include normalised tag counts for the mean of all replicates (where avaiable)

source_name: iPSC (OG2)

growth_protocol: MEFs were derived from E13.5 embryos from wildtype ICR genetic background, an OG2 or Oct4-GFP knock in mice. MEF cells were cultured in DMEM high-glucose media containing 10% FBS (GIBCO), 1 × GlutaMAX (GIBCO), and 1x nonessential amino acids (GIBCO), 0.5x Penicillin/Streptomycin (Hyclone). We generated immortalized MEF cell lines and used the  oncogenic genes: P53DD, SV40T, Hdac7SA, Mef2d, Bcl2, Myc, Ras, E1A.

extract_protocol:
Total RNA from cells was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocols. cDNA synesis by using a PrimeScript RT Master Mix (Takara, RR036A).
RNA-seq NEB Next Ultra RNA Library Prep Kit   cat.7530

treatment_protocol: WT (ICR) MEF and transformed MEFs in an OG2 reporter background were reprogrammed as described in Zhuang, 2018. Briefly, OKSM in lentivirus was transfected into 15,000 MEFs in one well of a 12-well plate. One day after transfection the medium was changed to reprogramming medium: DMEM high-glucose media containing 15% FBS (GIBCO), 1× GlutaMAX (GIBCO), 1x non-essential amino acids (GIBCO), 0.5x Penicillin/Streptomycin (Hyclone), 1mM sodium pyruvate (GIBCO), 0.1 mM 2-mercaptoethanol (GIBCO), 1000 U/ml leukemia inhibitory factor (LIF) (Millipore) and vitamin C, as indicated in the figures. Medium was changed daily. Inhibitors were added at the change to reprogramming medium: PD0325901, CHIR99021, Y23637, BIX-01294, and TSA.

value: iPSC (OG2)

tag: transgenes

value: OG2 reporter

value: PD+CHIR+Y+BIX


title: iPSC WT vc-chir-pd-y GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt vc-chir-pd-y gfpp rp1

value: PD+CHIR+Y


title: iPSC WT vc-chir-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt vc-chir-y-bix gfpp rp1

value: CHIR+Y+BIX


title: iPSC WT vc-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt vc-pd-y-bix gfpp rp1

value: PD+Y+BIX


title: sox4-2

description:
Cafs_gene_exp.txt
sox4-2_TPM


title: iPSC WT vc-chir-pd-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt vc-chir-pd-bix gfpp rp1

value: PD+CHIR+BIX


title: OSKM MEF (OG2) WT D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt D6 rp1

source_name: MEF (OG2)

value: MEF (OG2)


title: OSKM MEF (OG2) WT D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt D12 rp1


title: OSKM MEF (OG2) WT D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt D15 rp1


title: OSKM MEF (OG2) WT D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt D9 rp1


title: OSKM MEF (OG2) SV40T D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D6 rp2

value: SV40T, OSKM


title: iPSC-like SV40T vc-chir-pd-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t vc-chir-pd-bix gfpp rp1

source_name: iPSC-like (OG2)

value: iPSC-like (OG2)


title: OSKM MEF (OG2) SV40T D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D6 rp1


title: iPSC-like SV40T chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t chir-pd-y-bix gfpp rp1


title: iPSC-like SV40T vc-chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t vc-chir-pd-y-bix gfpp rp1


title: iPSC-like SV40T vc-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t vc-pd-y-bix gfpp rp1


title: OSKM MEF (OG2) SV40T D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D9 rp1


title: OSKM MEF (OG2) SV40T D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D9 rp2


title: OSKM MEF (OG2) SV40T D3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D3 rp2


title: iPSC-like SV40T vc-chir-pd-y GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t vc-chir-pd-y gfpp rp1


title: OSKM MEF (OG2) SV40T D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D3 rp1


title: OSKM MEF (OG2) SV40T D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D15 rp2


title: OSKM MEF (OG2) SV40T D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D15 rp1


title: OSKM MEF (OG2) SV40T D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D12 rp2


title: OSKM MEF (OG2) SV40T D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D12 rp1


title: OSKM MEF (OG2) SV40T D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D0 rp2


title: OSKM MEF (OG2) SV40T D0 Rep3

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D0 rp3


title: iPSC-like p53DD-Myc vc GFP+ line #2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc vc gfpp rp2

value: p53DD, Myc, OSKM


title: iPSC WT chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt chir-pd-y-bix gfpp rp1


title: OSKM MEF (OG2) SV40T D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 sv40t D0 rp1


title: OSKM MEF (OG2) WT D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 wt D3 rp1


title: OSKM MEF (OG2) p53DD-Myc D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc D15 rp2


title: OSKM MEF (OG2) p53DD-Myc D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc D6 rp2


title: OSKM MEF (OG2) p53DD-Myc D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc D12 rp2


title: p53ENZ-2

description:
Cafs_gene_exp.txt
p53ENZ-2_TPM

value: WT

value: enzalutamide 1 μM

value: isolated from PtenPC-/-; Trp53PC-/- mice


title: OSKM MEF (OG2) p53DD-E1A D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D9 rp2

value: p53DD, E1A, OSKM


title: OSKM MEF (OG2) p53DD-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc D0 rp2

value: p53DD, Myc


title: OSKM MEF (OG2) p53DD-E1A D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D12 rp2


title: OSKM MEF (OG2) p53DD-E1A D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D3 rp1


title: OSKM MEF (OG2) p53DD-E1A D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D15 rp2


title: OSKM MEF (OG2) p53DD-E1A D3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D3 rp2


title: OSKM MEF (OG2) p53DD-E1A D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D0 rp1

value: p53DD, E1A


title: OSKM MEF (OG2) p53DD-E1A D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D0 rp2


title: OSKM MEF (OG2) Hras-Myc D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D9 rp2

value: Hras, Myc, OSKM


title: OSKM MEF (OG2) Hras-Myc D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D6 rp2

value: OG2 reporter


title: OSKM MEF (OG2) Hras-Myc D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D3 rp1


title: OSKM MEF (OG2) Hras-Myc D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D15 rp2


title: iPSC-like p53DD-Myc vc GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc vc gfpp rp1


title: OSKM MEF (OG2) Hras-Myc D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D12 rp2


title: OSKM MEF (OG2) Hras-Myc D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D0 rp2

value: Hras, Myc


title: OSKM MEF (OG2) Hras-Myc D0 Rep3

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D0 rp3


title: OSKM MEF (OG2) Hras-Myc D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D12 rp1


title: OSKM MEF (OG2) Hras-Myc D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D9 rp1


title: OSKM MEF (OG2) Hras-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D0 rp1


title: OSKM MEF (OG2) Hras-Myc D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D6 rp1


title: OSKM MEF (OG2) Hdac7SA-Myc D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D6 rp1

value: Hdac7SA, Mef2d, OSKM


title: OSKM MEF (OG2) Hdac7SA-Myc D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D9 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D6 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D9 rp1


title: OSKM MEF (OG2) p53DD-Myc D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc D3 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D3 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D3 rp1


title: OSKM MEF (OG2) p53DD-E1A D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D6 rp1


title: OSKM MEF (OG2) p53DD-E1A D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D9 rp1


title: OSKM MEF (OG2) p53DD-E1A D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-e1a D6 rp2


title: OSKM MEF (OG2) Hras-Myc D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hras-myc D15 rp1


title: OSKM MEF (OG2) Hdac7SA-Myc D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D15 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D0 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D12 rp2


title: OSKM MEF (OG2) Hdac7SA-Myc D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D12 rp1


title: OSKM MEF (OG2) Hdac7SA-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D0 rp1


title: OSKM MEF (OG2) Hdac7SA-Mef2d D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D9 rp1


title: OSKM MEF (OG2) Hdac7SA-Mef2d D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D6 rp1


title: OSKM MEF (OG2) Hdac7SA-Mef2d D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D3 rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D15 rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D9 rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D15 rp1


title: OSKM MEF (OG2) Hdac7SA-Mef2d D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D6 rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D0 Rep3

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D0 rp3

value: Hdac7SA, Mef2d


title: OSKM MEF (OG2) Hdac7SA-Mef2d D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D12 rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D0 rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D0 rp1


title: OSKM MEF (OG2) Hdac7SA-E1A D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D9 rp2

value: Hdac7SA, E1A, OSKM


title: OSKM MEF (OG2) Hdac7SA-E1A D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D6 rp2


title: OSKM MEF (OG2) Hdac7SA-E1A D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D3 rp1


title: OSKM MEF (OG2) Hdac7SA-E1A D3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D3 rp2


title: OSKM MEF (OG2) Hdac7SA-E1A D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D15 rp1


title: OSKM MEF (OG2) Hdac7SA-E1A D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D6 rp1


title: OSKM MEF (OG2) Hdac7SA-E1A D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D9 rp1


title: OSKM MEF (OG2) Hdac7SA-Myc D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-myc D15 rp1


title: OSKM MEF (OG2) Hdac7SA-E1A D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D12 rp1


title: OSKM MEF (OG2) Hdac7SA-E1A D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D0 rp2

value: Hdac7SA, E1A


title: OSKM MEF (OG2) Hdac7SA-E1A D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D12 rp2

value: MEF (OG2)


title: iPSC-like Hdac7SA-Myc vc GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-myc vc gfpp rp1

value: Hdac7SA, Myc, OSKM


title: iPSC-like Hdac7SA-Mef2d vc-chir-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-chir-y-bix gfpp rp1

value: iPSC-like (OG2)

value: CHIR+Y+BIX


title: iPSC-like Hdac7SA-Mef2d vc-chir-pd-y-bix GFP+ line #2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-chir-pd-y-bix gfpp rp2

value: PD+CHIR+Y+BIX


title: iPSC-like Hdac7SA-Mef2d vc-chir-pd-y GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-chir-pd-y gfpp rp1

value: PD+CHIR+Y


title: iPSC-like Hdac7SA-Mef2d vc GFP+ line #5

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc gfpp rp5


title: iPSC-like Hdac7SA-Mef2d vc-chir-pd-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-chir-pd-bix gfpp rp1

value: PD+CHIR+BIX


title: iPSC-like Hdac7SA-Mef2d vc-chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-chir-pd-y-bix gfpp rp1


title: iPSC-like Hdac7SA-Mef2d vc GFP+ line #4

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc gfpp rp4


title: iPSC-like Hdac7SA-Mef2d vc-chir-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-chir-bix gfpp rp1

value: CHIR+BIX


title: iPSC-like E1A-ras vc-chir-pd-y GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-ras vc-chir-pd-y gfpp rp1

value: Hras, E1A, OSKM


title: OSKM MEF (OG2) Hdac7SA-E1A D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-e1a D15 rp2


title: iPSC-like E1A-ras vc-chir-pd-y-bix GFP+ line #2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-ras vc-chir-pd-y-bix gfpp rp2


title: OSKM MEF (OG2) Hdac7SA-Mef2d D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7sa-mef2d D12 rp1


title: iPSC-like Hdac7SA-Mef2d chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d chir-pd-y-bix gfpp rp1


title: OSKM MEF (OG2) p53DD-Myc D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 p53dd-myc D9 rp2

value: p53DD, Myc, OSKM


title: iPSC-like E1A-ras vc-chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-ras vc-chir-pd-y-bix gfpp rp1


title: iPSC-like E1A-ras vc-chir-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-ras vc-chir-y-bix gfpp rp1


title: iPSC-like E1A-ras vc-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-ras vc-pd-y-bix gfpp rp1

value: PD+Y+BIX


title: iPSC-like E1A-ras chir-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-ras chir-pd-y-bix gfpp rp1

value: OG2 reporter


title: OSKM MEF (OG2) E1A-Hras D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D6 rp1


title: OSKM MEF (OG2) E1A-Hras D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D9 rp2


title: OSKM MEF (OG2) E1A-Hras D3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D3 rp2


title: OSKM MEF (OG2) E1A-Hras D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D9 rp1


title: OSKM MEF (OG2) E1A-Hras D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D6 rp2


title: iPSC-like Hdac7SA-Mef2d vc-pd-y-bix GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 hdac7-mef2d vc-pd-y-bix gfpp rp1


title: OSKM MEF (OG2) E1A-Hras D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D12 rp1


title: OSKM MEF (OG2) E1A-Hras D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D12 rp2


title: OSKM MEF (OG2) E1A-Hras D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D15 rp1


title: OSKM MEF (OG2) E1A-Hras D0 Rep3

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D0 rp3

value: Hras, E1A


title: OSKM MEF (OG2) E1A-Hras D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D0 rp2


title: OSKM MEF (OG2) Bcl2-Myc D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D9 rp1

value: Bcl2, Myc, OSKM


title: OSKM MEF (OG2) E1A-Hras D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D0 rp1


title: OSKM MEF (OG2) Bcl2-Myc D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D6 rp1


title: OSKM MEF (OG2) Bcl2-Myc D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D6 rp2


title: OSKM MEF (OG2) Bcl2-Myc D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D3 rp1


title: OSKM MEF (OG2) Bcl2-Myc D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D0 rp3

value: Bcl2, Myc


title: OSKM MEF (OG2) Bcl2-Myc D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D15 rp1


title: OSKM MEF (OG2) Bcl2-Myc D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D9 rp2


title: OSKM MEF (OG2) E1A-Hras D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D3 rp1


title: OSKM MEF (OG2) Bcl2-Myc D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D12 rp1


title: OSKM MEF (OG2) Bcl2-Myc D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D12 rp2


title: iPSC-like Bcl2-E1A vc GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a vc gfpp rp1

value: Bcl2, E1A, OSKM


title: OSKM MEF (OG2) Bcl2-E1A D9 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D9 rp1


title: OSKM MEF (OG2) Bcl2-Myc D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D15 rp2


title: OSKM MEF (OG2) Bcl2-E1A D6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D6 rp1


title: OSKM MEF (OG2) Bcl2-E1A D3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D3 rp2


title: OSKM MEF (OG2) Bcl2-E1A D15 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D15 rp1


title: OSKM MEF (OG2) Bcl2-E1A D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D15 rp2


title: OSKM MEF (OG2) Bcl2-E1A D9 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D9 rp2


title: OSKM MEF (OG2) Bcl2-E1A D12 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D12 rp1


title: OSKM MEF (OG2) Bcl2-E1A D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D0 rp2

value: Bcl2, E1A


title: OSKM MEF (OG2) Bcl2-E1A D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D0 rp1

value: MEF (OG2)


title: OSKM MEF (OG2) Bcl2-E1A D12 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D12 rp2


title: OSKM MEF (OG2) E1A-Hras D15 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 e1a-hras D15 rp2


title: OSKM MEF (ICR) SV40T D0 Rep3

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr sv40t D0 rp3

source_name: MEF (ICR)

value: MEF (ICR)

value: wildtype


title: OSKM MEF (ICR) SV40T D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr sv40t D0 rp2


title: OSKM MEF (ICR) p53DD-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr p53dd-myc D0 rp1

value: p53DD, Myc


title: OSKM MEF (OG2) Bcl2-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-myc D0 rp1


title: OSKM MEF (ICR) Hras-Myc D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hras-myc D0 rp3

value: Hras, Myc


title: OSKM MEF (ICR) p53DD-E1A D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr p53dd-e1a D0 rp1


title: OSKM MEF (ICR) Hdac7SA-Mef2d D0

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hdac7sa-mef2d D0 rp3

value: Hdac7SA, Mef2d


title: OSKM MEF (ICR) Hdac7SA-Mef2d D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hdac7sa-mef2d D0 rp2


title: OSKM MEF (ICR) Hdac7SA-Mef2d D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hdac7sa-mef2d D0 rp1


title: OSKM MEF (ICR) E1A-Hras D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr e1a-hras D0 rp2


title: OSKM MEF (ICR) Hdac7SA-E1A D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hdac7sa-e1a D0 rp1

value: Hdac7SA, E1A


title: OSKM MEF (ICR) E1A-Hras D0

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr e1a-hras D0 rp3


title: OSKM MEF (ICR) E1A-Hras D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr e1a-hras D0 rp1


title: OSKM MEF (OG2) Bcl2-E1A D3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D3 rp1


title: OSKM MEF (ICR) Bcl2-Myc D0

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr bcl2-myc D0 rp3


title: OSKM MEF (ICR) Bcl2-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr bcl2-myc D0 rp1


title: OSKM MEF (ICR) Bcl2-Myc D0 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr bcl2-myc D0 rp2


title: OSKM MEF (ICR) Bcl2-E1A D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr bcl2-e1a D0 rp1


title: iPSC-like Hdac7SA-Mef2d GFP+ line #3

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 hdac7sa-mef2d gfpp rp3

value: Hdac7SA, Mef2d, OSKM


title: iPSC-like p53DD-htert GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 p53dd-htert gfpp rp1

value: p53DD, hTERT, OSKM


title: iPSC-like Hdac7SA-Mef2d GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 hdac7sa-mef2d gfpp rp1


title: iPSC-like Bcl2-Myc GFP+ line #1

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 bcl2-myc gfpp rp1


title: iPSC-like Bcl2-Myc GFP+ line #3

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 bcl2-myc gfpp rp3


title: iPSC-like Bcl2-Myc GFP+ line #2

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 bcl2-myc gfpp rp2


title: OSKM MEF (ICR) SV40T D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr sv40t D0 rp1


title: MEF (ICR) WT Passage 6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage6 rp2


title: OSKM MEF (ICR) Hras-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hras-myc D0 rp2


title: MEF (ICR) WT Passage 6 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage6 rp1


title: MEF (Oct4-GFP knockin) WT Passage 1

description:
genes_ntc_expression_nonmerged.tsv.gz
mefoct4ki wt passage1 rp1

source_name: MEF (Oct4-GFP knockin)

value: MEF (Oct4-GFP knockin)

value: Oct4-GFP knockin reporter


title: MEF (ICR) WT Passage 4 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage4 rp2


title: MEF (ICR) WT Passage 5 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage5 rp2


title: MEF (ICR) WT Passage 5 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage5 rp1


title: MEF (ICR) WT Passage 3 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage3 rp1


title: OSKM MEF (OG2) Bcl2-E1A D6 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog mefog2 bcl2-e1a D6 rp2

value: OG2 reporter


title: MEF (ICR) WT Passage 2 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage2 rp1


title: MEF (ICR) WT Passage 1 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage1 rp1


title: MEF (ICR) WT Passage 4 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage4 rp1


title: MEF (ICR) WT Passage 3 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage3 rp2


title: MEF (ICR) WT Passage 2 Rep2

description:
genes_ntc_expression_nonmerged.tsv.gz
meficr wt passage2 rp2


title: MEF Ras.Myc (ATAC-seq) rep2

data_processing:
Reads were aligned to the mm10 mouse genome with bowtie2 (v2.4.5) (Langmead and Salzberg, 2012)
Peaks were called with MACS2 (v2.2.7.1) (Zhang et al., 2008)
redefine_peaks function, was used to recover low-scoring peaks by sharing peak information across samples (Ma et al., 2021)
All other analysis was performed using glbase3 (Hutchins et al., 2014).
Assembly: mm10
Supplementary files format and content: peak BED files

source_name: OG2 MEFs

growth_protocol: MEFs were derived from E13.5 embryos from wildtype ICR genetic background. MEF cells were cultured in DMEM high-glucose media containing 10% FBS (GIBCO), 1 × GlutaMAX (GIBCO), and 1x nonessential amino acids (GIBCO), 0.5x Penicillin/Streptomycin (Hyclone). We generated immortalized MEF cell lines and used the  oncogenic genes: P53DD, PMM2-SV40T, PMM2-Hdac7SA, PMM2-Mef2d, Bcl2, PMM2-Myc, Ras, PMM2-E1A.

extract_protocol:
a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen). After selecting an appropriate PCR cycle number (See (Buenrostro et al., 2013)) samples were sequenced on an Illumina sequencer.
ATAC-seq library was generated using the Tn5 enzyme from the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501-02) as previously described (Buenrostro et al., 2013). Briefly, a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen).

treatment_protocol: MEFs were treated with the inhibitors PD0325901 and TSA for two days.

value: OG2 MEFs

value: MEF

value: Ras Myc immortalized


title: MEF Ras.Myc +PD (ATAC-seq) rep2


title: MEF Ras.Myc (ATAC-seq) rep1


title: MEF Ras.Myc +TSA (ATAC-seq) rep1

value: +TSA


title: MEF Hdac7SA.Mef2d (ATAC-seq) rep2

value: Hdac7SA Mef2d immortalized


title: MEF Hdac7SA.Mef2d (ATAC-seq) rep1


title: iPSC-like Hdac7SA-Mef2d GFP+ line #2

description:
genes_ntc_expression_nonmerged.tsv.gz
mefog2 hdac7sa-mef2d gfpp rp2

value: MEF (OG2)


title: MEF Ras.E1A (ATAC-seq) rep2

value: Ras E1A immortalized


title: OSKM MEF (ICR) Hdac7SA-Myc D0 Rep1

description:
genes_ntc_expression_nonmerged.tsv.gz
reprog meficr hdac7sa-myc D0 rp1

value: MEF (ICR)

value: Hdac7SA, Myc

value: wildtype


title: MEF Ras.E1A +TSA (ATAC-seq) rep1


title: NEJ-33-Exp

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline. First the raw reads were first trimmed (Trim-Galore version 0.60), mapped to mouse genome assembly (mm10) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (VM22).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: *.RSEM.genes.counts.txt: Tab-delimited text files include gene-level RSEM raw count, TPM, and FPKM.

source_name: Mouse liver tumor nodules

growth_protocol: Mouse liver tumor nodules and littermate normal mouse liver tissue.

extract_protocol:
Total RNA was extracted from xenograft tissues by RNeasy Mini Kit (cat. # 74034) from QIAGEN.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

value: Liver tumor nodules


title: NEJ-57-Exp


title: NEJ-31-Exp


title: MEF Ras.E1A +PD (ATAC-seq) rep2


title: NEJ-59-Ctrl

source_name: Mouse liver

value: Normal liver


title: MEF Ras.E1A +PD (ATAC-seq) rep1


title: NEJ-37-Ctrl


title: Ly6GTumor2

city: ChengDu

first: Bin

last: Shao

state: sichuan

address: No.14,3Rd Section Of Ren Min Nan Rd

institute: sichuan university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index ofthe reference genome was builtusing Hisat2 v2.0.5 andpaired-endcleanreadswerealignedtothereferencegenomeusingHisat2v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
total RNA was extracted using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Libraries were prepared according to Illumina's instructions of RNA sample. Paired-end method was adopted for further processes.

value: tumor


title: Ly6GTumor1


title: MEF Ras.Myc +PD (ATAC-seq) rep1


title: Ly6GSpleen2

value: spleen


title: Ly6CTumor2


title: Ly6GSpleen1


title: Ly6CTumor3


title: Ly6GTumor3


title: Ly6CSpleen3


title: MEF Ras.E1A (ATAC-seq) rep1


title: Ly6CSpleen1


title: Ly6CSpleen2


title: YC3-9_Occipital Lobe

city: South San Francisco

first: Xianglong

last: Zhang

state: CA

address: 1120 Veterans Blvd

institute: Amgen Inc

data_processing:
All read files were processed by fastp (v0.19.8) to remove poor quality reads and to trim poor quality 3’ bases. The filtered and trimmed reads were aligned and quantified using OmicSoft’s (Cary, NC, USA) Array Studio software (https://www.omicsoft.com/publish-studio; Oshell.exe v10.0) to reference genome NCBI Macaca_fascicularis_5.0. The transcriptomic annotation NCBI Macaca fascicularis Annotation Release 101 was used as the transcript model reference. The alignment algorithm OSA is documented in an OmicSoft whitepaper (http://omicsoft.com/downloads/whitepaper/OmicsoftAligner.pdf), and the gene/transcript quantification module is an OmicSoft implementation of the RSEM algorithm.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: RNA-Seq data — gene name, read count

organism: Macaca fascicularis

source_name: Occipital Lobe

extract_protocol:
Total RNA was extracted from 27 snap-froze tissues with RNeasy Micro/Mini Kit (QIAGEN, Germany, Cat. #74004/#74106), according to the manufacturer’s instructions. The quality of the isolated RNA was analyzed by Agilent Bioanalyzer 2100. Only the RNA samples with an RNA Integrity Number (RIN) value of 6.0 or higher were included for RNA sequencing.
RNA-seq libraries were constructed from RNA samples meeting QC criteria based on polyA+ selection of mRNA using a standard strand-specific protocol with VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme, China, Cat. #NR612). The quality of the sequencing libraries was analyzed by Agilent Bioanalyzer 4200 and the peak length ranged from 250~500 bp. Clusters were generated by cBot with the library diluted to 10 pM and then sequenced on Illumina HiSeq 2500 instruments with 2 × 150 bp paired-end sequencing. All libraries were sequenced to an average depth of 52 ± 8.8 (mean ± s.d.) million reads (corresponding to 26 ± 4.4 million paired-end reads).

tag: individual

tag: phenotype

value: Non-Obesity

value: Occipital Lobe


title: YC3-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: YC3-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: YC3-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: YC3-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: YC3-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: NEJ-38-Ctrl


title: YC3-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: YC3-28_Uterus

source_name: Uterus

value: Uterus


title: OmpGFP_WT_singlecellRNA

city: SAN FRANCISCO

first: Lea

last: Kiefer

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

description: single cell RNA-Seq

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: mOSNs

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.   For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.  For ChiP-Seq experiments, raw FASTQ files were aligned using Bowtie2 using hg19 reference genome upon adapter sequences removal using CutAdapt. Uniquely aligning reads were selected using Samtools and reads with alignment quality below 30 (-q 30) were removed. The HOMER software package was used to generate signal tracks.   For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For Crosslinked-ChIP and HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: mOSNs

value: ompgfp


title: YC3-21_Colon

source_name: Colon

value: Colon


title: Ly6CTumor1


title: YC3-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: YC3-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: YC3-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: Ly6GSpleen3


title: YC3-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: YC3-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: YC3-18_Biceps Femoris

source_name: Biceps Femoris

value: Non-Obesity

value: Biceps Femoris


title: YC3-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: YC3-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: YC3-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: YC3-14_Esophagus

source_name: Esophagus

value: Esophagus


title: YC3-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: YC2-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: YC2-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: YC3-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: YC2-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: YC3-10_Thalamus

source_name: Thalamus

value: Thalamus


title: YC2-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: YC3-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: YC2-4_Right Atrium


title: YC2-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: YC2-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: YC2-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: YC2-5_Renal Cortex

source_name: Renal Cortex

value: Non-Obesity

value: Renal Cortex


title: YC2-21_Colon

source_name: Colon

value: Colon


title: YC2-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: YC2-28_Uterus

source_name: Uterus

value: Uterus


title: YC2-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: YC2-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: YC2-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: YC2-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: YC2-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: YC3-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: YC2-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: YC2-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: YC1-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: YC2-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: YC2-14_Esophagus

source_name: Esophagus

value: Esophagus


title: YC1-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: YC2-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Non-Obesity

value: Lumbar Spinal Cord


title: YC1-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: YC2-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: YC1-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: YC1-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: YC1-28_Uterus

source_name: Uterus

value: Uterus


title: YC1-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: YC1-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: YC1-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: YC1-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: YC1-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: YC1-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: YC1-15_Pituitary Gland


title: YC1-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: YC1-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: YC1-21_Colon

source_name: Colon

value: Colon


title: YC1-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: YC1-13_Lower Lobe of the Right Lung

source_name: Lung

value: Non-Obesity

value: Lung


title: YC1-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: YC1-10_Thalamus

source_name: Thalamus

value: Thalamus


title: YC1-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: YC1-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: YC1-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: PD4-25_Brown Adipose Tissue

value: Obesity


title: PD4-26_Pericardial Fat


title: PD4-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: PD4-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: PD4-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: PD4-2_Right Ventricle

value: Right Ventricle


title: PD4-20_Brain Stem

value: Brain Stem


title: PD4-18_Biceps Femoris


title: PD4-19_Cerebellum


title: PD4-16_Adrenal Gland

value: Adrenal Gland


title: PD4-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: YC1-14_Esophagus

source_name: Esophagus

value: Esophagus


title: PD4-14_Esophagus


title: PD4-12_Optic Nerve


title: PD4-11_Lumbar Spinal Cord


title: PD4-13_Lower Lobe of the Right Lung


title: PD4-21_Colon

value: Colon


title: PD4-10_Thalamus


title: PD3-9_Occipital Lobe


title: PD4-1_Left Ventricle


title: PD3-7_Left Lobe of the Liver


title: PD3-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: PD4-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: PD4-5_Renal Cortex


title: PD3-6_Renal Medulla


title: PD3-5_Renal Cortex


title: PD3-4_Right Atrium


title: PD3-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: PD4-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: PD4-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: PD3-28_Uterus

source_name: Uterus

value: Uterus


title: PD3-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: PD3-26_Pericardial Fat

source_name: Visceral Fat

value: Obesity

value: Visceral Fat


title: PD3-20_Brain Stem

source_name: Brain Stem


title: PD3-2_Right Ventricle

source_name: Right Ventricle


title: PD3-17_White Adipose Tissue


title: PD3-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: PD3-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: PD3-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: PD3-16_Adrenal Gland

source_name: Adrenal Gland


title: PD3-14_Esophagus


title: PD3-15_Pituitary Gland


title: PD2-8_Tail of the Pancreas


title: PD3-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: YC1-23_Salivary Gland

value: Non-Obesity


title: PD3-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: PD3-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: PD3-10_Thalamus

source_name: Thalamus

value: Thalamus


title: PD2-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: PD2-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: PD2-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: PD3-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: PD2-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: PD3-21_Colon

source_name: Colon

value: Colon


title: PD2-28_Uterus

source_name: Uterus

value: Uterus


title: PD2-23_Salivary Gland

value: Obesity


title: PD2-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: PD2-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: PD2-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: PD2-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: PD2-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: PD2-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: PD2-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: PD2-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: PD2-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: PD2-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: PD2-14_Esophagus

source_name: Esophagus

value: Esophagus


title: PD2-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: PD1-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: PD2-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: PD1-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: PD2-10_Thalamus

source_name: Thalamus

value: Thalamus


title: PD1-8_Tail of the Pancreas

source_name: Pancreas

value: Obesity

value: Pancreas


title: PD1-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: PD1-26_Pericardial Fat


title: PD1-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: PD1-21_Colon

source_name: Colon

value: Colon


title: PD1-2_Right Ventricle


title: PD1-18_Biceps Femoris


title: PD1-17_White Adipose Tissue


title: PD1-15_Pituitary Gland


title: PD1-16_Adrenal Gland


title: PD1-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: PD1-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: PD1-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: PD1-11_Lumbar Spinal Cord


title: PD2-13_Lower Lobe of the Right Lung


title: PD1-10_Thalamus


title: PD1-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: PD2-12_Optic Nerve


title: PD1-1_Left Ventricle


title: OW2-9_Occipital Lobe

value: Non-Obesity


title: PD1-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: PT1_rep2_mtDOGMA_MASISO

city: New York

first: Caleb

last: Lareau

state: New York

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

institute: Memorial Sloan Kettering

description: Full length cDNA from multiome

library_source: transcriptomic single cell

data_processing:
Fastqs were generated using CellRanger-Arc mkfastq v1.0
Sequencing reads were aligned using CellRanger-Arc count to the hg38 reference genome and transcriptome
RNA/ATAC data were aggregated using CellRanger-Arc aggr v1.0 between the two replicates
Reads from the MAS-ISO-seq libraries were extracted using a pattern search for 16-mers  supporting either the wildtype or deleted mRNA molecule
Assembly: hg38
Supplementary files format and content: Aggregated gene expression counts with cells x peaks matrix (h5), ATAC fragments (tsv), and surface proteins (.csv) per cell, and full length transcripts (.txt) supporting the deletion or intact transcripts.

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

growth_protocol: Cryopreserved cells were thawed in RPMI with 10% FBS and washed in media prior to single cell genomics processing.

extract_protocol:
10x Genomics multiome protocol
10x Genomics multiome scRNA-seq with adaptations for mtDNA and surface proteins described here: https://www.nature.com/articles/s41587-021-00927-2 (DOGMA-seq) and further amplified to get full link transcripts (MAS-ISO-seq) described here: https://www.nature.com/articles/s41587-023-01815-7

value: PBMC


title: PT1_rep1_mtDOGMA_MASISO

description: Full length cDNA from multiome


title: PD1-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: PD1-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: OW2-8_Tail of the Pancreas


title: OSN_WaplcKO_HiC_r2

data_processing:
For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. Crosslinked ChIP-Seq samples were aligned with Bowtie2 (2.3.2) with default parameters. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1). For ChIP-seq, duplicate reads were marked with Picard and removed with samtools.
For ChIP-Seq, bigWig files  were generated using HOMER (4.7) (-fsize 1e20 -fragLength given). For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: Olfactory epithilium

extract_protocol: For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).

value: Olfactory epithilium


title: OW2-7_Left Lobe of the Liver

value: Liver


title: OW2-5_Renal Cortex


title: OSN_WaplcKO_HiC_r1


title: OW2-6_Renal Medulla


title: tetOWaplomptta_rep1_hic

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.   For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.   For in situ HiC was carried out according to Rao et al. 2014.  For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.   For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.    For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For  HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.


title: tetOWaplomptta_rep2_hic


title: OW2-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: PD1-14_Esophagus

source_name: Esophagus

value: Obesity

value: Esophagus


title: K562_chr_rep2

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

data_processing:
Basecalling (live with MinKNOW v20.10.3 or later)
Alignment (minimap2)
Poly(A) tail length estimation (nanopolish v0.13.3)
Determination of read splicing status (custom scripts available at https://github.com/churchmanlab/nano-COP)
Assembly: GRCh38
Supplementary files format and content: *_polyA_estimates.tsv: text files containing the poly(A) tail length estimate for each read
Supplementary files format and content: *_splicing_status_per_read.txt: text files containing the overall splicing status of each read

molecule: nuclear RNA

extract_protocol:
Trizol extraction
Poly(A) selection followed by direct RNA sequencing library preparation (SQK-RNA002)


title: K562_poly_rep2

molecule: polyA RNA


title: K562_chr_rep1


title: K562_cyto_rep1

molecule: cytoplasmic RNA


title: OW2-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: OW2-4_Right Atrium


title: K562_poly_rep1


title: OW2-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: OW2-20_Brain Stem


title: OW2-19_Cerebellum


title: OW2-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: Small prostate 2, scRNAseq

first: Tianyu

last: Cao

address: No. 100 Haining Road, Hongkou District

department: Urology

institute: Shanghai General Hospital

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Prostate

extract_protocol:
Tissue for scRNA-seq were minced and digested with 1000 U/mL Collagenase I + 1 mg/mL DNAse I + 1% antibiotic/antimycotic for 4 h while shaking at 37 °C, followed by treatment with TrypLE Express reagent as above. After cell washing and RBC lysis, cell suspensions were subjected to debris removal with Debris Removal Solution.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Whole cells

value: Prostate

tag: race

value: Asian

tag: age


title: Small prostate 1, scRNAseq

description: 10x Genomics


title: Small prostate 3, scRNAseq

description: 10x Genomics


title: K562_total_rep1


title: OW2-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: OW2-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Non-Obesity

value: Subcutaneous Fat


title: OW2-14_Esophagus


title: OW2-13_Lower Lobe of the Right Lung

value: Lung


title: Large prostate 1, scRNAseq

description: 10x Genomics


title: OW2-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: Large prostate 2, scRNAseq

description: 10x Genomics


title: StageII-JUNB-rep2

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .csv (comma separated values) file containing FPKM values of each gene in each sample.

extract_protocol:
Total RNA was isolated by using Direct-zol RNA MiniPrep Kit.
The NEBNext Ultra RNA Library Prep Kit (NEB England BioLabs, E7775) was used for RNA sequencing library construction.
Fragmented and randomly primed 2 × 150 bp paired-end libraries were sequenced using the Illumina HiSeq X Ten system.

value: human somatic cells during chemical reprogramming stage II

value: JUNB overexpression


title: StageII-JUNB-rep1


title: OW2-10_Thalamus

source_name: Thalamus

value: Thalamus


title: K562_total_rep2


title: StageII-JUN-rep2

value: JUN overexpression


title: StageII-JUN-rep1


title: StageII-FOSL2-rep2

value: FOSL2 overexpression


title: OW2-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: StageII-FOSL2-rep1


title: OW1-9_Occipital Lobe

source_name: Occipital Lobe

value: Obesity

value: Occipital Lobe


title: StageII-FOSL1-rep2

value: FOSL1 overexpression


title: OW1-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: OW1-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: StageII-FOSL1-rep1


title: OW1-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: Large prostate 3, scRNAseq

description: 10x Genomics

value: Whole cells

value: Prostate

value: Asian


title: StageII-FOS-rep2

value: FOS overexpression


title: OW1-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: StageII-FOS-rep1

value: human somatic cells during chemical reprogramming stage II


title: OW2-15_Pituitary Gland

source_name: Pituitary Gland

value: Non-Obesity

value: Pituitary Gland


title: K562_cyto_rep2


title: OW2-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: StageII-Ctrl-rep2

value: Ctrl


title: OW1-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: OW1-3_Left Atrium

source_name: Left Atrium

value: Obesity

value: Left Atrium


title: StageII-Ctrl-rep1


title: OW1-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: OW2-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: StageII-Day16, +TNFa, H3K27me3, rep2

description: StageII-Day16_+TNFa_H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)

data_processing:
Quality control was performed using FastQC.
The reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
After converting and sorting the output SAM files to BAM files using Samtools, we removed the duplicated reads and reads with low mapping quality using Picard and Samtools.
The pileup signal intensity for each sample was z-score normalized by subtract mean value and divided by standard error calculated using 1kb bins along whole genome.
Assembly: hg19
Supplementary files format and content: .bw file containing normalized  signal intensity of each sample
Library strategy: CUT&Tag

extract_protocol:
Approximately 1 x 10^5 cells of each sample were collected and analyzed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-02) following the recommended protocol.
Briefly, harvest fresh cultures and count 1 x 10^5 cells for each sample. Then bind cells to Concanavalin A beads at room temperature for 10 min. Next, remove liquid and add primary antibody with ice-cold Antibody Buffer and incubate overnight at 4 oC. The next day, remove liquid and add Guinea Pig Anti-Rabbit Antibody secondary antibody with Dig-Wash Buffer and incubate at room temperature for 1 h. Then, wash sufficiently and bind CUT&Tag pA/G-Tn5 Transposomes at room temperature for 1 h. After gently but throughly wash, tagmentation at 37 oC for 1 h and then performed DNA extraction with DNA extraction beads.
Finally, combine i7 and i5 Indexed Primer for PCR amplification and perform clean-up for quantification and illumina sequencing

value: human somatic cells during chemical reprogramming stage II with TNFa

tag: antibody


title: StageII-Day16, +TNFa, H3K27me3, rep1


title: OW1-25_Brown Adipose Tissue

value: Brown Adipose Tissue


title: OW1-23_Salivary Gland


title: OW1-21_Colon

source_name: Colon

value: Colon


title: StageII-Day16, +TNFa, H3K4me3, rep2

description: StageII-Day16_+TNFa_H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OW2-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: StageII-Day16, +TNFa, H3K27ac, rep1

description: StageII-Day16_+TNFa_H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: OW1-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: OW1-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: OW1-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: StageII-Day16, +TNFa, H3K4me1, rep2

description: StageII-Day16_+TNFa_H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: StageII-Day16, -JNKIN8, H3K27me3, rep2

description: StageII-Day16_-JNKIN8_H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)

value: human somatic cells during chemical reprogramming stage II without JNKIN8


title: StageII-Day16, -JNKIN8, H3K27me3, rep1


title: OW1-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: OW1-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: StageII-Day16, -JNKIN8, H3K27ac, rep2

description: StageII-Day16_-JNKIN8_H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: StageII-Day16, -JNKIN8, H3K27ac, rep1


title: StageII-Day16, -JNKIN8, H3K4me3, rep2

description: StageII-Day16_-JNKIN8_H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: StageII-Day16, +TNFa, H3K4me3, rep1


title: OW1-12_Optic Nerve


title: StageII-Day16, -JNKIN8, H3K4me3, rep1


title: OW1-11_Lumbar Spinal Cord


title: StageII-Day16, -JNKIN8, H3K4me1, rep2

description: StageII-Day16_-JNKIN8_H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: OW1-10_Thalamus

source_name: Thalamus

value: Thalamus


title: StageII-Day16, -JNKIN8, H3K4me1, rep1


title: StageII-Day16, +TNFa, H3K27ac, rep2


title: OB3-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: StageII-Day16, NC, H3K27me3, rep2

description: StageII-Day16_NC_H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)

value: human somatic cells during chemical reprogramming stage II


title: OW1-1_Left Ventricle

source_name: Left Ventricle

value: Obesity

value: Left Ventricle


title: OB3-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: StageII-Day16, NC, H3K27me3, rep1


title: StageII-Day16, NC, H3K27ac, rep2

description: StageII-Day16_NC_H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: StageII-Day16, NC, H3K27ac, rep1


title: OW1-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: StageII-Day16, +TNFa, H3K4me1, rep1

value: human somatic cells during chemical reprogramming stage II with TNFa


title: OB3-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: StageII-Day16, NC, H3K4me3, rep2

description: StageII-Day16_NC_H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OW1-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: OW1-14_Esophagus

source_name: Esophagus

value: Esophagus


title: OB3-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: OW1-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: OB3-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: OB3-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: OB3-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: StageII-Day16, NC, H3K4me3, rep1


title: StageII-Day16, NC, H3K4me1, rep1

description: StageII-Day16_NC_H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: OB3-28_Uterus

source_name: Uterus

value: Uterus


title: H9, H3K27me3, rep2

description: H9_H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)

value: hES cells H9


title: OB3-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: OB3-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: StageII-Day16, NC, H3K4me1, rep2

value: human somatic cells during chemical reprogramming stage II


title: H9, H3K27ac, rep2

description: H9_H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: H9, H3K27me3, rep1


title: H9, H3K27ac, rep1


title: OB3-21_Colon

source_name: Colon

value: Obesity

value: Colon


title: OB3-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: H9, H3K9me3, rep2

description: H9_H3K9me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OB3-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: H9, H3K4me3, rep2

description: H9_H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: H9, H3K9me3, rep1


title: OB3-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: OB3-18_Biceps Femoris

value: Biceps Femoris


title: H9, H3K4me1, rep2

description: H9_H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: OB3-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: OB3-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: OB3-15_Pituitary Gland

value: Pituitary Gland


title: H1, H3K27me3, rep2

description: H1_H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)

value: hES cells H1


title: H1, H3K27me3, rep1


title: H1, H3K27ac, rep2

description: H1_H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: OB3-13_Lower Lobe of the Right Lung

value: Lung


title: OB3-14_Esophagus

value: Esophagus


title: H1, H3K9me3, rep2

description: H1_H3K9me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OB3-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: OB3-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: H1, H3K4me3, rep2

description: H1_H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OB3-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: H1, H3K4me3, rep1


title: H1, H3K9me3, rep1


title: OB3-10_Thalamus

source_name: Thalamus

value: Thalamus


title: OB2-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: H9, H3K4me3, rep1

value: hES cells H9


title: OB2-8_Tail of the Pancreas

source_name: Pancreas

value: Obesity

value: Pancreas


title: H1, H3K4me1, rep2

description: H1_H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: H1, H3K4me1, rep1


title: OB2-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: OB2-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: OB3-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: OB2-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: OB2-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: hCiPSCs-1013-7, H3K27me3, rep1

description: hCiPSCs-1013-7__H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)

value: human chemically induced pluripotent stem cells


title: hCiPSCs-1013-7, H3K27me3, rep2


title: hCiPSCs-1013-7, H3K27ac, rep2

description: hCiPSCs-1013-7__H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: H9, H3K4me1, rep1


title: OB2-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: hCiPSCs-1013-7, H3K9me3, rep2

description: hCiPSCs-1013-7__H3K9me3_zscore.bw (in bigwig_files_2.tar.gz)


title: hCiPSCs-1013-7, H3K27ac, rep1


title: H1, H3K27ac, rep1

value: hES cells H1


title: OB2-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: hCiPSCs-1013-7, H3K9me3, rep1


title: OB2-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: hCiPSCs-1013-7, H3K4me3, rep2

description: hCiPSCs-1013-7__H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OB2-23_Salivary Gland

value: Salivary Gland


title: hCiPSCs-1013-7, H3K4me3, rep1


title: OB2-21_Colon

source_name: Colon

value: Colon


title: hCiPSCs-1013-7, H3K4me1, rep1

description: hCiPSCs-1013-7__H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: OB2-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: OB2-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: hCiPSCs-1013-7, H3K4me1, rep2


title: hCiPSCs-1013-3, H3K27me3, rep2

description: hCiPSCs-1013-3__H3K27me3_zscore.bw (in bigwig_files_2.tar.gz)


title: hCiPSCs-1013-3, H3K27me3, rep1


title: OB2-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: hCiPSCs-1013-3, H3K27ac, rep2

description: hCiPSCs-1013-3__H3K27ac_zscore.bw (in bigwig_files_2.tar.gz)


title: OB2-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Obesity

value: Subcutaneous Fat


title: hCiPSCs-1013-3, H3K9me3, rep2

description: hCiPSCs-1013-3__H3K9me3_zscore.bw (in bigwig_files_2.tar.gz)


title: hCiPSCs-1013-3, H3K9me3, rep1


title: OB2-14_Esophagus

source_name: Esophagus

value: Esophagus


title: hCiPSCs-1013-3, H3K27ac, rep1


title: hCiPSCs-1013-3, H3K4me3, rep2

description: hCiPSCs-1013-3__H3K4me3_zscore.bw (in bigwig_files_2.tar.gz)


title: OB2-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: hCiPSCs-1013-3, H3K4me1, rep2

description: hCiPSCs-1013-3__H3K4me1_zscore.bw (in bigwig_files_2.tar.gz)


title: OB2-10_Thalamus

source_name: Thalamus

value: Thalamus


title: hCiPSCs-1013-3, H3K4me1, rep1


title: OB2-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: StageII-Day16, H3K27me3, rep2

description: StageII-Day16_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)

value: human somatic cells during chemical reprogramming stage II


title: hCiPSCs-1013-3, H3K4me3, rep1

value: human chemically induced pluripotent stem cells


title: OB2-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: OB2-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: OB2-1_Left Ventricle

source_name: Left Ventricle

value: Left Ventricle


title: StageII-Day16, H3K27ac, rep2

description: StageII-Day16_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)


title: OB1-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: OB2-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: OB1-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: StageII-Day16, H3K27ac, rep1


title: StageII-Day16, H3K27me3, rep1


title: StageII-Day16, H3K9me3, rep2

description: StageII-Day16_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day16, H3K9me3, rep1


title: OB1-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: OB1-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: OB2-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: OB1-4_Right Atrium

source_name: Right Atrium

value: Obesity

value: Right Atrium


title: StageII-Day16, H3K4me3, rep1

description: StageII-Day16_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: OB1-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: StageII-Day16, H3K4me1, rep2

description: StageII-Day16_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: OB1-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: StageII-Day16, H3K4me1, rep1


title: StageII-Day12, H3K27me3, rep2

description: StageII-Day12_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)


title: OB1-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: StageII-Day12, H3K27me3, rep1


title: OB1-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: OB1-20_Brain Stem

source_name: Brain Stem

value: Brain Stem


title: OB1-19_Cerebellum


title: StageII-Day12, H3K9me3, rep2

description: StageII-Day12_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)

value: human somatic cells during chemical reprogramming stage II


title: OB1-7_Left Lobe of the Liver

source_name: Liver

value: Liver


title: OB1-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: StageII-Day12, H3K9me3, rep1


title: OB1-16_Adrenal Gland


title: OB1-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: StageII-Day12, H3K4me3, rep2

description: StageII-Day12_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: OB1-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: StageII-Day16, H3K4me3, rep2


title: OB1-14_Esophagus

source_name: Esophagus

value: Esophagus


title: StageII-Day12, H3K4me1, rep1

description: StageII-Day12_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: OB1-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: StageII-Day8, H3K27me3, rep2

description: StageII-Day8_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day12, H3K4me1, rep2


title: OB1-12_Optic Nerve

source_name: Optic Nerve

value: Optic Nerve


title: StageII-Day8, H3K27me3, rep1


title: OB1-25_Brown Adipose Tissue

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: OB1-11_Lumbar Spinal Cord

source_name: Lumbar Spinal Cord

value: Lumbar Spinal Cord


title: StageII-Day8, H3K27ac, rep2

description: StageII-Day8_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day8, H3K27ac, rep1


title: StageII-Day12, H3K27ac, rep1

description: StageII-Day12_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day12, H3K27ac, rep2


title: OB1-1_Left Ventricle

source_name: Left Ventricle

value: Obesity

value: Left Ventricle


title: OB1-10_Thalamus

source_name: Thalamus

value: Thalamus


title: DM6-9_Occipital Lobe

source_name: Occipital Lobe

value: Occipital Lobe


title: StageII-Day8, H3K9me3, rep2

description: StageII-Day8_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: DM6-8_Tail of the Pancreas

source_name: Pancreas

value: Pancreas


title: StageII-Day8, H3K4me3, rep2

description: StageII-Day8_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: DM6-7_Left Lobe of the Liver


title: StageII-Day8, H3K9me3, rep1


title: StageII-Day12, H3K4me3, rep1


title: DM6-5_Renal Cortex

source_name: Renal Cortex

value: Renal Cortex


title: DM6-6_Renal Medulla

source_name: Renal Medulla

value: Renal Medulla


title: StageII-Day8, H3K4me3, rep1

value: human somatic cells during chemical reprogramming stage II


title: DM6-4_Right Atrium

source_name: Right Atrium

value: Right Atrium


title: StageII-Day4, H3K27me3, rep2

description: StageII-Day4_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day4, H3K27me3, rep1


title: DM6-3_Left Atrium

source_name: Left Atrium

value: Left Atrium


title: StageII-Day4, H3K27ac, rep2

description: StageII-Day4_H3K27ac_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day8, H3K4me1, rep1

description: StageII-Day8_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: DM6-26_Pericardial Fat

source_name: Visceral Fat

value: Visceral Fat


title: DM6-24_Bone Marrow, Femur

source_name: Bone Marrow

value: Bone Marrow


title: DM6-23_Salivary Gland

source_name: Salivary Gland

value: Salivary Gland


title: DM6-21_Colon

source_name: Colon

value: Colon


title: StageII-Day4, H3K9me3, rep1

description: StageII-Day4_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day4, H3K4me3, rep2

description: StageII-Day4_H3K4me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageII-Day4, H3K4me3, rep1


title: DM6-19_Cerebellum

source_name: Cerebellum

value: Cerebellum


title: StageII-Day4, H3K4me1, rep2

description: StageII-Day4_H3K4me1_zscore.bw (in bigwig_files_1.tar.gz)


title: DM6-2_Right Ventricle

source_name: Right Ventricle

value: Right Ventricle


title: DM6-18_Biceps Femoris

source_name: Biceps Femoris

value: Biceps Femoris


title: DM6-17_White Adipose Tissue

source_name: Subcutaneous Fat

value: Subcutaneous Fat


title: StageII-Day8, H3K4me1, rep2


title: DM6-16_Adrenal Gland

source_name: Adrenal Gland

value: Adrenal Gland


title: StageI-Day8, H3K27me3, rep2

description: StageI-Day8_H3K27me3_zscore.bw (in bigwig_files_1.tar.gz)

value: human somatic cells during chemical reprogramming stage I


title: DM6-15_Pituitary Gland

source_name: Pituitary Gland

value: Pituitary Gland


title: DM6-13_Lower Lobe of the Right Lung

source_name: Lung

value: Lung


title: StageII-Day4, H3K27ac, rep1


title: StageI-Day8, H3K9me3, rep2

description: StageI-Day8_H3K9me3_zscore.bw (in bigwig_files_1.tar.gz)


title: StageI-Day8, H3K27me3, rep1