title: Dataset 1: Patient #32-DCIS-Stroma fraction (CD45- EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #389-Normal-Epithelium fraction (EpCAM+ CD10- CD45-)

status: Public on Feb 26 2026

type: SRA

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

country: USA

institute: Dana-Farber Cancer Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The sequenced reads were aligned to either the human reference genome hg18 or the rat reference genome Rn6. Demultiplexing, barcode calling, gene counting, and group aggregation were subsequently performed. These procedures were all carried out using the 10X Genomics Cell Ranger 7.0.1 and Cell Ranger Aggr. v7.0.1 on 10X Cloud (https://cloud.10xgenomics.com/)
For preprocessing and quality-control, the filtered count matrix files were processed in R using Seurat package. Stringent filtering parameters were set to filter out low-quality reads and dead cells (2000 <nCount < 60000 & percent mt < 20 & percent ribo RPS/RPL < 40). Doublets were identified and removed using DoubletFinder.
The data were normalized using SCTransform and integrated using SCTIntegration prior to decomposing into 30-dimension PCA, clustering and dimensional reduction by UMAP. Subclusters of immune, epithelial, stroma and subsequent T cells, myeloid, and fibroblast clusters were further subsetted and reclustered at same dimension but higher resolution.
DEGs of each seurat cluster at each step were computed using Seurat FindMarkers function. Cell identities were identified and annotated using up to a combination of three methods (1) DEGs of lineage markers, (2) gene modules from previous studies, (3) reference cell atlas such as Celltypist, ProjecTIL.
Downstream analyses relevant to the study include Milo neighborhood analysis, Trajectory analysis Monocle3, FCoEx, single-cell GSEA (Escape), ProjecTIL, CellChat, Gini index quantification, etc.
Assembly: hg18 (Dataset 1), rn6 (Dataset 2-3)
Supplementary files format and content: barcodes.tsv.gz (barcodes), features.tsv.gz (gene IDs), matrix.mtx.gz (gene expression count matrix), filtered_feature_bc_matrix.h5 (combined features, barcodes, matrix)
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Normal mammary tissues

extract_protocol:
For dataset 1, clinical specimens were shipped in DMEM media via dry ice and digested immediately upon arrival to the lab. For dataset 2-3, rats were sacrificed and tumors were extracted and minced gently prior to tissue digestion protocol. For both human and rat tissues, the minced tissues were placed in 2 mg/mL collagenase 4, 2 mg/kg hyaluronidase, 2 mg/mL BSA (5-6 fold-greater than tissue volume) and incubated with shaking at 37*C for 60 min (human tumor tissues and rat mammary gland tissue) or 80-90 min (rat tumor tissues). The digested tumors were serially filtered from 500um and 100um strainers and centrifuged at 1700 rpm for 7 min and resuspended in DMEM. For dataset 1 and 2, tissues were stained with FACS markers (CD45+, EpCAM+, CD10+, Live/Dead Aqua, 30min), washed, and filtered, and were subjected to FACS sorting at low speed followed by single-cell library construction targeting 5000 cells/sample. For dataset 3, the entired tumor tissues were digested briefly with TryLE Express Enzyme (7 min) and submited for scRNAseq library construction targeting 5000 cells/sample.
For dataset 1-2, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 3' HT v3 protocol targeting 5000 cells per sample. For dataset 3, cell and library construction were performed via the 10X Chromium NEXT GEM Single Cell 5' HT Reagent Kit v2 (Dual Index) protocol.
Equimolar libraries were sequenced on an Illumina NovaSeq6000 at the DFCI Molecular Biology Core Facility with at least 25000 reads per cells.

treatment_protocol: For dataset 2-3, tumor induction in Sprague-Dawley rats was performed via two injection of N-Nitroso-N-Methylurea(NMU, 50mg/kg, 7 days apart). Tumor volumes were measured daily following first detection of palpable tumors in the mammary areas.

tag: tissue

value: Normal mammary tissues

tag: cell type

value: Breast normal epithelium

tag: treatment

value: Untreated


title: Dataset 1: Patient #463-IDC-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics

source_name: Breast invasive carcinoma

value: Breast invasive carcinoma

value: Breast cancer epithelium


title: Dataset 1: Patient #463-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics

value: Breast immune cells


title: Dataset 1: Patient #449-DCIS-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics

source_name: Breast carcinoma in situ

value: Breast carcinoma in situ


title: Dataset 1: Patient #457-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #473-DCIS-Mixed fraction

description: 10X Genomics

value: Mixed breast cells


title: Dataset 1: Patient #36-DCIS-Mixed fraction

description: 10X Genomics


title: Dataset 1: Patient #464-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #449-DCIS-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #32-DCIS-Mixed fraction

description: 10X Genomics


title: Dataset 1: Patient #446-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #446-IDC-Stroma fraction (CD10- EpCAM- CD45-)

description: 10X Genomics

value: Breast stromal cells


title: Dataset 1: Patient #464-IDC-Stroma fraction (CD10- EpCAM- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #446-IDC-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #436-Normal-Myoepithelium fraction  (EpCAM+ CD10+ CD45-)

description: 10X Genomics

value: Breast myoepithelium


title: Dataset 1: Patient #464-IDC-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #36-DCIS-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #438-IDC-Myoepithelium fraction (CD10+EpCAM+CD45-)

description: 10X Genomics


title: Dataset 1: Patient #438-IDC-Stroma fraction (CD10- EpCAM- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #402-IDC-Stroma fraction (CD10- EpCAM- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #402-IDC-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #379-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #438-IDC-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: Dataset 1: Patient #438-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: Dataset 1: Patient #402-IDC-Immune fraction (CD45+ EpCAM- CD10-)

description: 10X Genomics


title: HaCaT cells, PHGDH-siRNA+Mix 2

city: Xi'an

first: Qinqin

last: Meng

state: Shaanxi

address: No.157 Xi Wu Road

department: Department of Dermatology

country: China

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

library_source: transcriptomic

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data by CASAVA base recognization. Raw data of fastq format were firstly processed through in-house perl scripts.The clean data were obtained.
Index of the reference genome was built using Hisat2 (V2.0.5) and paied-end reads were aligned to the reference genome using Hisat2 (V2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HaCaT cells

growth_protocol: HaCaT cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNAiso Plus (Takara, Japan). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

tag: cell line

value: HaCaT cells

value: human immortalized keratinocytes

tag: genotype

value: PHGDH-siRNA+Mix

value: We transfect PHGDH-siRNA to  HaCaT cells and stimulate HaCaT cells with mix for 24 h


title: HaCaT cells, PHGDH-siRNA+Mix 3


title: Dataset 1: Patient #379-IDC-Myoepithelium fraction (CD10+EpCAM+CD45-)

description: 10X Genomics


title: HaCaT cells, PHGDH-siRNA 3

value: PHGDH-siRNA

value: We transfect PHGDH-siRNA to  HaCaT cells


title: Dataset 1: Patient #379-IDC-Epithelium fraction (EpCAM+ CD10- CD45-)

description: 10X Genomics


title: HaCaT cells, PHGDH-siRNA 1


title: HaCaT cells, PHGDH-siRNA 2


title: HaCaT cells, Control-siRNA+Mix 2

value: Control-siRNA+Mix

value: We transfect control-siRNA to  HaCaT cells and stimulate HaCaT cells with mix for 24 h


title: HaCaT cells, Control-siRNA 3

value: Control-siRNA

value: We transfect control-siRNA to  HaCaT cells


title: HaCaT cells, Control-siRNA+Mix 1


title: HaCaT cells, Control-siRNA 1


title: HaCaT cells, Control-siRNA+Mix 3


title: HaCaT cells, PHGDH-siRNA+Mix 1


title: Dataset 1: Patient #379-IDC-Stroma fraction (CD10- EpCAM- CD45-)

description: 10X Genomics

value: Breast invasive carcinoma

value: Untreated


title: HaCaT cells, Control-siRNA 2


title: SS032

city: New York

first: Shanaz

middle: Adi

last: Ghandhi

state: NY

address: 630, W 168th street

department: Center for Radiological Research

institute: Columbia University Medical Center

description: Human donors

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (version 0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: Human: GRCm38
Supplementary files format and content: normalized counts

source_name: Whole blood

extract_protocol:
Blood samples were collected  and irradiated using a Clinac at dose rates between 1Gy/min and 10^5 Gy/sec (total dose 3Gy). After overnight freezing, the samples were thawed at room temperature and left for > 2 h before processing for total RNA isolation using the PAXgene® Blood RNA kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol. Isolated RNA was quantified using the Nanodrop One spectrophotometer (Thermofisher) and A260/ 280 ratios recorded.
RNA sequencing analysis for gene expression was performed according to standard RNA-seq pipeline at the Columbia University Medical Center Genome Center. We used the RIBOZERO workflow in which ribosomal depletion was performed to remove rRNAs from globin cleared total RNA. RINs of globin cleared RNA (catalog number AM1981 from Thermofisher) were in the acceptable range for 40-million reads RNAseq (75% of samples had RIN values >7.5).
After rRNA depletion, library construction was performed using Illumina TruSeq Stranded Total RNA kit.

value: Whole blood

value: 3Gy delivered at 3x105 Gy/sec

tag: dose (gy)

value: 3 Gy

tag: dose rate

value: FLASH

tag: time


title: SS031

description: Human donors


title: SS029

description: Human donors


title: SS023

description: Human donors

value: 3Gy delivered at 1 Gy/min

value: REF


title: SS027

description: Human donors


title: SS024

description: Human donors


title: SS025

description: Human donors


title: SS026

description: Human donors


title: SS028

description: Human donors


title: SS020

description: Human donors


title: SS021

description: Human donors


title: SS018

description: Human donors


title: SS017

description: Human donors


title: SS016

description: Human donors

value: 3Gy delivered at 600 Gy/sec

value: VHDR


title: SS004

description: Human donors

value: sham irradiation

value: 0 Gy

value: CTL


title: SS010

description: Human donors


title: SS007

description: Human donors


title: SS030

description: Human donors


title: SS008

description: Human donors


title: SS015

description: Human donors


title: SS012

description: Human donors


title: SS006

description: Human donors


title: SS002

description: Human donors


title: SS014

description: Human donors


title: SS003

description: Human donors


title: 62614_invitro_d14_sgRNA

city: Philadelphia

first: Jacqueline

middle: J

last: Peng

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description:
in vitro CRISPR screen, day 14 AML drug library, day 13 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.

library_source: other

data_processing:
10X Cell Ranger (verion 6.1.2) mkfastq for scRNA and sgRNA (if applicable)
10X Cell Ranger (verion 6.1.2) mkcount
Assembly: hg38 with GFP and mCherry
Supplementary files format and content: filtered_feature_bc_matrix from 10X Cell Ranger mkcount
Library strategy: CRISPR screen

molecule: other

source_name: AML PDX cells

growth_protocol: The primary AML samples/PDX samples were obtained from the Stem Cell and Xenograft Core Facility at The Perelman School of Medicine at the University of Pennsylvania or xxx, after informed consent in accordance with the Declaration of Helsinki. Protocols used for this study were approved by the University Pennsylvania’s institutional review board. The primary AML samples were frozen in FCS and 10% DMSO in liquid nitrogen for long-term storage. Patient clinical info is included in Table Sx. For short-term in vitro maintenance, cells were cultured in BM media (IMDM supplemented with 15% Fetal Bovine Serum (FBS), 1% P/S, 1% GlutaMAX) supplemented with human cytokines including 10ng/μl human IL-3 (200-03), 10ng/μl human FLT3 (300-19), 100ng/μl humanSCF (300-07), 20ng/μl humanIL-6 (200-06) and 10 ng/μl humanTPO (300-18) (all from Peprotech). Co-culture with stromal “feeder” cells (e.g. OP-9) may be recommended to maintain the primary cells (ref), although we did not see an obvious difference in cell growth with or without the feeder cells for specimens we studied.

extract_protocol:
For scRNA-seq, primary cells were thawed in PBS+5% FBS and treated with DNase I (AMPD1-1KT, Sigma) for 5 min at room temperature. Cells were washed and resuspended with PBS+0.04% BSA. Viability was checked by Trypan Blue (Thermo), and if viability was lower than 95%, live cells were purified by the Dead cell removal kit (MACS). Viable cells were subject to scRNA-seq following the Chromium Next GEM Single Cell 5' v2 protocol. For in vitro Perturb-seq, ells were transduced as described above and maintained in a dish for 9-14 days. For in vivo Perturb-seq, leukemia cells were harvested from BM on day 12 post-transplant. Sorted GFP/mCherry+ leukemia cells were washed 3 times and resuspended in PBS+0.04% BSA and checked for viability. Viable cells were subject to scRNA-seq following the Chromium Next GEM Single Cell 5' v2 protocol with spike-in of sgRNA amplification oligos.
For scRNA-seq, samples were prepared following the Chromium Next GEM Single Cell 5' v2 protocol. For Perturb-seq, samples were subject to the Perturb-seq protocol adapted from ECCITE-seq with small modifications, without antibody-hashtag labelling. Briefly, 2μM sg_RT_v4 (AGCAAGTGAGAAGCATCGTGTCAAAGCACCGACTCGGTGCCAC) oligo was spiked in to the cell suspension containing 20,000 live cells. Cells were barcoded on the 10xGenomics platform following the Chromium Next GEM Single Cell 5' v2 protocol. sgRNA was amplified together with cDNA using a spike-in Guide-tag_additive (AGCAAGTGAGAAGCATCGTGTC), and separated from cDNA by 0.6x SPRIselect beads (Beckman) (beads bind cDNA while supernatant contains sgRNAs). sgRNA was further amplified with primers incorporated with TotalSeq_A_Dual_Index, and purified by 1.2x SPRIselect beads (Beckman). cDNA was amplified and purified following the 10x Genomics protocol. Libraries were analyzed using the Qubit dsDNA HS assay kit (Thermo Fisher) and a High Sensitivity DNA Bioanalyzer Kit (Agilent), and quantified by NEBNext Library Quant Kit for Illumina. Libraries were pooled consisting of 90% cDNA and 10% sgRNA, and pair-end sequenced on a Nova-seq 6000 in Read 1 26, i7 index 10, i5 index 10, Read 2 90bp format.

treatment_protocol: For PDX/primary cell transduction, Retronectin (Takara) was used to avoid the cytotoxicity effect caused by the polybrene following the manufacturer’s instructions with minor modifications. Briefly, 12-well non-treated plates were coated with 1ml of 20ng/μl Rectronectin for 2 hr at 37°C or overnight at 4°C. The Retronectin was collected, and the plates were blocked with 1ml of 2% BSA for 30 min at RT. The BSA was aspirated, and the plates were washed with 1ml PBS or HBSS. Plates would be ready to use or can be stored at 4°C for up to a week. Retronectin can be recycled for up to 5 times. To boost the infection efficiency for large vectors (e.g. Cas9), 1ml virus containing supernatant was first applied to the plates and spun down at at 750 x g for 30 minutes to allow the virus to attach on the bottom. The supernatant was aspirated, and the above steps can be repeated multiple times to further enrich the virus. To transduce the cells, cells were mixed with virus, adjusted FBS (15% final) and human cytokines described above and 1:500 dilution of LentiBlast Premium (LBPX1500, OZBiosciences, which also enhances hematopoietic cell transduction), and the media was replenished the next day with BM media supplemented with cytokines.

tag: post infection

value: patient ID:062614

tag: molecule subtype

value: sgRNA


title: SS005

description: Human donors


title: 7031_invitro_d10_sgRNA

description:
in vitro CRISPR screen, day 10 AML drug lib, day 9 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.

source_name: Primary AML sample

value: patient ID:7031


title: 7031_invitro_d14_sgRNA

description:
in vitro CRISPR screen, day 14 AML drug lib, day 13 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.


title: SS022

description: Human donors


title: 2263_invitro_d15_sgRNA

description:
in vitro CRISPR screen, day 15 AML drug library, day 14 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.

value: patient ID:2263


title: SS009

description: Human donors


title: SS013

description: Human donors


title: SS001

description: Human donors


title: SS011

description: Human donors


title: 2263_invivo_d15_sgRNA

description:
in vivo CRISPR screen, day 15 AML drug library, day 14 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.


title: 62614_invitro_d9_sgRNA

description:
in vitro CRISPR screen, day 9 AML drug library, day 8 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.


title: 7050_invitro_DP_rep2_sgRNA

value: patient ID:7050


title: 2263_invitro_d10_sgRNA

description:
in vitro CRISPR screen, day 10 AML drug library, day 9 cas9 rerun
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.


title: 7050_invitro_DP_sgRNA


title: 2263_invitro_d10_rerun_sgRNA

description:
in vitro CRISPR screen, day 10 AML drug library, day 9 cas9 virus post-infection
processed data for sgRNA counts included in filtered_feature_bc_matrix available on the associated GEX sample.


title: 2263_invitro_d15_rerun_sgRNA


title: 7031_invitro_d14_cDNA

description: in vitro CRISPR screen, day 14 AML drug lib, day 13 cas9 virus post-infection

data_processing:
10X Cell Ranger (verion 6.1.2) mkfastq for scRNA and sgRNA (if applicable)
10X Cell Ranger (verion 6.1.2) mkcount
Assembly: hg38 with GFP and mCherry
Supplementary files format and content: filtered_feature_bc_matrix from 10X Cell Ranger mkcount

molecule: polyA RNA

value: cDNA


title: 7031_primary_d0_cDNA

description: Day 0 from frozen vial


title: 2263_invitro_d15_rerun_cDNA

description:
in vitro CRISPR screen, day 15 AML drug library, day 14 cas9 virus post-infection
processed data for this sample available on GSM6886575


title: 2263_invitro_d15_cDNA

description: in vitro CRISPR screen, day 15 AML drug library, day 14 cas9 virus post-infection


title: 62614_invitro_d14_cDNA

description: in vitro CRISPR screen, day 14 AML drug library, day 13 cas9 virus post-infection


title: 2263_invitro_d10_cDNA

description: in vitro CRISPR screen, day 10 AML drug library, day 9 cas9 virus post-infection


title: 62614_invitro_d9_cDNA

description: in vitro CRISPR screen, day 9 AML drug library, day 8 cas9 virus post-infection


title: 7050_invitro_DP_rep2_cDNA


title: 2263_invivo_d15_cDNA

description: in vivo CRISPR screen, day 15 AML drug library, day 14 cas9 virus post-infection


title: 2263_invitro_d10_rerun_cDNA

description:
in vitro CRISPR screen, day 10 AML drug library, day 9 cas9 virus post-infection
processed data for this sample available on GSM6886573


title: AML7050_DN_invivo_cDNA

description: in vitro culture 4 days, transplanted into NSG mice, 11 days post-transplant from BM


title: RNA-Seq of RPE cells exposed to PFOA at 7w (sample b)

city: Buffalo

first: G. Ekin

last: Atilla-Gokcumen

address: 120 Founders Promenade

department: Chemistry

institute: University at Buffalo

description: Library name: RPE1-7w-PFOA-b

data_processing:
Raw gene counts were normalized in TPMs.
Raw gene counts were inputed into DeSeq2 for differential expression across treatements.
Assembly: GRCh38
Supplementary files format and content: raw_gene_expression_data.csv: Comma-delimited file containing gene-level raw read counts for all samples. Rows correspond to Ensembl gene IDs and gene names; columns correspond to individual samples.
Supplementary files format and content: DESeq2_analysis.csv: comma-delimited file containing log2 fold change, p-value, and adjusted p-value for all comparisons (MeOH vs PFOA, MeOH vs PFOS, and PFOA vs PFOS) across all exposure durations.
Supplementary files format and content: README.txt: Text file describing the experimental design, sample structure, data processing workflow, and contents of all processed data files included in this submission.
Supplementary files format and content: TPM_gene_expression_data.csv: comma-delimited file containing TPM-normalized gene expression values.

source_name: retinal pigment epithelium

extract_protocol:
Frozen cell pellets treated individually with PFOA and PFOS for 24 hours, 7 weeks, 17 weeks, and 24 weeks (n=3) that were previously stored at −80 °C and were transported on dry ice to Azenta Life Sciences (South Plainfield, NJ) for RNA extraction and RNA-seq analysis. Azenta’s RNA-seq workflow comprises five steps, including experimental design, extraction, library preparation, sequencing, and data analysis. RNA from cells was extracted, and RNA molecules of interest were purified to ensure high quality and sufficient quantity prior to proceeding with analysis. After which, single-stranded RNA was converted to double-stranded complementary DNA (cDNA) strands in a reverse transcription reaction. Sequencing adapters and barcodes were then added to create RNA-seq libraries which were subsequently analyzed with Next Generation Sequencing (NGS) using Illumina NovaSeqTM6000 or Illumina Hiseq®X. The data were then evaluated, and biologically relevant information was extracted. Briefly, sequencing reads were pre-processed and trimmed to remove adapter sequences and low-quality bases. Trimmed reads were then mapped to the reference genome, followed by expression quantification and transcripts per million (TPM) calculation. Differential expression analysis was performed using DESeq2 , comparing treatments to the control: PFOA vs. MeOH, PFOS vs. MeOH, and PFOA vs. PFOS. Note that MeOH 24H was used a control for all time point comparisons involving both PFOA and PFOS. Gene Ontology (GO) enrichment analysis was conducted for significant genes (|log2foldchange|>1 & adjusted p < 0.05) in each comparison using gProfiler. To investigate shared gene expression patterns between PFOA and PFOS at 24 weeks, we identified differentially expressed genes (DEGs) common to both PFOA vs. MeOH and PFOS vs. MeOH comparisons at 24 weeks and performed GO enrichment analysis on this shared gene set.
RNA-seq libraries were prepared from polyA-enriched RNA using an Illumina-compatible stranded library preparation protocol. Libraries were sequenced using paired-end sequencing on an Illumina platform.

value: retinal pigment epithelium

value: hTERT RPE-1

value: retinal pigment epithelial cell

value: PFOA


title: 7031_invitro_d10_cDNA

description: in vitro CRISPR screen, day 10 AML drug lib, day 9 cas9 virus post-infection


title: RNA-Seq of RPE cells exposed to PFOA at 7w (sample a)

description: Library name: RPE1-7w-PFOA-a


title: RNA-Seq of RPE cells exposed to PFOA at 24w (sample c)

description: Library name: RPE1-24w-PFOA-c


title: AML7050_primary_cDNA

description: Day 0 from frozen vial


title: RNA-Seq of RPE cells exposed to PFOS at 24w (sample b)

description: Library name: RPE1-24w-PFOS-b

value: PFOS


title: RNA-Seq of RPE cells exposed to PFOA at 24w (sample b)

description: Library name: RPE1-24w-PFOA-b


title: RNA-Seq of RPE cells exposed to PFOS at 24w (sample a)

description: Library name: RPE1-24w-PFOS-a


title: RNA-Seq of RPE cells exposed to PFOS at 24w (sample c)

description: Library name: RPE1-24w-PFOS-c


title: RNA-Seq of RPE cells exposed to PFOS at 7w (sample a)

description: Library name: RPE1-7w-PFOS-a


title: SS019

description: Human donors

value: Whole blood

value: 3Gy delivered at 1 Gy/min

value: 3 Gy

value: REF


title: RNA-Seq of RPE cells exposed to PFOA at 17w (sample c)

description: Library name: RPE1-17w-PFOA-c


title: RNA-Seq of RPE cells exposed to PFOS at 7w (sample c)

description: Library name: RPE1-7w-PFOS-c


title: RNA-Seq of RPE cells exposed to PFOA at 7w (sample c)

description: Library name: RPE1-7w-PFOA-c


title: RNA-Seq of RPE cells exposed to MeOH (control) at 24h (sample a)

description: Library name: RPE1-24h-MeOH-a

value: MeOH

value: control


title: 7050_invitro_DP_cDNA


title: RNA-Seq of RPE cells exposed to MeOH (control) at 24h (sample c)

description: Library name: RPE1-24h-MeOH-c


title: RNA-Seq of RPE cells exposed to PFOS at 24h (sample a)

description: Library name: RPE1-24h-PFOS-a


title: RNA-Seq of RPE cells exposed to PFOS at 17w (sample c)

description: Library name: RPE1-17w-PFOS-c


title: RNA-Seq of RPE cells exposed to PFOA at 17w (sample b)

description: Library name: RPE1-17w-PFOA-b


title: RNA-Seq of RPE cells exposed to PFOA at 24w (sample a)

description: Library name: RPE1-24w-PFOA-a


title: RNA-Seq of RPE cells exposed to PFOA at 24h (sample c)

description: Library name: RPE1-24h-PFOA-c


title: RNA-Seq of RPE cells exposed to PFOS at 17w (sample b)

description: Library name: RPE1-17w-PFOS-b


title: RNA-Seq of RPE cells exposed to PFOS at 24h (sample c)

description: Library name: RPE1-24h-PFOS-c


title: RNA-Seq of RPE cells exposed to PFOS at 17w (sample a)

description: Library name: RPE1-17w-PFOS-a


title: RNA-Seq of RPE cells exposed to PFOA at 17w (sample a)

description: Library name: RPE1-17w-PFOA-a


title: RNA-Seq of RPE cells exposed to PFOA at 24h (sample a)

description: Library name: RPE1-24h-PFOA-a


title: RNA-Seq of RPE cells exposed to PFOS at 24h (sample b)

description: Library name: RPE1-24h-PFOS-b


title: RNA-Seq of RPE cells exposed to PFOA at 24h (sample b)

description: Library name: RPE1-24h-PFOA-b


title: C&R, OV4, OVARIAN, IgG, REP2

first: Sophie

last: Hanina

address: 630 West 168th Street

institute: Columbia University

description: Library name: CnR_OV4_IgG_rep2

library_source: genomic

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC. Version 2.3.4.1 of bowtie2 employed to align reads to human assembly hg38 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0. ATAC-seq peaks for each replicate were identified using MACS2 and filtered for blacklisted regions
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Ovarian PDX

extract_protocol:
CUT&RUN was performed on cells using the CUTANA™ ChIC/CUT&RUN Kit following the manufacturer’s instructions. The following antibodies were used: rabbit anti-H3K4me3; rabbit anti-H3K27me3; rabbit anti-EZH2 ; negative control rabbit IgG .
After quantification of the recovered DNA fragments, libraries were prepared using the ThruPLEX®DNA-Seq kit following the manufacturer’s instructions, purified with AMPure XP magnetic beads, and quantified using a Qubit fluorometer and a TapeStation, and sequenced on a NovaSeq 6000.

value: Ovarian PDX

tag: disease state

value: HGSOC


title: C&R, K7, KIDNEY, CD70Pos, D0, H3K4me3, REP3

description: Library name: CnR_K7_2p3K_CD70_Pos_d0_H3K4me3_rep3

source_name: Kidney PDX

value: Kidney PDX

value: ccRCC


title: C&R, OV4, OVARIAN, H3K4me3, REP1

description: Library name: CnR_OV4_H3K4me3_rep1


title: C&R, OV4, OVARIAN, IgG, REP1

description: Library name: CnR_OV4_IgG_rep1


title: RNA-Seq of RPE cells exposed to PFOS at 7w (sample b)

description: Library name: RPE1-7w-PFOS-b


title: C&R, OV4, OVARIAN, H3K4me3, REP3

description: Library name: CnR_OV4_H3K4me3_rep3


title: C&R, OV4, OVARIAN, H3K27me3, REP3

description: Library name: CnR_OV4_H3K27me3_rep3


title: C&R, OV4, OVARIAN, H3K27me3, REP1

description: Library name: CnR_OV4_H3K27me3_rep1


title: C&R, OV4, OVARIAN, H3K4me3, REP2

description: Library name: CnR_OV4_H3K4me3_rep2


title: C&R, OV4, OVARIAN, EZH2, REP3

description: Library name: CnR_OV4_EZH2_rep3


title: C&R, OV4, OVARIAN, EZH2, REP2

description: Library name: CnR_OV4_EZH2_rep2


title: RNA-Seq of RPE cells exposed to MeOH (control) at 24h (sample b)

description: Library name: RPE1-24h-MeOH-b


title: C&R, OV4, OVARIAN, H3K27me3, REP2

description: Library name: CnR_OV4_H3K27me3_rep2


title: C&R, OV4, OVARIAN, CD70Pos, H3K4me3, REP3

description: Library name: CnR_CD70pos_H3K4me3_rep3_10p3


title: C&R, OV4, OVARIAN, CD70Pos, H3K4me3, REP4

description: Library name: CnR_CD70pos_H3K4me3_rep4_10p4


title: C&R, OV4, OVARIAN, CD70Pos, IgG, REP2

description: Library name: CnR_CD70pos_IgG_rep2_10p2


title: C&R, OV4, OVARIAN, EZH2, REP1

description: Library name: CnR_OV4_EZH2_rep1


title: C&R, OV4, OVARIAN, CD70Pos, EZH2, REP4

description: Library name: CnR_CD70pos_EZH2_rep4_10p4


title: C&R, OV4, OVARIAN, CD70Pos, H3K4me3, REP2

description: Library name: CnR_CD70pos_H3K4me3_rep2_10p2


title: C&R, OV4, OVARIAN, CD70Pos, H3K4me3, REP1

description: Library name: CnR_CD70pos_H3K4me3_rep1_10p1


title: C&R, OV4, OVARIAN, CD70Pos, H3K27me3, REP2

description: Library name: CnR_CD70pos_H3K27me3_rep2_10p2


title: C&R, OV4, OVARIAN, CD70lo, IgG, REP2

description: Library name: CnR_CD70lo_IgG_rep2_10p2


title: C&R, OV4, OVARIAN, CD70Pos, EZH2, REP3

description: Library name: CnR_CD70pos_EZH2_rep3_10p3


title: C&R, OV4, OVARIAN, CD70Pos, H3K27me3, REP4

description: Library name: CnR_CD70pos_H3K27me3_rep4_10p4


title: C&R, OV4, OVARIAN, CD70lo, H3K4me3, REP1

description: Library name: CnR_CD70lo_H3K4me3_rep1_10p1


title: C&R, OV4, OVARIAN, CD70Pos, IgG, REP1

description: Library name: CnR_CD70pos_IgG_rep1_10p1


title: C&R, OV4, OVARIAN, CD70Pos, EZH2, REP1

description: Library name: CnR_CD70pos_EZH2_rep1_10p1


title: C&R, OV4, OVARIAN, CD70lo, H3K4me3, REP4

description: Library name: CnR_CD70lo_H3K4me3_rep4_10p4


title: C&R, OV4, OVARIAN, CD70lo, H3K4me3, REP2

description: Library name: CnR_CD70lo_H3K4me3_rep2_10p2


title: C&R, OV4, OVARIAN, CD70lo, H3K27me3, REP2

description: Library name: CnR_CD70lo_H3K27me3_rep2_10p2


title: C&R, OV4, OVARIAN, CD70lo, H3K27me3, REP3

description: Library name: CnR_CD70lo_H3K27me3_rep3_10p3


title: C&R, OV4, OVARIAN, CD70Pos, H3K27me3, REP1

description: Library name: CnR_CD70pos_H3K27me3_rep1_10p1


title: C&R, OV4, OVARIAN, CD70lo, EZH2, REP2

description: Library name: CnR_CD70lo_EZH2_rep2_10p2


title: C&R, OV4, OVARIAN, CD70lo, IgG, REP3

description: Library name: CnR_CD70lo_IgG_rep3_10p3


title: C&R, OV4, OVARIAN, CD70lo, EZH2, REP3

description: Library name: CnR_CD70lo_EZH2_rep3_10p3


title: C&R, OV4, OVARIAN, CD70lo, H3K4me3, REP3

description: Library name: CnR_CD70lo_H3K4me3_rep3_10p3


title: C&R, OV4, OVARIAN, CD70lo, H3K27me3, REP4

description: Library name: CnR_CD70lo_H3K27me3_rep4_10p4


title: C&R, OV4, OVARIAN, CD70lo, EZH2, REP1

description: Library name: CnR_CD70lo_EZH2_rep1_10p1


title: C&R, K7, KIDNEY, CD70Pos, D0, H3K27me3, REP2

description: Library name: CnR_K7_2p2K_CD70_Pos_d0_H3K27me3_rep2


title: C&R, K7, KIDNEY, CD70Pos, D0, IgG, REP2

description: Library name: CnR_K7_2p2K_CD70_Pos_d0_IgG_rep2


title: C&R, K7, KIDNEY, CD70lo, D0, IgG, REP2

description: Library name: CnR_K7_2p2K_CD70_lo_d0_IgG_rep2


title: C&R, K7, KIDNEY, CD70lo, D0, H3K27me3, REP2

description: Library name: CnR_K7_2p2K_CD70_lo_d0_H3K27me3_rep2


title: C&R, OV4, OVARIAN, IgG, REP3

description: Library name: CnR_OV4_IgG_rep3


title: C&R, K7, KIDNEY, CD70lo, D0, H3K4me3, REP2

description: Library name: CnR_K7_2p2K_CD70_lo_d0_H3K4me3_rep2


title: C&R, OV4, OVARIAN, CD70lo, EZH2, REP4

description: Library name: CnR_CD70lo_EZH2_rep4_10p4


title: C&R, OV4, OVARIAN, CD70Pos, H3K27me3, REP3

description: Library name: CnR_CD70pos_H3K27me3_rep3_10p3


title: C&R, K7, KIDNEY, CD70Pos, D0, IgG, REP1

description: Library name: CnR_K7_2p1K_CD70_Pos_d0_IgG_rep1


title: C&R, K7, KIDNEY, CD70Pos, D0, H3K4me3, REP1

description: Library name: CnR_K7_2p1K_CD70_Pos_d0_H3K4me3_rep1


title: C&R, K7, KIDNEY, CD70Pos, D0, H3K27me3, REP1

description: Library name: CnR_K7_2p1K_CD70_Pos_d0_H3K27me3_rep1


title: C&R, K7, KIDNEY, CD70lo, D0, IgG, REP1

description: Library name: CnR_K7_2p1K_CD70_lo_d0_IgG_rep1


title: C&R, K7, KIDNEY, CD70lo, D0, H3K4me3, REP1

description: Library name: CnR_K7_2p1K_CD70_lo_d0_H3K4me3_rep1


title: C&R, K5, KIDNEY, CD70lo, D8, H3K4me3

description: Library name: CD70lo_kidney_K5_d8_H3K4me3_SM-425-5_hg38_sorted.RmDup.10mNorm.bw


title: C&R, K5, KIDNEY, CD70Pos, D8, IgG, REP2

description: Library name: CnR_K5_1K_CD70Pos_d8_IgG_rep2


title: C&R, K5, KIDNEY, CD70Pos, D8, IgG, REP1

description: Library name: CnR_K5_1K_CD70Pos_d8_IgG_rep1


title: C&R, K5, KIDNEY, CD70Pos, D8, H3K4me3, REP3, Pooled

description: Library name: CnR_K5_Pooled_CD70Pos_d8_H3K4me3_rep3


title: C&R, K5, KIDNEY, CD70Pos, D8, EZH2, REP1

description: Library name: CnR_K5_1K_CD70Pos_d8_EZH2_rep1


title: C&R, K5, KIDNEY, CD70lo, D8, IgG, REP1

description: Library name: CnR_K5_1K_CD70lo_d8_IgG_rep1


title: C&R, K5, KIDNEY, CD70lo, D8, H3K4me3, REP1

description: Library name: CnR_K5_1K_CD70lo_d8_H3K4me3_rep1


title: C&R, K5, KIDNEY, CD70Pos, D8, H3K4me3, REP3

description: Library name: CnR_K5_1K_CD70Pos_d8_H3K4me3_rep2


title: C&R, K5, KIDNEY, CD70lo, D8, IgG, REP2

description: Library name: CnR_K5_1K_CD70lo_d8_IgG_rep2


title: C&R, K7, KIDNEY, CD70lo, D0, H3K27me3, REP1

description: Library name: CnR_K7_2p1K_CD70_lo_d0_H3K27me3_rep1


title: C&R, K5, KIDNEY, CD70Pos, D8, EZH2, REP2

description: Library name: CnR_K5_1K_CD70Pos_d8_EZH2_rep2


title: C&R, K5, KIDNEY, CD70lo, D8, H3K27me3, REP1

description: Library name: CnR_K5_1K_CD70lo_d8_H3K27me3_rep1


title: C&R, K5, KIDNEY, CD70lo, D8, EZH2, REP1

description: Library name: CnR_K5_1K_CD70lo_d8_EZH2_rep1


title: C&R, K5, KIDNEY, CD70Pos, D8, H3K27me3, REP2

description: Library name: CnR_K5_1K_CD70Pos_d8_H3K27me3_rep2


title: C&R, K5, KIDNEY, CD70lo, D8, H3K27me3

description: Library name: CD70lo_kidney_K5_d8_H3K27me3_SM-425-4_hg38_sorted.RmDup.10mNorm.bw


title: C&R, K5, KIDNEY, CD70Pos, D0, EZH2, REP2

description: Library name: CnR_K5_1p4K_CD70Pos_d0_EZH2_rep2


title: C&R, K5, KIDNEY, CD70Pos, D8, H3K27me3, REP1

description: Library name: CnR_K5_1K_CD70Pos_d8_H3K27me3_rep1


title: C&R, K5, KIDNEY, CD70Pos, D0, IgG, REP2

description: Library name: CnR_K5_1p4K_CD70Pos_d0_IgG_rep2


title: C&R, K5, KIDNEY, CD70Pos, D0, H3K4me3, REP2

description: Library name: CnR_K5_1p4K_CD70Pos_d0_H3K4me3_rep2


title: C&R, K5, KIDNEY, CD70lo, D8, EZH2, REP2

description: Library name: CnR_K5_1K_CD70lo_d8_EZH2_rep2


title: C&R, K5, KIDNEY, CD70lo, D0, EZH2, REP2

description: Library name: CnR_K5_1p4K_CD70lo_d0_EZH2_rep2


title: C&R, K5, KIDNEY, CD70Pos, D0, EZH2, REP1

description: Library name: CnR_K5_1p3K_CD70Pos_d0_EZH2_rep1


title: C&R, K5, KIDNEY, CD70Pos, D0, IgG, REP1

description: Library name: CnR_K5_1p3K_CD70Pos_d0_IgG_rep1


title: C&R, K5, KIDNEY, CD70lo, D0, H3K27me3, REP2

description: Library name: CnR_K5_1p4K_CD70lo_d0_H3K27me3_rep2


title: C&R, K5, KIDNEY, CD70lo, D0, H3K4me3, REP1

description: Library name: CnR_K5_1p3K_CD70lo_d0_H3K4me3_rep1


title: C&R, K5, KIDNEY, CD70Pos, D0, H3K27me3, REP1

description: Library name: CnR_K5_1p3K_CD70Pos_d0_H3K27me3_rep1


title: C&R, K5, KIDNEY, CD70lo, D0, IgG, REP2

description: Library name: CnR_K5_1p4K_CD70lo_d0_IgG_rep2


title: C&R, K5, KIDNEY, CD70lo, D0, H3K4me3, REP2

description: Library name: CnR_K5_1p4K_CD70lo_d0_H3K4me3_rep2


title: C&R, K5, KIDNEY, CD70Pos, D0, H3K27me3, REP2

description: Library name: CnR_K5_1p4K_CD70Pos_d0_H3K27me3_rep2


title: C&R, K5, KIDNEY, CD70lo, D0, EZH2, REP1

description: Library name: CnR_K5_1p3K_CD70lo_d0_EZH2_rep1


title: ATAC-seq, OV, IN VITRO, CD70LO, REP 2

description: Library name: ATAC_OV4_invitro_rep2_100K

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC. Version 2.3.4.1 of bowtie2 employed to align reads to human assembly hg38 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0. ATAC-seq peaks for each replicate were identified using MACS2 and filtered for blacklisted regions
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Human kidney tumor from PDX models were digested into single cell suspensions using the Tumor Dissociation Kit, human (Miltenyi Biotec) according to the manufacturer’s instructions. Red cell blood lysis was performed using ACK buffer (Lonza).
ATAC was performed on cells using the Tagment DNA TDE1 Enzyme (Illumina, #20034198). Sequencing libraries were purified with AMPure XP magnetic beads (Beckman Coulter, A63881), and quantified using a Qubit fluorometer (ThermoFisher Scientific) and a TapeStation (Agilent).


title: ATAC-seq, OV, IN VITRO, CD70LO, REP 1

description: Library name: ATAC_OV4_invitro_rep1_100K


title: C&R, K5, KIDNEY, CD70lo, D0, IgG, REP1

description: Library name: CnR_K5_1p3K_CD70lo_d0_IgG_rep1


title: C&R, K5, KIDNEY, CD70Pos, D0, H3K4me3, REP1

description: Library name: CnR_K5_1p3K_CD70Pos_d0_H3K4me3_rep1


title: C&R, K5, KIDNEY, CD70lo, D0, H3K27me3, REP1

description: Library name: CnR_K5_1p3K_CD70lo_d0_H3K27me3_rep1


title: ATAC-seq, OV, CD70POS, REP 1

description: Library name: ATAC_CD70_pos_rep1_100K


title: ATAC-seq, OV, CD70POS, REP 4

description: Library name: ATAC_CD70_pos_rep4_100K


title: ATAC-seq, OV, CD70POS, REP 3

description: Library name: ATAC_CD70_pos_rep3_100K


title: ATAC-seq, OV, CD70LO, REP 4

description: Library name: ATAC_CD70_lo_rep4_60K


title: ATAC-seq, OV, CD70LO, REP 2

description: Library name: ATAC_CD70_lo_rep2_100K


title: ATAC-seq, OV, CD70POS, REP 2

description: Library name: ATAC_CD70_pos_rep2_100K


title: ATAC-seq, K5, IN VITRO, REP 1

description: Library name: ATAC_K5_px9_rep1


title: ATAC-seq, K5, KIDNEY, CD70POS, D8, REP 3

description: Library name: ATAC_K5_1p5K_CD70Pos_d8_rep3


title: ATAC-seq, K5, IN VITRO, REP 2

description: Library name: ATAC_K5_px9_rep2


title: ATAC-seq, OV, CD70LO, REP 1

description: Library name: ATAC_CD70_lo_rep1_60K


title: ATAC-seq, K5, KIDNEY, CD70POS, D0, REP 3

description: Library name: ATAC_K5_1p5K_CD70Pos_d0_rep3


title: ATAC-seq, K5, Lung, D0, REP 3

description: Library name: ATAC_K5_Lung_d0_rep3


title: ATAC-seq, OV, CD70LO, REP 3

description: Library name: ATAC_CD70_lo_rep3_80K


title: ATAC-seq, K5, Lung, D0, REP 1

description: Library name: ATAC_K5_Lung_d0_rep1


title: ATAC-seq, K5, KIDNEY, CD70POS, D0, REP 1

description: Library name: ATAC_K5_1p3K_CD70Pos_d0_rep1


title: ATAC-seq, K5, KIDNEY, CD70POS, D0, REP 2

description: Library name: ATAC_K5_1p4K_CD70Pos_d0_rep2


title: ATAC-seq, K5, KIDNEY, CD70LO, D0, REP 3

description: Library name: ATAC_K5_1p5K_CD70lo_d0_rep3


title: ATAC-seq, K5, KIDNEY, CD70LO, D2, REP 3

description: Library name: ATAC_K5_1p5K_CD70lo_d2_rep3


title: ATAC-seq, K5, KIDNEY, CD70LO, D0, REP 1

description: Library name: ATAC_K5_1p3K_CD70lo_d0_rep1


title: ATAC-seq, K5, KIDNEY, CD70LO, D8, REP 3

description: Library name: ATAC_K5_1p5K_CD70lo_d8_rep3


title: ATAC-seq, K5, Lung, D0, REP 2

description: Library name: ATAC_K5_Lung_d0_rep2


title: ATAC-seq, K5, KIDNEY, CD70LO, D0, REP 2

description: Library name: ATAC_K5_1p4K_CD70lo_d0_rep2


title: ATAC-seq, K5, KIDNEY, CD70POS, D2, REP 1, POOLED

description: Library name: ATAC_K5_kidneypooledCD70Pos_d2_rep1


title: ATAC-seq, K7, IN VITRO, REP 3

description: Library name: ATAC_K7_px4_invitro_rep3


title: ATAC-seq, K7, IN VITRO, REP 2

description: Library name: ATAC_K7_px4_invitro_rep2


title: ATAC-seq, K7, Lung, D0, REP 3

description: Library name: ATAC_K7_Lung_d0_rep3


title: ATAC-seq, K7, KIDNEY, CD70POS, D0, REP 3

description: Library name: ATAC_K7_CD70Pos_d0_rep3


title: ATAC-seq, K7, IN VITRO, REP 1

description: Library name: ATAC_K7_px4_invitro_rep1


title: ATAC-seq, K7, Lung, D0, REP 1

description: Library name: ATAC_K7_Lung_d0_rep1


title: ATAC-seq, K7, KIDNEY, CD70POS, D0, REP 2

description: Library name: ATAC_K7_CD70Pos_d0_rep2


title: ATAC-seq, K7, Lung, D0, REP 2

description: Library name: ATAC_K7_Lung_d0_rep2


title: ATAC-seq, K7, KIDNEY, CD70POS, D0, REP 1

description: Library name: ATAC_K7_CD70Pos_d0_rep1


title: ATAC-seq, K7, KIDNEY, CD70LO, D0, REP 3

description: Library name: ATAC_K7_CD70lo_d0_rep3


title: ATAC-seq, K7, KIDNEY, CD70LO, D0, REP 1

description: Library name: ATAC_K7_CD70lo_d0_rep1


title: ATAC-seq, K7, KIDNEY, CD70LO, D0, REP 2

description: Library name: ATAC_K7_CD70lo_d0_rep2


title: D7_Combo1.r3

city: Milwaukee

first: Angela

last: Mathison

state: WI

address: 8701 Watertown Plank Rd, HM034, HRC5125

department: Department of Surgery

institute: Medical College of Wisconsin

description: Library name: R2024-379

data_processing:
Sequencing reads were processed through Cutadapt, STAR, FastQC, FastQ Screen, and RSeQC.
Differential expression was determined using EdgeR (McCarthy et al., 2012), with differentially expressed genes (DEGs) defined as those with a false discovery rate (FDR) < 0.05 and an absolute fold change (FC) ≥ 2 called relative to control.
Pathway analysis of DEGs was performed in Partek using the Molecular Signatures Database (MSigDB) cancer hallmark gene set, as well as KEGG, Gene Ontology, Reactome, and WikiPathways databases. Pathways with q-values < 0.05 were considered significantly enriched.
Assembly: Gencode v43 (GRCh38)
Supplementary files format and content: L3.6_EPZ_Prex_Combo_FeatureCounts.xlsx; xlsx file includes raw counts for each sample
Supplementary files format and content: L3.6_EPZ_Prex_Combo_CPM.xlsx; xlsx file includes linear RPMK values for each sample
Supplementary files format and content: L3.6_EPZ_Prex_Combo_Differential.xlsx; xlsx file includes differential expression fold change and statistical test for various sample comparisons, vehicle DMSO control combined for both 5 day and 7 day comparisons, D5 and D7 indicated in separate tabs

source_name: human pancreatic cancer cells (L3.6pl)

extract_protocol:
RNA extraction was done following the miRNeasy Mini Kit protocol (Qiagen), with cells lysed and collected in 700µL QIAzol lysis reagent (Qiagen) per sample.
Illumina TruSeq RNA v2 library preparation

treatment_protocol: L3.6pl cells plated and then treated with DMSO (vehicle), 200nM EPZ015938, 1.95nM prexasertib, 2.34nM prexasertib, and then the combinations of 200nM EPZ015938 with 1.95nM prexasertib (Combo 1) or 200nM EPZ015938 with 2.34nM prexasertib (Combo 2).  Cells were grown for 5 days (D5) or 7 days (D7), washed twice in PBS, and lysed in RNA extraction buffer.

value: human pancreatic cancer cells (L3.6pl)

value: 200nM EPZ015938 and 1.95nM prexasertib (Combo 1)

tag: treatment duration

value: 7 days

tag: batch


title: D7_Prex2.r3

description: Library name: R2024-378

value: 2.34nM prexasertib


title: D7_Combo2.r3

description: Library name: R2024-380

value: 200nM EPZ015938 and 2.34nM prexasertib (Combo 2)


title: D7_EPZ.r3

description: Library name: R2024-376


title: D7_Prex1.r3

description: Library name: R2024-377

value: 1.95nM prexasertib


title: D5_Combo1.r3

description: Library name: R2024-373

value: 5 days


title: D5_Combo2.r3

description: Library name: R2024-374


title: D7_Prex2.r2

description: Library name: R2024-366


title: D5_EPZ.r3

description: Library name: R2024-370


title: D5_Prex1.r3

description: Library name: R2024-371


title: D5_Prex2.r2

description: Library name: R2024-360


title: D5_Prex1.r2

description: Library name: R2024-359


title: D7_Prex1.r2

description: Library name: R2024-365


title: D7_DMSO.r3

description: Library name: R2024-375

value: vehicle, DMSO


title: D5_Combo2.r2

description: Library name: R2024-362


title: D7_DMSO.r2

description: Library name: R2024-363


title: D7_Combo2.r1

description: Library name: R2024-356


title: D5_Combo1.r2

description: Library name: R2024-361


title: D5_Prex2.r3

description: Library name: R2024-372


title: D5_DMSO.r3

description: Library name: R2024-369


title: D7_Prex2.r1

description: Library name: R2024-354


title: D7_Prex1.r1

description: Library name: R2024-353


title: D7_EPZ.r1

description: Library name: R2024-352


title: D7_Combo1.r1

description: Library name: R2024-355


title: D7_Combo1.r2

description: Library name: R2024-367


title: D7_EPZ.r2

description: Library name: R2024-364


title: D7_Combo2.r2

description: Library name: R2024-368


title: D7_DMSO.r1

description: Library name: R2024-351


title: D5_EPZ.r2

description: Library name: R2024-358


title: D5_DMSO.r2

description: Library name: R2024-357


title: D5_Combo2.r1

description: Library name: R2024-350


title: D5_Combo1.r1

description: Library name: R2024-349


title: D5_Prex2.r1

description: Library name: R2024-348


title: D5_EPZ.r1

description: Library name: R2024-346


title: D5_Prex1.r1

description: Library name: R2024-347


title: RGG deletion mutant replicate 2

first: Michael

middle: D

last: Blower

state: MA

address: 72 E. Concord St. K123C

department: Biochemistry and Cell Biology

institute: Boston University

description:
Library name: DeltaRGG_2
RGG_1_CKDL220011617-1a_HVV77DSX3_L2_1

data_processing:
linkers were timmed and duplicates were removed using fastp
reads were aligned to the genome using Subread
reads were quantitated agains Entrez Gene annotations using feature Counts
Separately Allele-specific expression was quantitated using PAC
Seperately splicing changes were measured using rMATs
Assembly: hn38 (UCSC)
Supplementary files format and content: tab delimited text. Summaries of analysis or RNA-seq data.

growth_protocol: cells were grown in DMEM/F12 with 10% FBS, sodium bicorbonate, Pen/Strep at 37C with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol
rRNA was depleted with the NEB rRNA depletion kit and libraries were constructed using the NEB Next Directional RNA kit

treatment_protocol: cells were treated with doxycycline and IAA for 24 hours

value: retinal pigment epithelium

value: RPE1 SAF-A-AID-mCherry dox RGG

value: doxycycline 24h IAA 24h


title: Walker B deletion mutant replicate 1

description:
Library name: DeltaWalkerB_1
DA_1_CKDL220007726-1a_HK72FDSX3_L1_1

value: RPE1 SAF-A-AID-mCherry dox Walker B


title: Walker A deletion mutant replicate 1

description:
Library name: DeltaWalkerA_1
KA_1_CKDL220007724-1a_HK5WJDSX3_L1_1

value: RPE1 SAF-A-AID-mCherry dox Walker A


title: Walker A deletion mutant replicate 2

description:
Library name: DeltaWalkerA_2
KA_2_CKDL220007725-1a_HK7JCDSX3_L1_1


title: RNA-seq of human lung adenocarcinoma:H1299 cell line ZNF200 KD replicate

city: hefei

first: xiaozheng

last: wei

address: tanghelu

institute: Anhui Medical University

description:
Library name: H1299_ZNF200_2
Following ZNF200 knockdown in H1299 cells, RNA was extracted for sequencing.

data_processing:
Quality control: Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
Reads mapping: The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
we used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: GRCh38
Supplementary files format and content: FPKM

source_name: lung

growth_protocol: H1299 cells were cultured in DMEM medium (Vivocell) with 10% FBS. They were all cultured at 37 °C with 5% CO2.

extract_protocol:
Total RNA was harvested using RNA isolater Total RNA Extraction Reagent(Vazyme) . 2ug of total RNA  was used for construction of sequencing libraries.
RNA library for RNA-seq was prepared follwing manufacturer's protocols.

treatment_protocol: H1299 cells were transfected with ZNF200 knockdown virus or control virus.

value: lung

value: Human non-small cell lung cancer cells

value: ZNF200 knockdown


title: RNA-seq of human lung adenocarcinoma:H1299 cell line control replicate

description:
Library name: H1299_NC_2
RNA was extracted from H1299 cells unloaded for sequencing

value: WT


title: monocytes_periphery_input_MG3

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: human_Inputmonocytesperiphery3_H3K27acChIP_rep3

data_processing:
All epigenetic libraries were mapped to hg38 genome using STAR (v2.7.9a) with default parameters and converted into HOMER tag directories. The findPeaks command from HOMER was used to call peaks. For ChIP-seq, only peaks with an Irreproducible Discovery Rate (IDR) < 0.05 was used for downstream analysis. ATAC peak lists were merged with HOMER’s mergePeaks and annotated for H3K27ac reads with HOMER’s annotatePeaks. DESeq2 was used to identify ATAC peaks that are differentially acetylated between celltypes and environments. Overlapping differentially acetylated ATAC peaks with IDR peaks were determined using the package GenomicRanges (v.1.54.1).
Assembly: hg38
Supplementary files format and content: Bedgraph.gz

source_name: umbilical cord blood

extract_protocol:
Chromatin ImmunoPreciptation-seq library preparation was performed as previously described on 1,000,000 cells per cell line per replicate. For H3K27ac ChIP, the cells were fixed in 1% PFA, pelleted at 1000 x g for 5 min at 4°C, and flash frozen. Frozen cell pellets were lysed on ice in ice-cold LB3 (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylarcisine, 1X protease inhibitor cocktail).
For ChIP-seq, library preparation was performed using the NebNext Ultra II DNA Library Prep Kit (New England Biolabs E7645). Crosslinking was reversed with overnight proteinase K treatment. The DNA was purified using SpeedBeads (Thermo Scientific Fisher 651520505025) in 20% PEG8000, 1.5 M NaCl to final 12% PEG concentration and then amplified using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs MO541). The final library was purified by gel excision of 200-500 bp fragments and single-end sequenced.

value: umbilical cord blood

value: Monocytes

value: Peripheral engraftment


title: RNA-seq of human lung adenocarcinoma:H1299 cell line ZNF200 KD

description:
Library name: H1299_ZNF200_1
Following ZNF200 knockdown in H1299 cells, RNA was extracted for sequencing.


title: monocytes_CNS_input_MG1

description: Library name: human_InputmonocytesCNS1_H3K27acChIP_rep1

value: CNS engraftment


title: monocytes_periphery_input_MG1

description: Library name: human_Inputmonocytesperiphery1_H3K27acChIP_rep1


title: iHPC_periphery_input_MG2

description: Library name: human_InputiHPCliver2_H3K27acChIP_rep2

source_name: iPSC-derived cells

value: iPSC-derived cells

value: iHPC


title: iHPC_CNS_input_MG2

description: Library name: human_InputiHPCCNS2_H3K27acChIP_rep2


title: D5_DMSO.r1

description: Library name: R2024-345

value: human pancreatic cancer cells (L3.6pl)

value: 5 days


title: monocytes_periphery_input_MG2

description: Library name: human_Inputmonocytesperiphery2_H3K27acChIP_rep2


title: CD34_periphery_input_MG4

description: Library name: human_InputCD34periphery4_H3K27acChIP_rep4


title: CD34_CNS_input_MG1

description: Library name: human_InputCD34CNS1_H3K27acChIP_rep1


title: CD34_periphery_input_MG1

description: Library name: human_InputCD34periphery1_H3K27acChIP_rep1


title: monocytes_CNS_input_MG2

description: Library name: human_InputmonocytesCNS2_H3K27acChIP_rep2


title: CD34_periphery_input_MG2

description: Library name: human_InputCD34periphery2_H3K27acChIP_rep2


title: Walker B deletion mutant replicate 2

description:
Library name: DeltaWalkerB_2
DA_2_CKDL220007727-1a_HK5LKDSX3_L2_1

value: retinal pigment epithelium


title: CD34_periphery_input_MG3

description: Library name: human_InputCD34periphery3_H3K27acChIP_rep3


title: CD34_CNS_input_MG2

description: Library name: human_InputCD34CNS2_H3K27acChIP_rep2


title: monocytes_periphery_H3K27ac_MG3

description: Library name: human_ChIPmonocytesperiphery3_H3K27acChIP_rep3


title: RNA-seq of human lung adenocarcinoma:H1299 cell line control

description:
Library name: H1299_NC_1
RNA was extracted from H1299 cells unloaded for sequencing


title: monocytes_periphery_H3K27ac_MG2

description: Library name: human_ChIPmonocytesperiphery2_H3K27acChIP_rep2


title: iHPC_periphery_input_MG1

description: Library name: human_InputiHPCliver1_H3K27acChIP_rep1


title: monocytes_periphery_input_MG4

description: Library name: human_Inputmonocytesperiphery4_H3K27acChIP_rep4


title: monocytes_CNS_H3K27ac_MG2

description: Library name: human_ChIPmonocytesCNS2_H3K27acChIP_rep2


title: iHPC_CNS_input_MG1

description: Library name: human_InputiHPCCNS1_H3K27acChIP_rep1


title: monocytes_periphery_H3K27ac_MG4

description: Library name: human_ChIPmonocytesperiphery4_H3K27acChIP_rep4


title: RGG deletion mutant replicate 1

description:
Library name: DeltaRGG_1
RGG1_CKDL230043098-1A_HGCGYDSX7_L2_1

value: RPE1 SAF-A-AID-mCherry dox RGG


title: monocytes_CNS_H3K27ac_MG1

description: Library name: human_ChIPmonocytesCNS1_H3K27acChIP_rep1


title: monocytes_periphery_H3K27ac_MG1

description: Library name: human_ChIPmonocytesperiphery1_H3K27acChIP_rep1


title: iHPC_CNS_H3K27ac_MG2

description: Library name: human_ChIPiHPCCNS2_H3K27acChIP_rep2


title: iHPC_periphery_H3K27ac_MG1

description: Library name: human_ChIPiHPCliver1_H3K27acChIP_rep1


title: iHPC_CNS_H3K27ac_MG1

description: Library name: human_ChIPiHPCCNS1_H3K27acChIP_rep1


title: CD34_periphery_H3K27ac_MG4

description: Library name: human_ChIPCD34periphery4_H3K27acChIP_rep4


title: iHPC_periphery_H3K27ac_MG2

description: Library name: human_ChIPiHPCliver2_H3K27acChIP_rep2


title: CD34_periphery_H3K27ac_MG3

description: Library name: human_ChIPCD34periphery3_H3K27acChIP_rep3


title: CD34_periphery_H3K27ac_MG1

description: Library name: human_ChIPCD34periphery1_H3K27acChIP_rep1


title: CD34_CNS_H3K27ac_MG1

description: Library name: human_ChIPCD34CNS1_H3K27acChIP_rep1


title: CD34_periphery_H3K27ac_MG2

description: Library name: human_ChIPCD34periphery2_H3K27acChIP_rep2


title: iHPC_invitro_MG2

description: Library name: human_iHPCinvitro2_ATAC_rep2

data_processing:
ATAC libraries were trimmed to 30bp and were mapped to hg38 genome using bowtie2 (Langmead and Salzberg, 2012) with default parameters. HOMER (Heinz et al., 2010) tag directories were created for mapped samples. Peaks were called using HOMER‚ findPeaks command with the following parameters: ‚-style factor -size 200 - minDist 200‚  for ATAC-seq experiments. Peaks were merged with HOMER‚ mergePeaks and annotated using HOMER‚ annotatePeaks.pl using all tag directories.
Assembly: hg38
Supplementary files format and content: tab-delimited text peak file

extract_protocol:
For ATAC-seq, live cells were rinsed with 1X PBS and lysed with cold 50 mL lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 x g for 10 min at 4°C, the resulting nuclei pellet was re-suspended in 50 mL tranposase reaction mix (Illumnia #20034197) and incubated at 37°C for 30 min.
For ATAC-seq, Zymo ChIP DNA Clean and Concentrator-5 kit (Zymo Research D5205) was used to purify the DNA, which was then amplified with Nextera primers (1.25 M) using NebNext High-Fidelity 2X PCR Master Mix (New England Biolabs MO541). The final libraries were purified by gel excision of 155-250 bp fragments and single-end sequenced.

value: InVitro


title: iHPC_invitro_MG1

description: Library name: human_iHPCinvitro1_ATAC_rep1


title: CD34_invitro_MG2

description: Library name: human_CD34invitro2_ATAC_rep2


title: CD34_invitro_MG1

description: Library name: human_CD34invitro1_ATAC_rep1


title: iHPC_invitro_MG3

description: Library name: human_iHPCinvitro3_ATAC_rep3


title: monocytes_periphery_MG3

description: Library name: human_monocytesperipheryMG3_ATAC_rep3


title: monocytes_periphery_MG2

description: Library name: human_monocytesperipheryMG2_ATAC_rep2


title: monocytes_periphery_MG4

description: Library name: human_monocytesperipheryMG4_ATAC_rep4


title: monocytes_CNS_MG3

description: Library name: human_monocytesCNSMG3_ATAC_rep3


title: iHPC_CNS_MG1

description: Library name: human_iHPCCNSMG1_ATAC_rep1


title: monocytes_CNS_MG2

description: Library name: human_monocytesCNSMG2_ATAC_rep2


title: monocytes_periphery_MG5

description: Library name: human_monocytesperipheryMG5_ATAC_rep5


title: CD34_CNS_H3K27ac_MG2

description: Library name: human_ChIPCD34CNS2_H3K27acChIP_rep2


title: monocytes_periphery_MG1

description: Library name: human_monocytesperipheryMG1_ATAC_rep1


title: iHPC_periphery_MG1

description: Library name: human_iHPCperipheryMG1_ATAC_rep1


title: monocytes_CNS_MG1

description: Library name: human_monocytesCNSMG1_ATAC_rep1


title: CD34_periphery_MG1

description: Library name: human_cd34peripheryMG1_ATAC_rep1


title: CD34_CNS_MG5

description: Library name: human_cd34CNSMG5_ATAC_rep5


title: iHPC_periphery_MG3

description: Library name: human_iHPCperipheryMG3_ATAC_rep3


title: monocytes_CNS_MG4

description: Library name: human_monocytesCNSMG4_ATAC_rep4


title: CD34_CNS_MG2

description: Library name: human_cd34CNSMG2_ATAC_rep2


title: CD34_periphery_MG4

description: Library name: human_cd34peripheryMG4_ATAC_rep4


title: iHPC_CNS_MG2

description: Library name: human_iHPCCNSMG2_ATAC_rep2


title: iHPC_CNS_MG4

description: Library name: human_iHPCCNSMG5_ATAC_rep4


title: iHPC_CNS_MG3

description: Library name: human_iHPCCNSMG4_ATAC_rep3


title: CD34_CNS_MG4

description: Library name: human_cd34CNSMG4_ATAC_rep4


title: CD34_periphery_MG2

description: Library name: human_cd34peripheryMG2_ATAC_rep2


title: CD34_CNS_MG1

description: Library name: human_cd34CNSMG1_ATAC_rep1


title: CD34_periphery_MG3

description: Library name: human_cd34peripheryMG3_ATAC_rep3


title: CD34_CNS_MG3

description: Library name: human_cd34CNSMG3_ATAC_rep3


title: dpSTR_HEK293T_gDNA_Rep3

city: La Jolla

first: Alon

last: Goren

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

description:
Library name: dpSTR_HEK293T_gDNA_Rep3
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.

data_processing:
The FASTQ reads from the MPRA library were first subjected to quality control and adaptor trimming using Cutadapt, ensuring that low-quality bases and residual adaptor sequences were removed.
Following this preprocessing step, the cleaned reads were aligned to the appropriate variant reference library using BWA (Burrows-Wheeler Aligner), allowing accurate mapping of reads to their corresponding designed variants.
After alignment, read counts were computed for each variant to quantify their abundance in the library, forming the basis for downstream expression analysis.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file or CSV containing raw read counts for each variant in each sample.
Supplementary files format and content: A barcode-to-variant association table should be provided in TSV format.

growth_protocol: HEK293T cells were cultured in DMEM, high glucose, supplemented with 10% heat inactivated fetal bovine serum (FBS-HI) and 2 mM L-Glutamine in humidified incubator with 5% CO2 at 37 ºC. HeLa S3 cells were cultured in DMEM, high glucose, pyruvate supplemented with 10% heat inactivated fetal bovine serum (FBS-HI) and 2 mM L-Glutamine in humidified incubator with 5% CO2 at 37 ºC.

extract_protocol:
After 40-42 hours post-transfection, RNA and DNA were harvested using the AllPrep DNA/RNA mini Kit (Qiagen, 80204).
RNA was converted to cDNA using Superscript  Libraries were prepared using two rounds of PCR to attach Illumina barcodes and adaptors. Libraries were amplified using XX cycles on the thermocycler.

treatment_protocol: Cells were transfected using Lipofectamine 3000 to deliver the expression plasmid.

value: embryonic kidney epithelial

value: Untreated


title: dpSTR_HEK293T_gDNA_Rep2

description:
Library name: dpSTR_HEK293T_gDNA_Rep2
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: dpSTR_HEK293T_cDNA_Rep2

description:
Library name: dpSTR_HEK293T_cDNA_Rep2
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: dpSTR_HEK293T_cDNA_Rep3

description:
Library name: dpSTR_HEK293T_cDNA_Rep3
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: dpSTR_HEK293T_gDNA_Rep1

description:
Library name: dpSTR_HEK293T_gDNA_Rep1
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: hSTR1_HEK293T_gDNA_Rep3

description:
Library name: hSTR1_HEK293T_gDNA_Rep3
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: dpSTR_HEK293T_cDNA_Rep1

description:
Library name: dpSTR_HEK293T_cDNA_Rep1
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: hSTR1_HEK293T_gDNA_Rep2

description:
Library name: hSTR1_HEK293T_gDNA_Rep2
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: hSTR1_HEK293T_cDNA_Rep2

description:
Library name: hSTR1_HEK293T_cDNA_Rep2
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: hSTR1_HEK293T_gDNA_Rep1

description:
Library name: hSTR1_HEK293T_gDNA_Rep1
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: hSTR1_HEK293T_cDNA_Rep1

description:
Library name: hSTR1_HEK293T_cDNA_Rep1
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: hSTR1_association_Illumina

description:
Library name: hSTR1_association_Illumina
Plasmid library containing barcoded regulatory variants; barcode-variant pairs identified by sequencing plasmid DNA.

value: plasmid


title: hSTR1_HEK293T_cDNA_Rep3

description:
Library name: hSTR1_HEK293T_cDNA_Rep3
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: hSTR2_association_Illumina

description:
Library name: hSTR2_association_Illumina
Plasmid library containing barcoded regulatory variants; barcode-variant pairs identified by sequencing plasmid DNA.


title: RNA-seq, K7, LUNG, CD70HI, D0, REP 1

description:
Library name: K7-Lung-d0
k7_lung_d0_hi_TRUE_rep1

data_processing:
Raw RNA-seq reads were trimmed and filtered using fastp v0.23.4. Reads were aligned to the reference human genome hg38 using STAR(20) aligner v2.7.10. Transcript annotations from Gencode(21) (Release 44 GRCh38.p14) were used for the genomic location of transcripts. Transcript abundances were quantified using the alignment-based mode of Salmon(22) v0.13.1. Transcript abundances were then aggregated into gene-level counts using tximport v1.22.0 package in R (4.1.2) with gene models from Gencode v44.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
Cell pellets were resuspended in RLT and nucleic acids were extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN catalog # 80204) according to the manufacturer’s instructions. RNA was eluted in nuclease-free water and DNA in 0.5X Buffer EB.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 125-500 ng of total RNA with RIN values of 8.3-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.

value: Kidney PDX

value: ccRCC

tag: library type

value: mRNA


title: RNA-seq, K7, LUNG, CD70HI, D0, REP 2

description:
Library name: K7-Lung-d0_2
k7_lung_d0_hi_TRUE_rep2


title: RNA-seq, K7, IN VITRO, REP 2

description:
Library name: K7-p4-b
k7_in_vitro_d0_na_FALSE_rep2


title: RNA-seq, K7, LUNG, CD70HI, D0, REP 3

description:
Library name: K7-Lung-d0_3
k7_lung_d0_hi_TRUE_rep3


title: dpSTR_association_Illumina

description:
Library name: dpSTR_association_Illumina
Plasmid library containing barcoded regulatory variants; barcode-variant pairs identified by sequencing plasmid DNA.


title: RNA-seq, K7, KIDNEY, CD70HI, D0, REP 2, Pooled

description:
Library name: K7-kidneypooledCD70pos-d0_2
k7_kidney_d0_hi_TRUE_rep2


title: RNA-seq, K7, KIDNEY, CD70HI, D0, REP 1, Pooled

description:
Library name: K7-kidneypooledCD70pos-d0
k7_kidney_d0_hi_TRUE_rep1


title: RNA-seq, K7, IN VITRO, REP 3

description:
Library name: K7-p4-c
k7_in_vitro_d0_na_FALSE_rep3


title: RNA-seq, K7, IN VITRO, REP 1

description:
Library name: K7-p5-a
k7_in_vitro_d0_na_FALSE_rep1


title: RNA-seq, K7, KIDNEY, CD70LO, D8, REP 3

description:
Library name: K7-2-3K-CD70lo-d8
k7_kidney_d8_lo_FALSE_rep3


title: RNA-seq, K7, KIDNEY, CD70LO, D8, REP 2

description:
Library name: K7-2-2K-CD70lo-d8
k7_kidney_d8_lo_FALSE_rep2


title: RNA-seq, K7, KIDNEY, CD70LO, D0, REP 3

description:
Library name: K7-2-3K-CD70-lo-d0
k7_kidney_d0_lo_FALSE_rep3


title: RNA-seq, K7, KIDNEY, CD70LO, D0, REP 2

description:
Library name: K7-2-2K-CD70-lo-d0
k7_kidney_d0_lo_FALSE_rep2


title: RNA-seq, K7, KIDNEY, CD70HI, D8, REP 1, Pooled

description:
Library name: K7-Pooled-Kidney-CD70-Pos_d8
k7_kidney_d8_hi_TRUE_rep1


title: RNA-seq, K7, KIDNEY, CD70HI, D8, REP 3, Pooled

description:
Library name: K7-Pooled-Kidney-CD70-Pos_d8_3
k7_kidney_d8_hi_TRUE_rep3


title: RNA-seq, K7, KIDNEY, CD70LO, D2, REP 2

description:
Library name: K7-2-2K-CD70-lo-d2_2
k7_kidney_d2_lo_TRUE_rep2


title: iHPC_periphery_MG2

description: Library name: human_iHPCperipheryMG2_ATAC_rep2


title: RNA-seq, K7, KIDNEY, CD70LO, D2, REP 1

description:
Library name: K7-2-2K-CD70-lo-d2
k7_kidney_d2_lo_TRUE_rep1


title: RNA-seq, K7, KIDNEY, CD70LO, D8, REP 1

description:
Library name: K7-2-1K-CD70lo-d8
k7_kidney_d8_lo_FALSE_rep1


title: RNA-seq, K7, KIDNEY, CD70HI, D8,  REP 2, Pooled

description:
Library name: K7-Pooled-Kidney-CD70-Pos_d8_2
k7_kidney_d8_hi_TRUE_rep2


title: RNA-seq, K7, KIDNEY, CD70LO, D2

description:
Library name: K7-2-1K-CD70-lo-d2
k7_kidney_d2_lo_FALSE_rep1


title: RNA-seq, K7, KIDNEY, CD70LO, D0, REP 1

description:
Library name: K7-2-1K-CD70-lo-d0
k7_kidney_d0_lo_FALSE_rep1


title: RNA-seq, K5, KIDNEY, CD70HI, D8, REP 2, Pooled

description:
Library name: K5-Pooled-kidney-CD70Pos-d8_2
k5_kidney_d8_hi_TRUE_rep2


title: RNA-seq, K7, KIDNEY, CD70HI, D0, REP 3, Pooled

description:
Library name: K7-kidneypooledCD70pos-d0_3
k7_kidney_d0_hi_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70HI, D8, REP 1, Pooled

description:
Library name: K5-Pooled-kidney-CD70Pos-d8
k5_kidney_d8_hi_TRUE_rep1


title: RNA-seq, K5, KIDNEY, CD70HI, D2, REP 3, Pooled

description:
Library name: K5-Pooled-kidney-CD70Pos-d2_3
k5_kidney_d2_hi_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70HI, D2, REP 2, Pooled

description:
Library name: K5-Pooled-kidney-CD70Pos-d2_2
k5_kidney_d2_hi_TRUE_rep2


title: RNA-seq, K5, KIDNEY, CD70HI, D8, REP 3, Pooled

description:
Library name: K5-Pooled-kidney-CD70Pos-d8_3
k5_kidney_d8_hi_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70HI, D2, REP 1, Pooled

description:
Library name: K5-Pooled-kidney-CD70Pos-d2
k5_kidney_d2_hi_TRUE_rep1


title: RNA-seq, K5, KIDNEY, CD70HI, D0, REP 1, Pooled

description:
Library name: K5-Pooled-Kidney-CD70Pos-d0
k5_kidney_d0_hi_TRUE_rep1


title: RNA-seq, K5, KIDNEY, CD70HI, D0, REP 2, Pooled

description:
Library name: K5-Pooled-Kidney-CD70Pos-d0_2
k5_kidney_d0_hi_TRUE_rep2


title: RNA-seq, K5, KIDNEY, CD70LO, D8, REP 2, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d8_2
k5_kidney_d8_lo_TRUE_rep2


title: RNA-seq, K5, KIDNEY, CD70HI, D0, REP 3, Pooled

description:
Library name: K5-Pooled-Kidney-CD70Pos-d0_3
k5_kidney_d0_hi_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70LO, D2, REP 2, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d2_2
k5_kidney_d2_lo_TRUE_rep2


title: RNA-seq, K5, KIDNEY, CD70LO, D2, REP 3, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d2_3
k5_kidney_d2_lo_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70LO, D2, REP 1, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d2
k5_kidney_d2_lo_TRUE_rep1


title: RNA-seq, K7, KIDNEY, CD70LO, D2, REP 3

description:
Library name: K7-2-2K-CD70-lo-d2_3
k7_kidney_d2_lo_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70LO, D0, REP 2, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d0_2
k5_kidney_d0_lo_TRUE_rep2


title: RNA-seq, K5, KIDNEY, CD70LO, D0, REP 1, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d0
k5_kidney_d0_lo_TRUE_rep1


title: RNA-seq, K5, IN VITRO, REP 2

description:
Library name: K5-p9-b
k5_in_vitro_d0_na_FALSE_rep2


title: RNA-seq, K5, KIDNEY, CD70LO, D0, REP 3, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d0_3
k5_kidney_d0_lo_TRUE_rep3


title: RNA-seq, K5, IN VITRO, REP 3

description:
Library name: K5-p9-c
k5_in_vitro_d0_na_FALSE_rep3


title: RNA-seq, K5, KIDNEY, CD70LO, D8, REP 3, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d8_3
k5_kidney_d8_lo_TRUE_rep3


title: RNA-seq, K5, IN VITRO, REP 1

description:
Library name: K5-p9-a
k5_in_vitro_d0_na_FALSE_rep1


title: RNA-seq, K5, KIDNEY, CD70LO, D8, REP 1, Pooled

description:
Library name: K5-Pooled-Kidney-CD70lo-d8
k5_kidney_d8_lo_TRUE_rep1


title: RNA-seq, K5, LUNG, CD70HI, D0, REP 3

description:
Library name: K5-Lung-d0_3
k5_lung_d0_hi_TRUE_rep3


title: RNA-seq, K5, KIDNEY, CD70LO, D8, REP 3

description:
Library name: K5-1-5K-CD70lo-d8
k5_kidney_d8_lo_FALSE_rep3


title: RNA-seq, K5, LUNG, CD70HI, D0, REP 2

description:
Library name: K5-Lung-d0_2
k5_lung_d0_hi_TRUE_rep2


title: RNA-seq, K5, LUNG, CD70HI, D0, REP 1

description:
Library name: K5-Lung-d0
k5_lung_d0_hi_TRUE_rep1


title: RNA-seq, K5, KIDNEY, CD70HI, D0, REP1

description:
Library name: K5-1-3K-CD70Pos-d0
k5_kidney_d0_hi_FALSE_rep1


title: RNA-seq, K5, KIDNEY, CD70LO, D0, REP 3

description:
Library name: K5-1-5k-CD70lo-d0
k5_kidney_d0_lo_FALSE_rep3


title: inVitro,REP 3

description:
Library name: OV4_3
inVitro_na_rep3

source_name: Ovary PDX

value: Ovary PDX

value: Ovarian Cancer


title: RNA-seq, K5, KIDNEY, CD70LO, D0, REP 2

description:
Library name: K5-1-4k-CD70lo-d0
k5_kidney_d0_lo_FALSE_rep2


title: RNA-seq, K5, KIDNEY, CD70LO, D8, REP 1

description:
Library name: K5-1-3K-CD70lo-d8
k5_kidney_d8_lo_FALSE_rep1


title: RNA-seq, K5, KIDNEY, CD70HI, D0, REP 3

description:
Library name: K5-1-5K-CD70Pos-d0
k5_kidney_d0_hi_FALSE_rep3


title: RNA-seq, K5, KIDNEY, CD70LO, D0, REP 1

description:
Library name: K5-1-3k-CD70lo-d0
k5_kidney_d0_lo_FALSE_rep1


title: inVitro,REP 2

description:
Library name: OV4_2
inVitro_na_rep2


title: inVitro,REP 1

description:
Library name: OV4_1
inVitro_na_rep1


title: RNA-seq, K5, KIDNEY, CD70LO, D8, REP 2

description:
Library name: K5-1-4K-CD70lo-d8
k5_kidney_d8_lo_FALSE_rep2


title: RNA-seq, K5, KIDNEY, CD70HI, D0, REP 2

description:
Library name: K5-1-4K-CD70Pos-d0
k5_kidney_d0_hi_FALSE_rep2


title: exVivo,CD70 Low,REP 2

description:
Library name: 9_3_CD70LO
exVivo_lo_rep2


title: exVivo,CD70 Low,REP 3

description:
Library name: 9_4_CD70LO
exVivo_lo_rep3


title: exVivo,CD70 High,REP 1

description:
Library name: 9_2_CD70POS
exVivo_hi_rep1


title: exVivo,CD70 Low,REP 1

description:
Library name: 9_2_CD70LO
exVivo_lo_rep1


title: BJ_OSK_BRD2a

city: Fort Worth

first: Kejin

last: Hu

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

description:
Library name: OSK353a
allSamples_NormalizedCounts.xlsx

data_processing:
Original image data file from high-throughput sequencing (Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The human reference genome (assembly GRCH38, release 114) was indexed  using STAR (STAR version 2.7.11b) (runMode  genomeGenerate) on Cheaha supercomputer, and the read fragments of each FASTQ file was aligned to human reference genome using the STAR aligner (version 2.7.11b).
The BAM files were sorted and indexed using SAMtools (version 1.12), and the counting was achieved using FeatureCounts in bioocontainer on Texas Advanced Computing Center (TACC).
The statistics and normalization of the RNA-seq were conducted using the DESeq2 software (version 1.48.1) on a Dell PC.
Assembly: GRCH38, release 113
Supplementary files format and content: normalized read counts in Excel xlsx
Supplementary files format and content: allSamples_NormalizedCounts.xlsx

source_name: male

growth_protocol: Human iPS cells were cultured in standard feeder-free and serum-free chemically defined E8 media. Human fibroblast BJ cells were cultured in fibroblast media: DMEM/F12 media supplemented with 10% FBS and 5 ng/mL human bFGF

extract_protocol:
BJ fibroblast cells (ATCC, CRL-2522, foreskin fibroblasts) were cultured in six well plates at a density of 2 00000 cells per well. At 24 hrs post seeding, the medium was removed and 2 mL fresh medium containing polybrene (final concentration = 5 µg/mL) was added to the wells. The viruse preparations were then added into respective wells (day 0). At 18 hrs after virus addition, the virus-containing spent media were removed, and fresh fibroblast medium was added. At 72 hrs (or indicated times) after virus removal (on Day 4), the spent medium was removed and 1 mL of TRIzol (Invitrogen; Cat no. 15596018) was added directly to each well. RNA was extracted following manufacturer’s protocol. After extraction, the RNA was further purified using Quick RNA Miniprep kit (Zymo Research; Cat. no. R1055) using manufacturer’s protocol.   RNA for the nontreated BJ was extracted the same way but without virus transduction. RNA from humna iPSCs or ESCs was prepared using the same kits. Human PSCs were grown in E8 medium
Briefly, mRNA from BJ or human PSCs is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by the addition of fragmentation buffer. The Novogene ENB library protocol was used as briefed below (from Novogene). ENB library: Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization (1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of the indicated genes, shRNA, CRISPR KO constructs or BRD2 mutants (MOI, OCT4, 8; SOX2, 5, KLF4, 5; and all others are 3). At 18 hours post transduction, virus-containing spent media were removed and RNAs were extracted 72 hours (or as indicated) after virus removal using extraction protocols described.

value: male

value: BJ

value: On reprogramming

value: with random lentivirus integration of reprogramming factors

value: overexpressing OCT4, SOX2, KLF4 and BRD2 (WT)


title: BJ_OSK_BRD2b

description:
Library name: OSK353b
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and WT BRD2


title: BJ_OSK_LucSHRNA2

description:
Library name: OSHLUC2
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and luciderase shRNA


title: BJ_OSK_LucSHRNA1

description:
Library name: OSHLUC1
allSamples_NormalizedCounts.xlsx


title: BJ_OSK72BRD2KO2

description:
Library name: O72K2
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and knockout BRD2 with inducible CRISPR. RNA was extracted 72 hours post KO


title: BJ_OSK72BRD2KO1

description:
Library name: O72K1
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and knockout BRD2 with inducible CRISPR, RNA was extracted 72 hours post KO


title: BJ_OSK_BRD2shRNA1

description:
Library name: OSHB1
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and BRD2 shRNA


title: BJ_OSK_BRD2dETa

description:
Library name: O356a
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

value: with random lentivirus integration of reprogramming factors overexpressing OCT4, SOX2, KLF4 and BRD2 with its ET tail deleted

value: overexpressing OCT4, SOX2, KLF4 and BRD2dET (i.e., BRD2 with ET tail deleted)


title: BJ_OSK48BRD2KO1

description:
Library name: O48K1
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and knockout BRD2 with inducible CRISPR. RNA was extracted  48 hours post induction.


title: NCI-H446 UHRF1 KO 5wk tumor 1

city: Irvine

first: Claudia

last: Benavente

address: 839 Health Sciences Road, Sprague Hall B200

institute: University of California, Irvine

description:
Library name: Sample 16
Column name in processed_human_counts.xlsx matche with sample title

data_processing:
All data processing steps were conducted on Galaxy platform. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic. Trimmed sequence reads were mapped to hg38 for human and mm10 for mouse samples using HISAT2. Read count extraction and normalization were performed using featurecounts/Kallistro counts.
Assembly: hg38 for human, mm10 for mouse
Supplementary files format and content: txt or xls files include raw counts for each sample

source_name: small cell lung cancer

extract_protocol:
Total RNA from homogenized tumors was isolated using RNeasy Mini Kit (Qiagen). After quality check with Agilent BioAnalyzer and Qubit, 1 µg RNA per sample was used for poly(A) mRNA isolation.
cDNA libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina, following manufacturer instructions. Barcode-indexed libraries were purified with AMPure XP beads (Beckman Coulter) and checked for library quality using Agilent BioAnalyzer DNA Chip and quantified using KAPA qPCR.

value: small cell lung cancer

value: UHRF1 KO


title: BJ_OSK_BRD2dETb

description:
Library name: O356b
allSamples_NormalizedCounts.xlsx


title: NCI-H446 UHRF1 KO 5wk tumor 2

description:
Library name: Sample 17
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H526 UHRF1 KO 5wk tumor 5

description:
Library name: Sample 10
Column name in processed_human_counts.xlsx matche with sample title


title: BJ_OSK48BRD2KO2

description:
Library name: O48K2
allSamples_NormalizedCounts.xlsx

value: overexpressing OCT4, SOX2, KLF4 and knockout BRD2 with inducible CRISPR. RNA was prepared 48 hours post induction.


title: NCI-H446 VC 5wk tumor 1

description:
Library name: Sample 11
Column name in processed_human_counts.xlsx matche with sample title

value: VC


title: NCI-H446 UHRF1 KO 5wk tumor 3

description:
Library name: Sample 18
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H526 UHRF1 KO 5wk tumor 4

description:
Library name: Sample 9
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H526 UHRF1 KO 5wk tumor 2

description:
Library name: Sample 7
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H446 VC 5wk tumor 5

description:
Library name: Sample 15
Column name in processed_human_counts.xlsx matche with sample title


title: BJ_OSK_BRD2shRNA2

description:
Library name: OSHB2
allSamples_NormalizedCounts.xlsx

value: male


title: NCI-H526 UHRF1 KO 5wk tumor 3

description:
Library name: Sample 8
Column name in processed_human_counts.xlsx matche with sample title


title: exVivo,CD70 High,REP 2

description:
Library name: 9_3_CD70POS
exVivo_hi_rep2

value: Ovary PDX

value: Ovarian Cancer

value: mRNA


title: NCI-H526 VC 5wk tumor 3

description:
Library name: Sample 3
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H526 VC 5wk tumor 2

description:
Library name: Sample 2
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H446 VC 5wk tumor 4

description:
Library name: Sample 14
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H446 VC 5wk tumor 3

description:
Library name: Sample 13
Column name in processed_human_counts.xlsx matche with sample title


title: KNS60_NMDi14_rep1

city: Worcester

first: Athma

middle: A

last: pai

address: 55 Lake Avenue North

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

description: Library name: KNNM1

data_processing:
Adapters were trimmed and removed from reads with trimmomatic v0.32. Adapter removal was verified by running fastqc v0.11.565 on trimmed fastqc files. Overlapping read-mates were merged with PEAR v0.9.1166 and merged overlapping read-mates, non-overlapping read 1 and non-overlapping read 2 for each sample were pooled into a single fastq file per library. Fastq files for cell lines were subsampling to 112.67M reads to match the depth of the library with the lowest sequencing depth  using seqtk v1.3. Fastq files for K562 transcriptional noise experiments were subsampled to 33.1M reads to match the depth of library with the lowest sequencing depth.
Subsampled reads were mapped to GRCH38 genome by STAR v2.7.0e69 using default parameters with the following modifications or additions: --outSAMattributes All --outSJfilterOverhangMin 40 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --alignIntronMin 100 --alignIntronMax 250000 --limitOutSJcollapsed 2000000 --outSJfilterDistToOtherSJmin 20 0 10 10 --alignSJstitchMismatchNmax 2 2 2 2
Assembly: Grch38
Supplementary files format and content: Sj.out.tab  output from STAR

growth_protocol: K562 cells were grown in IMDM supplemented with 10% FBS. KNS60 cells were grown in DMEM supplemented with 5% FBS. AM38 cells were grown in EMEM supplemented with 20% FBS. HepG2 cells were grown in DMEM supplemented with 10% FBS. SH-SY5Y cells were grown in DMEM:F12 supplemented with 10% FBS. All cell lines were maintained at 37°C and 5% CO2 until 70% confluent.

extract_protocol:
Nuclear extraction: Nuclear isolation from total cells was performed following a previously established protocol(Nabbi and Riabowol 2015). Briefly, trypsinized cells were pelleted, washed with ice cold 1X PBS, and resuspended in ice cold Nuclear Isolation Buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.3% NP40, Roche EDTA-free protease inhibitor (Millipore Sigma, 11836153001), Sigma PhosSTOP phosphatase inhibitor (Millipore Sigma, 4906845001). The suspension was briefly centrifuged again to pellet the nuclei. The supernatant was removed (cytoplasmic fraction) and the pellet was resuspended in ice cold Nuclear Isolation Buffer. The suspension was centrifuged at 10,000 RCF and supernatant removed. The nuclear pellet was resuspended in TRIzol (Invitrogen, 15596018) before RNA isolation. Nascent RNA isolation from nuclei: Cells were incubated with 1mM 4-thiouridine (Sigma, T4509), dissolved in wter, for 8 minutes and spun down to pellet cells. The pellet was resuspended in Trizol and flash frozen in liquid nitrogen. After nuclear isolation and RNA isolation and described below, 4sU pulldowns were performed using MTSEA biotin-XX (VWR, 89139-636) 4sU-containing (nascent) transcripts were purified following previously established protocols(Garibaldi et al. 2017; Duffy and Simon 2016).  RNA was extracted from whole cells or nuclear pellets using TRIzol reagent to separate the aqueous RNA phase from the DNA and protein phases. The aqueous RNA phase was carried forward into column purification using a Zymo-25 RNA Clean & Concentrator kit (Zymo, R1018)
Library preparation for polyA RNA, CHX-treated, NMDi14-treated, and DMSO-treated samples was performed using the KAPA Stranded mRNA-Seq Kit for Illumina Platforms (KK8421). Library preparation for the nuclear and 4sU-labeled samples was performed using Kapa Biosystems KAPA RNA HyperPrep Kit with RiboErase (KK8561). Libraries were sequenced commercially at Novogene using an Illumina Novaseq 6000,  Illumina Nextseq 2000. SIRV libraries were made with both KAPA Stranded mRNA-Seq Kit and KAPA RNA HyperPrep Kit and sequenced on Illumina NextSeq 500

treatment_protocol: For 4sU labelleing experiments, K562 and KNS60 cells were labelled with either 500uM  or 1mM 4sU (Sigma, T4509) for 8 mins, whereas AM38, SY5Y and HepG2 cells were labelled with 1mM 4SU for 8 mins. For cychoheximide experiments, K562 or KNS60 cells were treated 50ug/mL cycloheximide (CHX) (Sigma, C7698) resuspended in DMSO for 3 hours (or only DMSO as a control). For NMDi14 experiments, K562 and KNS60 cells were  treated with 50uM NMDi14 (Sigma, SML1538) resuspended in DMSO for 6 hours. For transcriptional noise experiments, K562 cells were treated with 10uM 5-Iodo-2’-deoxyuridine (IdU) resuspended in DMSO for 24 hours and media containing 1mM 4sU (Sigma, T4509) was added during the last 8 minutes for subsequent nuclear isolation and nascent mRNA enrichment, as described below. Control cells were treated with equivalent amounts of DMSO without CHX, NMDi14, or IdU for 3, 6, and 24 hours, respectively. Uridine treatment: Control cells were treated 1mM uridine (ChemGenes, RP-1186) dissolved in water for 8 minutes or with 1mM 4sU for 24 hours. For synthetic SIRV: Synthetic Spike-In RNA Variant (SIRV-Set1; Lexogen 025.03 & SIRV-Set4: Lexogen 141.01) were pooled before library prep

value: glioblastoma

value: WT

value: 50 uM NMDi14, 6 hour


title: NCI-H526 UHRF1 KO 5wk tumor 1

description:
Library name: Sample 6
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H526 VC 5wk tumor 5

description:
Library name: Sample 5
Column name in processed_human_counts.xlsx matche with sample title


title: exVivo,CD70 High,REP 3

description:
Library name: 9_4_CD70POS
exVivo_hi_rep3


title: NCI-H446 UHRF1 KO 5wk tumor 4

description:
Library name: Sample 19
Column name in processed_human_counts.xlsx matche with sample title


title: NCI-H526 VC 5wk tumor 4

description:
Library name: Sample 4
Column name in processed_human_counts.xlsx matche with sample title


title: K562_DMSO_rep1

description: Library name: K5NMDMSO1

value: chronic myeloid leukemia

value: DMSO, 6 hour


title: NCI-H446 UHRF1 KO 5wk tumor 5

description:
Library name: Sample 20
Column name in processed_human_counts.xlsx matche with sample title


title: K562_DMSO_rep2

description: Library name: K5NMDMSO2


title: KNS60_CHX_rep1

description: Library name: KNCHX1

value: 50 ug/ml cycloheximide, 3 hour


title: K562_NMDi14_rep2

description: Library name: K5NM2


title: K562_uridine8min_rep1

description: Library name: K58mU1

value: 1 mM Uridine, 8min


title: K562_uridine8min_rep2

description: Library name: K58mU2


title: NCI-H526 VC 5wk tumor 1

description:
Library name: Sample 1
Column name in processed_human_counts.xlsx matche with sample title


title: KNS60_CHX_rep2

description: Library name: KNCHX2


title: K562_CHX_rep1

description: Library name: K5CHX1


title: KNS60_NMDi14_rep2

description: Library name: KNNM2


title: K562_4SU8min_rep2

description: Library name: K58m4sU2

value: 1 mM 4SU, 8min


title: K562_NMDi14_rep1

description: Library name: K5NM1


title: SY5Y_nascent_rep2

description: Library name: SHNAS2

molecule: nuclear RNA

value: neuroblastoma

value: 1 mM 4SU, 8 min


title: K562_4SU24hr_rep1

description: Library name: K524h4sU1

value: 1 mM 4SU, 24 hour


title: SY5Y_nuclear_rep2

description: Library name: SHNUC2

value: untreated


title: HEPG2_polyA_rep1

description: Library name: HEPPOLY1

value: hepatoblastoma


title: K562_4SU24hr_rep2

description: Library name: K524h4sU2


title: SY5Y_nascent_rep1

description: Library name: SHNAS1


title: SY5Y_polyA_rep2

description: Library name: SHPOLY2


title: HEPG2_polyA_rep2

description: Library name: HEPPOLY2


title: HEPG2_nuclear_rep1

description: Library name: HEPNUC1


title: HEPG2_nuclear_rep2

description: Library name: HEPNUC2


title: K562_4SU8min_rep1

description: Library name: K58m4sU1


title: HEPG2_nascent_rep2

description: Library name: HEPNAS2


title: AM38_polyA_rep2

description: Library name: AMPOLY2


title: AM38_polyA_rep1

description: Library name: AMPOLY1


title: HEPG2_nascent_rep1

description: Library name: HEPNAS1


title: AM38_nascent_rep1

description: Library name: AMNAS1


title: KNS60_polyA_rep4

description: Library name: KNL5POL


title: KNS60_polyA_rep3

description: Library name: KNL4POL


title: KNS60_nascent_rep3

description: Library name: KNL4NAS


title: KNS60_nuclear_rep2

description: Library name: KNL3NUC


title: KNS60_nuclear_rep3

description: Library name: KNL4NUC


title: KNS60_nascent_rep1

description: Library name: KNL2NAS

value: 500 uM 4SU, 8 min


title: KNS60_polyA_rep2

description: Library name: KNL3POL


title: AM38_nuclear_rep2

description: Library name: AMNUC2


title: K562_polyA_rep4

description: Library name: K5L5POL


title: KNS60_nascent_rep2

description: Library name: KNL3NAS


title: KNS60_nuclear_rep1

description: Library name: KNL2NUC


title: K562_nascent_rep4

description: Library name: K5L5NAS


title: K562_nuclear_rep4

description: Library name: K5L5NUC


title: AM38_nuclear_rep1

description: Library name: AMNUC1


title: AM38_nascent_rep2

description: Library name: AMNAS2


title: K562_polyA_rep3

description: Library name: K5L4POL


title: KNS60_polyA_rep1

description: Library name: KNL2POL


title: KNS60_nuclear_rep4

description: Library name: KNL5NUC


title: K562_nascent_rep2

description: Library name: K5L3NAS


title: K562_nascent_rep3

description: Library name: K5L4NAS


title: KNS60_nascent_rep4

description: Library name: KNL5NAS


title: K562_polyA_rep2

description: Library name: K5L3POL


title: K562_nuclear_rep1

description: Library name: K5L2NUC


title: K562_polyA_rep1

description: Library name: K5L2POL


title: K562_nuclear_rep3

description: Library name: K5L4NUC


title: monocytes_periphery6

description: Library name: MNC_xMGliver_rep6

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.11b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Batch correction was performed using CombatSeq and the sva package (v3.52.0)
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.44.0) to determine differential expression between groups, within the R statistical computing environment (v4.4.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: umbilical cord blood

value: Monocytes

value: Peripheral engraftment


title: K562_nascent_rep1

description: Library name: K5L2NAS


title: K562_nuclear_rep2

description: Library name: K5L3NUC


title: monocytes_periphery5

description: Library name: MNC_xMGliver_rep5


title: monocytes_periphery3

description: Library name: MNC_xMGliver_rep3


title: monocytes_periphery1

description: Library name: MNC_xMGliver_rep1


title: monocytes_periphery4

description: Library name: MNC_xMGliver_rep4


title: monocytes_periphery2

description: Library name: MNC_xMGliver_rep2


title: CD34_periphery6

description: Library name: CD34_xMGliver_rep6


title: CD34_periphery3

description: Library name: CD34_xMGliver_rep3


title: CD34_periphery2

description: Library name: CD34_xMGliver_rep2


title: monocytes_brain6

description: Library name: MNC_xMGbrain_rep6

value: CNS engraftment


title: CD34_periphery4

description: Library name: CD34_xMGliver_rep4


title: monocytes_brain5

description: Library name: MNC_xMGbrain_rep5


title: monocytes_brain3

description: Library name: MNC_xMGbrain_rep3


title: monocytes_brain7

description: Library name: MNC_xMGbrain_rep7


title: monocytes_brain4

description: Library name: MNC_xMGbrain_rep4


title: monocytes_brain1

description: Library name: MNC_xMGbrain_rep1


title: CD34_brain4

description: Library name: CD34_xMGbrain_rep4


title: CD34_periphery1

description: Library name: CD34_xMGliver_rep1


title: CD34_brain1

description: Library name: CD34_xMGbrain_rep1


title: CD34_brain6

description: Library name: CD34_xMGbrain_rep6


title: ec11_periphery6

description: Library name: EC11_xMGliver_rep6

value: iPSC-derived cells

value: iHPC


title: CD34_brain5

description: Library name: CD34_xMGbrain_rep5


title: CD34_periphery5

description: Library name: CD34_xMGliver_rep5


title: ec11_periphery4

description: Library name: EC11_xMGliver_rep4


title: CD34_brain2

description: Library name: CD34_xMGbrain_rep2


title: ec11_periphery5

description: Library name: EC11_xMGliver_rep5


title: CD34_brain3

description: Library name: CD34_xMGbrain_rep3


title: ec11_periphery3

description: Library name: EC11_xMGliver_rep3


title: monocytes_brain2

description: Library name: MNC_xMGbrain_rep2


title: ec11_periphery2

description: Library name: EC11_xMGliver_rep2


title: ec11_brain4

description: Library name: EC11_xMGbrain_rep4


title: ec11_brain3

description: Library name: EC11_xMGbrain_rep3


title: ec11_brain6

description: Library name: EC11_xMGbrain_rep6


title: ec11_brain5

description: Library name: EC11_xMGbrain_rep5


title: ec11_brain2

description: Library name: EC11_xMGbrain_rep2


title: ec11_periphery1

description: Library name: EC11_xMGliver_rep1


title: ec11_brain1

description: Library name: EC11_xMGbrain_rep1


title: genomic DNA from PHGDH-siRNA treated HaCaT cells 2

type: genomic

hyb_protocol: The genomic DNA underwent bisulfite conversion and the bisulfite modified DNA was then whole-genome amplified, fragmented by an enzymatic process and hybridized to the HumanMethylatio850 BeadChip by the manufacturer

scan_protocol: Scanning and imaging Beadchip with iScan

data_processing:
R-package minifi (V1.30.0)
Average Beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: PHGDH-siRNA treated HaCaT cells 2

label_protocol: Standard Illumina Protocol

extract_protocol: genome DNA was extracted and purified from HaCaT cells using Qiagen DNeasy Blood and Tissue Kit according to standard instructions

value: PHGDH knockdown


title: AML_7575_cDNA

description:
Library name: Sample 32
in vitro CRISPR screen

value: patient ID:7575


title: genomic DNA from PHGDH-siRNA treated HaCaT cells 1

source_name: PHGDH-siRNA treated HaCaT cells 1