title: Library 2 CITE-seq CD8+ T cells, Feature Barcode (HTO)

description:
Library name: Library_2_HTO
10x Genomics Chromium Feature Barcode hashing library from lineage-traced CD8+ T cells.

value: B16-F10 melanoma; tamoxifen (days 8-10)


title: snATAC-seq from GM23338 (ENCLB085MLJ)

status: Public on Jul 24 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR446QJT/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line PGP1
experiment encode accession: ENCSR446QJT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB085MLJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens GM23338 cell line nuclear fraction

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

tag: source

value: George Church

tag: link

value: ENCBS763JVU at ENCODE; https://www.encodeproject.org/ENCBS763JVU/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: U87MG cells, 3d Etoposide, Rep1

city: Providence

first: Abigail

middle: K

last: Brown

state: RI

address: 70 Ship Street

department: Molecular Biology, Cell Biology, Biochemistry

institute: Brown University

data_processing:
Sequences were trimmed for Illumina adaptors using Trimgalore.
Reads were then aligned to the human geneome (hg19) using Bowtie2 v. 2.3.0
Mitochondrial and PCR duplicate reads were removed using.
Peaks were called using MACS2 v.2.1.1 with a significance cutoff q value of 0.01
Assembly: hg19
Supplementary files format and content: narrowPeak files

source_name: cell line

growth_protocol: U87MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% PenStrep in humidfied atmosphere with 5% CO2 at 37C.

extract_protocol:
50,000 cells per time point were collected and washed in 1X PBS and centrifuged at 500g at 4oC for 5 minutes. Three independent replicates were performed. After collection, cells were lysed and the nuclei extracted by incubation in cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and then immediately centrifuged at 500g at 4oC for 10 minutes. Transposition was then performed on whole nuclei by resuspending the nuclei in 50 µl of Transposition mix (22.5 µl of 1X TD Buffer and 2.5 µl of Tn5 enzyme) and then incubation at 37oC for 30 minutes. DNA was then isolated using the MinElute PCR purification kit (Qiagen). DNA was amplified using 9 PCR cycles, and libraries were then purified using the MinElute PCR purification kit.
ATAC-seq was used to probe chromatin accessibility.

treatment_protocol: 1. For FOXO3 activation cells were infected with lentiviral media for 24 hours. Activation of FOXO3 (8 and 16 hours) and GFP expression was induced using doxycycline. 2. For FOXO3 knockdown, cells were infected with FOXO3 shRNA lentivirus. 3. Senescence was induced in cells using 10µM etoposide for designated times.

tag: tissue

tag: cell line

tag: cell type

value: Glioblastoma

tag: genotype

value: Wildtype

tag: treatment

value: Etoposide 3 days


title: U87MG, FOXO3 Act.16hrs w PFI3, Rep3

value: FOXO3 activation and PFI3 16hrs


title: Library 2 CITE-seq CD8+ T cells, Gene Expression

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

description:
Library name: Library_2_GEX
10x Genomics Chromium Single Cell 5' Gene Expression library from lineage-traced CD8+ T cells.

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were obtained either as demultiplexed FASTQ files from the sequencing facility or converted from BCL files using Illumina bcl2fastq. The resulting FASTQ files were processed using Cell Ranger (10x Genomics).
Gene expression FASTQ files were processed using Cell Ranger (10x Genomics) against the mm10 reference genome to generate filtered gene-barcode matrices.
Feature Barcode (CITE-seq) libraries were processed using Cell Ranger Feature Barcode to generate antibody-derived tag (ADT) count matrices.
TCR libraries were processed using Cell Ranger VDJ to assemble TCR α and β chain sequences and generate filtered contig annotations.
Filtered gene expression matrices, ADT matrices, and TCR annotations were imported into Seurat (v4) for downstream quality control, normalization, sample demultiplexing, integration, clustering, and visualization.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Sparse gene expression count matrices generated by Cell Ranger, including matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz, representing UMI counts for each gene in each cell.
Supplementary files format and content: Cell Ranger V(D)J filtered contig annotation files (filtered_contig_annotations.csv) containing assembled TCR α/β sequences, clonotype assignments, CDR3 sequences, and V(D)J gene usage. Feature Barcode (CITE-seq) count matrices (UMI_matrix.mtx.gz, UMI_features.tsv.gz, and UMI_barcodes.tsv.gz) containing antibody-derived tag (ADT) counts for each cell.

molecule: polyA RNA

organism: Mus musculus

source_name: Tumor and lymph node

growth_protocol: Lag3^iCreERT2^ Rosa26^LSL-tdTomato^ mice on a C57BL/6 background were maintained under specific pathogen-free conditions. Mice were subcutaneously inoculated with B16-F10 melanoma cells and monitored until tissue collection.

extract_protocol:
Single-cell suspensions were prepared from tumors and lymphoid tissues by mechanical and enzymatic dissociation. CD8+ T cell populations were enriched and stained with fluorophore-conjugated antibodies and TotalSeq™ oligonucleotide-conjugated antibodies. Cell populations were sorted by flow cytometry based on tdTomato, LAG3, CD44, and additional surface markers. Viable sorted cells were immediately processed using the 10x Genomics Chromium platform.
Single-cell libraries were generated using the 10x Genomics Chromium Single Cell 5' Library & Gel Bead Kit according to the manufacturer's protocol. Three libraries were generated from each sample: (1) Gene Expression (GEX), (2) Feature Barcode libraries for CITE-seq (TotalSeq antibodies), and (3) V(D)J TCR libraries. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Tumor-bearing mice received tamoxifen by oral gavage on days 8–10 after tumor implantation to induce Cre-mediated lineage labeling of Lag3-expressing cells. Tumors and lymphoid tissues were harvested at the indicated experimental time points (Day 11, Day 19, or Day 72).

value: Tumor and lymph node

value: Sorted CD8+ T cells

value: LAG3-tdT-, LAG3-tdT+, LAG3+tdT+, CD44+tdT-

tag: batch


title: U87MG, FOXO3 Act.16hrs w PFI3, Rep1


title: Library 1 CITE-seq CD8+ T cells, V(D)J TCR

description:
Library name: Library_1_tcr
10x Genomics Chromium Single Cell 5' V(D)J TCR library from lineage-traced CD8+ T cells.

library_source: other

molecule: other

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day19, Day74


title: U87MG, FOXO3 Act.16hrs w PFI3, Rep2

value: cell line


title: U87MG, FOXO3 Act.8hrs w PFI3, Rep3

value: FOXO3 activation and PFI3 8hrs


title: snATAC-seq from heart right ventricle (ENCLB587ZAE)

description:
https://www.encodeproject.org/experiments/ENCSR442RZO/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR442RZO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB587ZAE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (61 years) heart right ventricle tissue nuclear fraction

value: heart right ventricle

value: tissue

value: male

tag: health state

value: nonischemic (EF 11% LVEDD 7.7; RV severe dilation, severe dysfunction)

value: adult

value: 61 year

value: Shin Lin

value: ENCBS459KEQ at ENCODE; https://www.encodeproject.org/ENCBS459KEQ/

value: Derived from ENCODE donor ENCDO808ASZ; https://www.encodeproject.org/ENCDO808ASZ/


title: Control ChIP-seq from HepG2 (ENCLB044POH)

description:
https://www.encodeproject.org/experiments/ENCSR441NSM/
***************
biological replicate number: 1
technical replicate number: 1
description: NR2F2 ChIP-seq on HepG2 cells treated with vector control shRNA
experiment encode accession: ENCSR441NSM
assay title: Control ChIP-seq
possible controls: ENCSR482BUK
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB044POH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line

tag: antibody

tag: encode accession

tag: note

value: Homo sapiens HepG2 cell line genetically modified using CRISPR via transient transfection. CEBPB locus was targeted using sgRNA.

value: hepatocellular carcinoma

value: child

value: 15 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS348HRE at ENCODE; https://www.encodeproject.org/ENCBS348HRE/


title: Library 1 CITE-seq CD8+ T cells, Feature Barcode (HTO)

description:
Library name: Library_1_hto
10x Genomics Chromium Feature Barcode hashing library from lineage-traced CD8+ T cells.

molecule: protein

value: Tumor and lymph node

value: Sorted CD8+ T cells

value: LAG3-tdT-, LAG3-tdT+, LAG3+tdT+, CD44+tdT-

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day19, Day73


title: U87MG, FOXO3 Act.8hrs w PFI3, Rep1

value: cell line

value: Glioblastoma

value: Wildtype

value: FOXO3 activation and PFI3 8hrs


title: U87MG, FOXO3 Act.8hrs w PFI3, Rep2


title: snATAC-seq from Calu3 (ENCLB029UCY)

description:
https://www.encodeproject.org/experiments/ENCSR443NJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR443NJZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB029UCY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens Calu3 cell line nuclear fraction

tag: line

tag: biosample encode accession

tag: Sex

value: male

value: Lung adenocarcinoma

value: adult

value: 25 year

value: Mats Ljungman, UMichigan

value: nucleus

value: ENCBS414ISM at ENCODE; https://www.encodeproject.org/ENCBS414ISM/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: U87MG cells, GFP control w PFI3, Rep3

value: GFP control PFI3 treatment


title: U87MG cells, GFP control w PFI3, Rep2


title: Library 1 CITE-seq CD8+ T cells, Gene Expression

description:
Library name: Library_1_GEX
10x Genomics Chromium Single Cell 5' Gene Expression library from lineage-traced CD8+ T cells.

value: Tumor and lymph node

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day19, Day72


title: Control ChIP-seq from HepG2 (ENCLB479LCL)

description:
https://www.encodeproject.org/experiments/ENCSR441NSM/
***************
biological replicate number: 2
technical replicate number: 1
description: NR2F2 ChIP-seq on HepG2 cells treated with vector control shRNA
experiment encode accession: ENCSR441NSM
assay title: Control ChIP-seq
possible controls: ENCSR482BUK
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB479LCL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: Homo sapiens HepG2 cell line transduced with doxycycline-inducible shRNA targeting non-targeting control. Cells were treated for 72 hours with 4ug/mL doxycycline prior to experiment harvest.

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS238BKJ at ENCODE; https://www.encodeproject.org/ENCBS238BKJ/


title: Tumor tdTomato+ CD8+ T cells ATAC-seq (replicate 3)

description:
Library name: TUMOR_TDT_SP_rep3
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.

data_processing:
Raw sequencing reads were processed using the atacseq pipeline.
Reads were trimmed when necessary and aligned to the Mus musculus GRCm38 (mm10) reference genome using BWA-MEM.
Duplicate, mitochondrial, and low-quality reads were removed according to the atacseq workflow. Library quality metrics, including fragment size distribution and transcription start site (TSS) enrichment, were generated during pipeline execution.
Accessible chromatin regions were identified using MACS2 to generate narrowPeak and summit files.
Normalized genome-wide chromatin accessibility tracks were generated in BigWig format for visualization in genome browsers.
Assembly: GRCm38 (mm10)
Supplementary files format and content: MACS2 narrowPeak files containing genomic regions of accessible chromatin identified for each ATAC-seq sample, and summits.bed files containing the summit position of each called peak.
Supplementary files format and content: BigWig files containing normalized genome-wide chromatin accessibility signal generated from aligned ATAC-seq reads for visualization in genome browsers.

source_name: Tumor

growth_protocol: Lag3^iCreERT2^ Rosa26^LSL-tdTomato^ mice on a C57BL/6 background were maintained under specific pathogen-free conditions. B16-F10 melanoma cells were cultured according to ATCC recommendations and implanted into recipient mice. Tumors, draining lymph nodes (DLNs), and non-draining lymph nodes (NDLNs) were collected at the indicated experimental time points for downstream analysis.

extract_protocol:
Tumors, draining lymph nodes (DLNs), and non-draining lymph nodes (NDLNs) were harvested from tumor-bearing mice. Tumor-infiltrating lymphocytes were isolated by enzymatic digestion with collagenase IV (1 mg/mL), dispase (1 mg/mL), and DNase (5 mg/mL) at 37°C for 30 min, followed by mechanical dissociation and red blood cell lysis. Lymph node samples were processed into single-cell suspensions. CD8^+^ T cell subsets (LAG3^-^tdT^-^, LAG3^+^tdT^+^, LAG3^-^tdT^+^, and CD44^+^tdT^+^ where applicable) were flow sorted prior to 10x Genomics single-cell RNA-seq/CITE-seq/TCR-seq or ATAC-seq library preparation.
Nuclei were isolated from fluorescence-activated cell sorted CD8+ T cell subsets. Chromatin accessibility libraries were generated using the Omni-ATAC protocol as previously described. Briefly, nuclei were incubated with Tn5 transposase to simultaneously fragment genomic DNA and insert sequencing adapters. Following transposition, libraries were PCR amplified, purified, quality assessed, and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol: Mice were implanted with B16-F10 melanoma cells and received three consecutive intraperitoneal injections of tamoxifen (2 mg in 5% ethanol/sunflower oil) on days 8–10 after tumor implantation to induce Cre-mediated lineage tracing. Vehicle-treated mice served as controls where indicated. Tissues were harvested at the specified time points for single-cell RNA-seq and ATAC-seq analyses.

value: Tumor

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: U87MG cells, GFP control w PFI3, Rep1

value: cell line

value: Glioblastoma

value: Wildtype


title: U87MG cells, GFP control, Rep3

value: GFP control


title: U87MG cells, GFP control, Rep2


title: snATAC-seq from CD8-positive, alpha-beta T cell (ENCLB905AOL)

description:
https://www.encodeproject.org/experiments/ENCSR438DII/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR438DII
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB905AOL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell nuclear fraction

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

tag: source

value: AllCells

tag: link

value: ENCBS243UCY at ENCODE; https://www.encodeproject.org/ENCBS243UCY/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: U87MG cells, GFP control, Rep1

tag: tissue

tag: cell line

tag: cell type


title: snATAC-seq from heart left ventricle (ENCLB614CJN)

description:
https://www.encodeproject.org/experiments/ENCSR435CGY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR435CGY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB614CJN
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (41 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: nonischemic

value: 41 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS041JJC at ENCODE; https://www.encodeproject.org/ENCBS041JJC/

value: Derived from ENCODE donor ENCDO216BMM; https://www.encodeproject.org/ENCDO216BMM/


title: U87MG cells, FOXO3 Act.16hrs, Rep3

value: cell line

value: Glioblastoma

tag: genotype

value: Wildtype

tag: treatment

value: FOXO3 activation 16hrs


title: Tumor tdTomato+ CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: TUMOR_TDT_SP_rep2
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.

value: Tumor

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19

tag: batch


title: U87MG cells, FOXO3 Act.16hrs, Rep2


title: Tumor tdTomato+ CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: TUMOR_TDT_SP_rep1
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.


title: U87MG cells, FOXO3 Act.16hrs, Rep1


title: Tumor LAG3-tdTomato+ CD8+ T cells ATAC-seq (replicate 3)

description:
Library name: TUMOR_LAG3_SP_rep3
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato+ CD8+ T cells.


title: snATAC-seq from mucosa of urinary bladder (ENCLB063HLH)

description:
https://www.encodeproject.org/experiments/ENCSR427SIL/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human mucosa of urinary bladder
experiment encode accession: ENCSR427SIL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB063HLH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (47 years) mucosa of urinary bladder tissue, preserved by flash-freezing nuclear fraction

value: mucosa of urinary bladder

value: female

tag: health state

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 47 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS211JBC at ENCODE; https://www.encodeproject.org/ENCBS211JBC/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: U87MG cells, FOXO3 Act.8hrs, Rep3

value: cell line

value: Glioblastoma

value: FOXO3 activation 8hrs


title: snATAC-seq from left ventricle myocardium superior (ENCLB022VQR)

description:
https://www.encodeproject.org/experiments/ENCSR425CZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR079LVG).
experiment encode accession: ENCSR425CZQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB022VQR
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (60 years) left ventricle myocardium superior tissue, preserved by flash-freezing nuclear fraction

value: left ventricle myocardium superior

value: tissue

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: 60 year

value: Michael Snyder, Stanford

value: ENCBS999XQG at ENCODE; https://www.encodeproject.org/ENCBS999XQG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: U87MG cells, FOXO3 Act.8hrs, Rep2

value: Wildtype


title: Tumor LAG3-tdTomato+ CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: TUMOR_LAG3_SP_rep2
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato+ CD8+ T cells.

value: Tumor

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: U87MG cells, FOXO3 Act.8hrs, Rep1

value: cell line


title: snATAC-seq from adrenal gland (ENCLB006QEF)

description:
https://www.encodeproject.org/experiments/ENCSR420EWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR362YDM).
experiment encode accession: ENCSR420EWQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB006QEF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (26 years) adrenal gland tissue, preserved by flash-freezing nuclear fraction

value: adrenal gland

value: DM:no; HTN:no; CAD:no

value: adult

value: 26 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS099KRU at ENCODE; https://www.encodeproject.org/ENCBS099KRU/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: lung endothelial cells, Tie1-CR, rep 5

city: Mannheim

first: Lorna

last: Wessels

address: Ludolf-Krehl-Straße 13-17

country: Germany

institute: European Center for Angioscience

description:
Library name: Sample 9
MK73-24_PBS_mut

library_source: transcriptomic

data_processing:
Sequence reads were aligned to GRCm38 using STAR Aligner (version 2.7) with default parameters
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: csv file with TPM values for each sample if TPM was greater than 10 in at least one sample

molecule: total RNA

source_name: lung

extract_protocol:
RNA was harvested using Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific). 50-100 ng of total RNA was used for the construction of sequencing libraries.
SMARTer Ultra Low RNA kit for Illumina sequencing (Clontech) was used for library construction.

value: lung

value: endothelial cells


title: Tumor LAG3-tdTomato+ CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: TUMOR_LAG3_SP_rep1
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato+ CD8+ T cells.


title: lung endothelial cells, Tie1-CR, rep 4

description:
Library name: Sample 8
MK73-23_PBS_mut


title: snATAC-seq from progenitor cell of endocrine pancreas (ENCLB349DVN)

description:
https://www.encodeproject.org/experiments/ENCSR413MCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR413MCQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB349DVN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells nuclear fraction

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

tag: description

value: WA09 derived pancreatic progenitor cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS791GDZ at ENCODE; https://www.encodeproject.org/ENCBS791GDZ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: lung endothelial cells, Tie1-CR, rep 3

description:
Library name: Sample 7
MK73-22_PBS_mut


title: Tumor LAG3+tdTomato+ CD8+ T cells ATAC-seq (replicate 4)

description:
Library name: TUMOR_DP_rep4
Bulk ATAC-seq of FACS-isolated LAG3+ tdTomato+ CD8+ T cells.

value: Tumor

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: snATAC-seq from heart left ventricle (ENCLB236ULJ)

description:
https://www.encodeproject.org/experiments/ENCSR412VTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR412VTJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB236ULJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: male

value: nonischemic (EF 27%, LVEDD 7.9)

value: adult

value: 54 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS530IBJ at ENCODE; https://www.encodeproject.org/ENCBS530IBJ/

value: Derived from ENCODE donor ENCDO593PZY; https://www.encodeproject.org/ENCDO593PZY/


title: lung endothelial cells, Tie1-CR, rep 2

description:
Library name: Sample 6
MK73-20_PBS_mut

value: lung

value: endothelial cells


title: lung endothelial cells, Tie1-CR, rep 1

description:
Library name: Sample 5
MK73-19_PBS_mut


title: Tumor LAG3+tdTomato+ CD8+ T cells ATAC-seq (replicate 3)

description:
Library name: TUMOR_DP_rep3
Bulk ATAC-seq of FACS-isolated LAG3+ tdTomato+ CD8+ T cells.

value: Tumor

value: B16-F10 melanoma


title: lung endothelial cells, Tie1-WT, rep 4

description:
Library name: Sample 4
MK73-18_PBS_wt


title: snATAC-seq from CD14-positive monocyte (ENCLB698LOJ)

description:
https://www.encodeproject.org/experiments/ENCSR410OWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410OWB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB698LOJ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (30 years) CD14-positive monocyte primary cell nuclear fraction

value: CD14-positive monocyte

value: primary cell

value: 30 year

value: Yijun Ruan, JAX

value: nucleus

value: AllCells

value: ENCBS881OAV at ENCODE; https://www.encodeproject.org/ENCBS881OAV/

value: Derived from ENCODE donor ENCDO544CHQ; https://www.encodeproject.org/ENCDO544CHQ/


title: lung endothelial cells, Tie1-WT, rep 3

description:
Library name: Sample 3
MK73-17_PBS_wt


title: Tumor LAG3+tdTomato+ CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: TUMOR_DP_rep2
Bulk ATAC-seq of FACS-isolated LAG3+ tdTomato+ CD8+ T cells.

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: lung endothelial cells, Tie1-WT, rep 2

description:
Library name: Sample 2
MK73-16_PBS_wt


title: lung endothelial cells, Tie1-WT, rep 1

description:
Library name: Sample 1
MK73-15_PBS_wt


title: snATAC-seq from heart left ventricle (ENCLB198QFN)

description:
https://www.encodeproject.org/experiments/ENCSR409QLZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR409QLZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB198QFN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: female

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Shin Lin

value: giant cell (EF <20%)

value: ENCBS133HQW at ENCODE; https://www.encodeproject.org/ENCBS133HQW/

value: Derived from ENCODE donor ENCDO121UJI; https://www.encodeproject.org/ENCDO121UJI/


title: Tumor LAG3+tdTomato+ CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: TUMOR_DP_rep1
Bulk ATAC-seq of FACS-isolated LAG3+ tdTomato+ CD8+ T cells.

value: Tumor

value: B16-F10 melanoma


title: total RNA-seq from T-helper 1 cell (ENCLB091GSW)

description:
https://www.encodeproject.org/experiments/ENCSR997HFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR997HFD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB091GSW

source_name: Homo sapiens female adult (33 years) T-helper 1 primary cell treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours

value: T-helper 1 cell

value: primary cell

tag: encode accession

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:16; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS380YWV at ENCODE; https://www.encodeproject.org/ENCBS380YWV/


title: snATAC-seq from heart left ventricle (ENCLB308CHG)

description:
https://www.encodeproject.org/experiments/ENCSR406CJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR406CJH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB308CHG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (68 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: biosample encode accession

tag: Sex

value: male

value: ischemic

value: 68 year

value: ENCBS437OBX at ENCODE; https://www.encodeproject.org/ENCBS437OBX/

value: Derived from ENCODE donor ENCDO184BIH; https://www.encodeproject.org/ENCDO184BIH/


title: total RNA-seq from T-cell (ENCLB014SQE)

description:
https://www.encodeproject.org/experiments/ENCSR990GHM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR990GHM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB014SQE

source_name: Homo sapiens male adult (42 years) T-cell primary cell

value: T-cell

tag: dev stage

value: adult

tag: age

value: 42 year

value: ENCBS758FVD at ENCODE; https://www.encodeproject.org/ENCBS758FVD/


title: Tumor DN CD8+ T cells ATAC-seq (replicate 4)

description:
Library name: TUMOR_DN_rep4
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

value: Tumor

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB057NVJ)

description:
https://www.encodeproject.org/experiments/ENCSR992FYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR992FYQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB057NVJ

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 34 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS102KAQ at ENCODE; https://www.encodeproject.org/ENCBS102KAQ/


title: snATAC-seq from right lobe of liver (ENCLB163UEU)

description:
https://www.encodeproject.org/experiments/ENCSR402PKA/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human right lobe of liver
experiment encode accession: ENCSR402PKA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB163UEU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female child (16 years) right lobe of liver tissue, preserved by cryopreservation nuclear fraction

value: right lobe of liver

value: tissue

value: Child biosample for Chang/Greenleaf lab

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

value: ENCBS188MBW at ENCODE; https://www.encodeproject.org/ENCBS188MBW/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB141MEJ)

description:
https://www.encodeproject.org/experiments/ENCSR983YCJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR983YCJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141MEJ

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

tag: link

value: ENCBS319KCN at ENCODE; https://www.encodeproject.org/ENCBS319KCN/


title: Tumor DN CD8+ T cells ATAC-seq (replicate 3)

description:
Library name: TUMOR_DN_rep3
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

tag: tissue

value: Tumor

tag: cell line

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB183VYC)

description:
https://www.encodeproject.org/experiments/ENCSR982RIX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR982RIX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB183VYC

value: female

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS324AHU at ENCODE; https://www.encodeproject.org/ENCBS324AHU/


title: Control ChIP-seq from K562 (ENCLB296OXR)

description:
https://www.encodeproject.org/experiments/ENCSR402HVP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input for K562 cells treated with vector control shRNA
experiment encode accession: ENCSR402HVP
assay title: Control ChIP-seq
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB296OXR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: note

value: Homo sapiens HepG2 cell line genetically modified using CRISPR via transient transfection. CEBPB locus was targeted using sgRNA.

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS338VJZ at ENCODE; https://www.encodeproject.org/ENCBS338VJZ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB640KGN)

description:
https://www.encodeproject.org/experiments/ENCSR975NWR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR975NWR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB640KGN

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 40 year

value: ENCBS038WDG at ENCODE; https://www.encodeproject.org/ENCBS038WDG/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB019WAF)

description:
https://www.encodeproject.org/experiments/ENCSR979GPU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR979GPU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB019WAF

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: male

value: 38 year

value: ENCBS759TTE at ENCODE; https://www.encodeproject.org/ENCBS759TTE/


title: Tumor DN CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: TUMOR_DN_rep2
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

source_name: Tumor

value: Tumor

value: B16-F10 melanoma

tag: cell type

value: Sorted CD8+ T cells

tag: genotype

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

tag: treatment

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19

tag: batch


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB584MKA)

description:
https://www.encodeproject.org/experiments/ENCSR975MXT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR975MXT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB584MKA

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

tag: encode accession

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS980WCI at ENCODE; https://www.encodeproject.org/ENCBS980WCI/


title: snATAC-seq from lower lobe of left lung (ENCLB392OFR)

description:
https://www.encodeproject.org/experiments/ENCSR391BWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR391BWM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB392OFR
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (59 years) lower lobe of left lung tissue, preserved by flash-freezing nuclear fraction

value: lower lobe of left lung

value: tissue

tag: biosample encode accession

value: female

tag: health state

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS287DGI at ENCODE; https://www.encodeproject.org/ENCBS287DGI/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: Tumor DN CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: TUMOR_DN_rep1
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

value: Tumor

value: B16-F10 melanoma

value: Sorted CD8+ T cells


title: snATAC-seq from mucosa of descending colon (ENCLB616FKZ)

description:
https://www.encodeproject.org/experiments/ENCSR384AYS/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR384AYS
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB616FKZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (26 years) mucosa of descending colon tissue, preserved by cryopreservation nuclear fraction

value: mucosa of descending colon

tag: Sex

value: male

value: DM:no; HTN:no; CAD:no

tag: dev stage

value: adult

value: 26 year

value: ENCBS480WQR at ENCODE; https://www.encodeproject.org/ENCBS480WQR/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: snATAC-seq from Panc1 (ENCLB527WVM)

description:
https://www.encodeproject.org/experiments/ENCSR974TUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR974TUB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB527WVM
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens Panc1 cell line nuclear fraction

value: cell line

value: pancreatic carcinoma

tag: age

value: 56 year

tag: lab

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS683ZNT at ENCODE; https://www.encodeproject.org/ENCBS683ZNT/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB799BAK)

description:
https://www.encodeproject.org/experiments/ENCSR971LSO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971LSO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB799BAK

source_name: Homo sapiens male adult (56 years) effector memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

value: ENCBS617UCN at ENCODE; https://www.encodeproject.org/ENCBS617UCN/


title: snATAC-seq from bile duct (ENCLB628PMH)

description:
https://www.encodeproject.org/experiments/ENCSR381NFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR381NFT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB628PMH
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (47 years) bile duct tissue, preserved by flash-freezing nuclear fraction

value: bile duct

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS335IVP at ENCODE; https://www.encodeproject.org/ENCBS335IVP/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: total RNA-seq from inflammatory macrophage (ENCLB400YSE)

description:
https://www.encodeproject.org/experiments/ENCSR971KZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971KZD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB400YSE

source_name: Homo sapiens male adult (24 years) inflammatory macrophage primary cell

value: inflammatory macrophage

value: male

value: adult

value: 24 year

value: Shelly Heimfeld

value: ENCBS375PHX at ENCODE; https://www.encodeproject.org/ENCBS375PHX/


title: NDLN tdTomato+ CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: NDLN_TDT_SP_rep2
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.

source_name: Non-draining lymph node

tag: tissue

value: Non-draining lymph node

tag: cell line

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from T-cell (ENCLB846RHM)

description:
https://www.encodeproject.org/experiments/ENCSR969WFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR969WFV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB846RHM

value: T-cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS876UMS at ENCODE; https://www.encodeproject.org/ENCBS876UMS/


title: NDLN tdTomato+ CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: NDLN_TDT_SP_rep1
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.


title: TF ChIP-seq from K562 (ENCLB938OGM)

description:
https://www.encodeproject.org/experiments/ENCSR965UZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPB ChIP-seq on K562 cells treated with shRNA targeting MAFF
experiment encode accession: ENCSR965UZJ
assay title: TF ChIP-seq
possible controls: ENCSR915CFB, ENCSR538UCE
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB938OGM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line expressing RNAi targeting H. sapiens MAFF

tag: antibody

value: CEBPB

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS129XXB at ENCODE; https://www.encodeproject.org/ENCBS129XXB/


title: snATAC-seq from colonic mucosa (ENCLB981MXQ)

description:
https://www.encodeproject.org/experiments/ENCSR375XCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human colonic mucosa
experiment encode accession: ENCSR375XCZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB981MXQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female child (16 years) colonic mucosa tissue, preserved by cryopreservation nuclear fraction

value: colonic mucosa

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS447NED at ENCODE; https://www.encodeproject.org/ENCBS447NED/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB181DAN)

description:
https://www.encodeproject.org/experiments/ENCSR961UKV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961UKV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB181DAN

source_name: Homo sapiens female adult (33 years) effector memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS682DSX at ENCODE; https://www.encodeproject.org/ENCBS682DSX/


title: NDLN LAG3-tdTomato+ CD8+ T cells ATAC-seq

description:
Library name: NDLN_LAG3_SP_rep1
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato+ CD8+ T cells.

value: Non-draining lymph node

value: B16-F10 melanoma

tag: cell type

value: Sorted CD8+ T cells

tag: genotype

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB013PYY)

description:
https://www.encodeproject.org/experiments/ENCSR961CKN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961CKN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB013PYY

value: CD4-positive, alpha-beta T cell

value: male

value: 38 year

value: ENCBS131ALG at ENCODE; https://www.encodeproject.org/ENCBS131ALG/


title: snATAC-seq from GM12878 (ENCLB326EVB)

description:
https://www.encodeproject.org/experiments/ENCSR371ZNU/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line GM12878
experiment encode accession: ENCSR371ZNU
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB326EVB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens GM12878 cell line nuclear fraction

value: cell line

value: female

value: unknown

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: ATCC

value: ENCBS870LLN at ENCODE; https://www.encodeproject.org/ENCBS870LLN/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB516ODX)

description:
https://www.encodeproject.org/experiments/ENCSR961BYL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961BYL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB516ODX

source_name: Homo sapiens male adult (42 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS983EJZ at ENCODE; https://www.encodeproject.org/ENCBS983EJZ/


title: NDLN DN CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: NDLN_DN_rep2
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

value: Non-draining lymph node

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

tag: treatment

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19

tag: batch


title: total RNA-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB887OEP)

description:
https://www.encodeproject.org/experiments/ENCSR955OOH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR955OOH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB887OEP

source_name: Homo sapiens male adult (38 years) effector memory CD8-positive, alpha-beta T primary cell

tag: biosample encode accession

tag: encode accession

value: male

value: 38 year

value: ENCBS698PNQ at ENCODE; https://www.encodeproject.org/ENCBS698PNQ/


title: snATAC-seq from right lobe of liver (ENCLB733MWM)

description:
https://www.encodeproject.org/experiments/ENCSR364FHN/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human right lobe of liver
experiment encode accession: ENCSR364FHN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB733MWM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue, preserved by cryopreservation nuclear fraction

value: right lobe of liver

value: tissue

tag: description

value: Child biosample for Chang/Greenleaf lab

tag: Sex

value: female

tag: health state

value: DM:no; HTN:no; CAD:no

value: 41 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS914OMQ at ENCODE; https://www.encodeproject.org/ENCBS914OMQ/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB703XJX)

description:
https://www.encodeproject.org/experiments/ENCSR955XIA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR955XIA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB703XJX

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: dev stage

value: adult

tag: age

value: 40 year

tag: lab

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS397XGW at ENCODE; https://www.encodeproject.org/ENCBS397XGW/


title: NDLN DN CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: NDLN_DN_rep1
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

value: Non-draining lymph node

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB208ZKZ)

description:
https://www.encodeproject.org/experiments/ENCSR953MDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR953MDI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB208ZKZ

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: female

value: 34 year

tag: source

tag: link

value: ENCBS054MXW at ENCODE; https://www.encodeproject.org/ENCBS054MXW/


title: snATAC-seq from spleen (ENCLB064CLE)

description:
https://www.encodeproject.org/experiments/ENCSR363EAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human spleen
experiment encode accession: ENCSR363EAJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB064CLE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) spleen tissue, preserved by cryopreservation nuclear fraction

value: spleen

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS816WHM at ENCODE; https://www.encodeproject.org/ENCBS816WHM/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Control ChIP-seq from HepG2 (ENCLB126WNW)

description:
https://www.encodeproject.org/experiments/ENCSR943SJY/
***************
biological replicate number: 1
technical replicate number: 1
description: JUND ChIP-seq on HepG2 cells treated with control sgRNA
experiment encode accession: ENCSR943SJY
assay title: Control ChIP-seq
possible controls: ENCSR482BUK
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB126WNW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line

tag: antibody

value: JUND

value: cell line

tag: note

value: Homo sapiens HepG2 cell line transduced with doxycycline-inducible shRNA targeting FOXA3. Cells were treated for 72 hours with 4ug/mL doxycycline prior to experiment harvest.

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS510GKN at ENCODE; https://www.encodeproject.org/ENCBS510GKN/


title: DLN tdTomato+ CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: DLN_TDT_SP_rep2
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.

source_name: Draining lymph node

tag: tissue

value: Draining lymph node

tag: cell line

value: B16-F10 melanoma

tag: cell type

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB087YLT)

description:
https://www.encodeproject.org/experiments/ENCSR940NCC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR940NCC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB087YLT

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS594UPN at ENCODE; https://www.encodeproject.org/ENCBS594UPN/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB416KHQ)

description:
https://www.encodeproject.org/experiments/ENCSR940DDA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR940DDA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB416KHQ

value: female

value: 40 year

value: ENCBS142XNA at ENCODE; https://www.encodeproject.org/ENCBS142XNA/


title: snATAC-seq from posterior vena cava (ENCLB129ZXQ)

description:
https://www.encodeproject.org/experiments/ENCSR352RMS/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR716VLR).
experiment encode accession: ENCSR352RMS
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB129ZXQ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (26 years) posterior vena cava tissue, preserved by flash-freezing nuclear fraction

value: posterior vena cava

value: tissue

value: male

value: DM:no; HTN:no; CAD:no

value: 26 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS769AKF at ENCODE; https://www.encodeproject.org/ENCBS769AKF/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: DLN tdTomato+ CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: DLN_TDT_SP_rep1
Bulk ATAC-seq of FACS-isolated tdTomato+ CD8+ T cells.

value: Draining lymph node

value: B16-F10 melanoma

value: Sorted CD8+ T cells

tag: genotype

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

tag: treatment

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19

tag: batch


title: snATAC-seq from PC-9 (ENCLB493LAJ)

description:
https://www.encodeproject.org/experiments/ENCSR338KBR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338KBR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB493LAJ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens PC-9 cell line nuclear fraction

tag: line

value: cell line

tag: biosample encode accession

value: not collected

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS810TWF at ENCODE; https://www.encodeproject.org/ENCBS810TWF/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB928AUD)

description:
https://www.encodeproject.org/experiments/ENCSR932JIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR932JIV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB928AUD

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

tag: Sex

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS607ZRM at ENCODE; https://www.encodeproject.org/ENCBS607ZRM/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB422VPC)

description:
https://www.encodeproject.org/experiments/ENCSR934JNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR934JNT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB422VPC

value: female

tag: dev stage

tag: age

value: 40 year

value: ENCBS596LGH at ENCODE; https://www.encodeproject.org/ENCBS596LGH/


title: DLN LAG3-tdTomato+ CD8+ T cells ATAC-seq

description:
Library name: DLN_LAG3_SP_rep1
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato+ CD8+ T cells.

value: Draining lymph node

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB295QYE)

description:
https://www.encodeproject.org/experiments/ENCSR931NIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR931NIE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB295QYE

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: 38 year

tag: lab

tag: source

value: ENCBS432RIQ at ENCODE; https://www.encodeproject.org/ENCBS432RIQ/


title: snATAC-seq from psoas muscle (ENCLB704VBG)

description:
https://www.encodeproject.org/experiments/ENCSR332XEW/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on human psoas muscle. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR005TCL).
experiment encode accession: ENCSR332XEW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB704VBG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (47 years) psoas muscle tissue, preserved by flash-freezing nuclear fraction

value: psoas muscle

value: tissue

tag: health state

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS481BQH at ENCODE; https://www.encodeproject.org/ENCBS481BQH/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB863XQJ)

description:
https://www.encodeproject.org/experiments/ENCSR930GNS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR930GNS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB863XQJ

value: CD8-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS072ZHD at ENCODE; https://www.encodeproject.org/ENCBS072ZHD/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB576GCD)

description:
https://www.encodeproject.org/experiments/ENCSR928QLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR928QLV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB576GCD

source_name: Homo sapiens female adult (33 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: female

value: 33 year

value: ENCBS482UGK at ENCODE; https://www.encodeproject.org/ENCBS482UGK/


title: DLN DN CD8+ T cells ATAC-seq (replicate 2)

description:
Library name: DLN_DN_rep2
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

tag: tissue

value: Draining lymph node

value: B16-F10 melanoma

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: snATAC-seq from K562 (ENCLB227NCE)

description:
https://www.encodeproject.org/experiments/ENCSR332SXG/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line K562
experiment encode accession: ENCSR332SXG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB227NCE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens K562 cell line nuclear fraction

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: nucleus

value: ATCC

value: ENCBS991GWL at ENCODE; https://www.encodeproject.org/ENCBS991GWL/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB850TSC)

description:
https://www.encodeproject.org/experiments/ENCSR920XLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR920XLL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB850TSC

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS810BPG at ENCODE; https://www.encodeproject.org/ENCBS810BPG/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB781VLJ)

description:
https://www.encodeproject.org/experiments/ENCSR918XMD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR918XMD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB781VLJ

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 24 hours

value: female

value: 34 year

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS203DAR at ENCODE; https://www.encodeproject.org/ENCBS203DAR/


title: DLN DN CD8+ T cells ATAC-seq (replicate 1)

description:
Library name: DLN_DN_rep1
Bulk ATAC-seq of FACS-isolated LAG3- tdTomato- CD8+ T cells.

value: Draining lymph node

tag: cell line

value: B16-F10 melanoma

tag: cell type

value: Sorted CD8+ T cells

value: Lag3-iCreERT2 Rosa26-LSL-tdTomato

value: B16-F10 melanoma; tamoxifen (days 8-10); harvested Day 19


title: snATAC-seq from ovary (ENCLB411GCE)

description:
https://www.encodeproject.org/experiments/ENCSR322LEY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR322LEY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB411GCE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (61 years) ovary tissue, preserved by flash-freezing nuclear fraction

value: ovary

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS720BUN at ENCODE; https://www.encodeproject.org/ENCBS720BUN/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Control ChIP-seq from K562 (ENCLB319GKR)

description:
https://www.encodeproject.org/experiments/ENCSR915CFB/
***************
biological replicate number: 1
technical replicate number: 1
description: CEBPB ChIP-seq on K562 cells treated with vector control shRNA
experiment encode accession: ENCSR915CFB
assay title: Control ChIP-seq
possible controls: ENCSR402HVP
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB319GKR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: antibody

value: CEBPB

value: cell line

tag: note

value: Homo sapiens K562 cell line genetically modified using CRISPR via transient transfection. CEBPB locus was targeted using sgRNA.

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS436BLB at ENCODE; https://www.encodeproject.org/ENCBS436BLB/


title: total RNA-seq from T-cell (ENCLB138KNI)

description:
https://www.encodeproject.org/experiments/ENCSR910HYR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR910HYR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB138KNI

source_name: Homo sapiens male adult (38 years) T-cell primary cell

value: T-cell

value: primary cell

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS590VXV at ENCODE; https://www.encodeproject.org/ENCBS590VXV/


title: M16 Pool 2

city: Rochester

first: Regina

last: Rowe

state: NY

address: 601 Elmwood Ave, Box 850

institute: University of Rochester

description:
Library name: Sample34
1646 cells

data_processing:
Samples were demultiplexed and aligned using CellRanger Multi 6.0.2 using default parameters
Assembly: mm10-2020-A
Supplementary files format and content: h5 sample feature barcode matrix

source_name: MOE

extract_protocol:
On day 7, mice were euthanized by isoflurane inhalation and decapitation. The turbinates were then removed from the nasal cavity and collected in freshly prepared oxygenated Ringer’s solution containing 115 mM NaCl, 5 mM KCl, 2 mM MgCl2 hexahydrate, 2 mM CaCl2 dihydrate, 25 mM NaHCO3, 10 mM HEPES, and 10 mM glucose with a pH of 7.4 at 4°C. The olfactory epithelium was dissected from the turbinates, minced with fine forceps, then dissociated for 45 minutes at 37°C with tissue dissociation cocktail: dispase II (2 mg/mL), Collagenase Type 1 (2 mg/mL), Papain (0.25 mg/mL), and DNase (2 mg/mL) in Ringer’s solution). The reaction was terminated with Ringer’s-FBS (FBS-10%) and the cells were triturated, filtered, and centrifuged. The cell suspension was filtered once more through a 40-micrometer strainer, centrifuged, and resuspended in 500 μl of Ringer's solution. Dissociated single cell suspensions were used for single cell capture via 10x Genomics platform. Tissue harvesting, dissociations, and captures were repeated on subsequent days to perform the experiment on 8 total animals (1 male and 1 female for 4 conditions) in a sequencing experiment. Male and female mice were processed on subsequent days/batches. This experiment was performed twice for a total of 16 animals (8 male, 8 female, 4 per condition). In addition to the 16 exposed mice, we also included 2 male mice taken directly from the cage (no exposure) which were processed similarly. These mice (A1 and B1) in the data provided here were used only for cell clustering and not used for differential gene analysis.
Samples were barcoded using the 10x Genomics CellPlex cell hashing protocol per manufacturer’s recommendations (10x Genomics, Pleasanton, CA). Barcoded samples were pooled and captured on the 10x Genomics Chromium platform per manufacturer’s instructions. Pooled samples from 4 MOEs (one male or female from each exposure condition) were captured across 2 independent captures to facilitate sufficient cells per animal/sample and decrease batch effects. Total RNA was isolated, cDNA libraries constructed (single cell 3’ v3 protocol, 10x Genomics), and libraries were sequenced on the Illumina NovaSeq6000 (Illumina, San Diego, CA) for a target of 100,000 reads per cell for gene expression + 5000 reads per cell for the cell multiplexing libraries.

treatment_protocol: Wild-type male and female C57BL/6J mice (Strain #:000664) aged 6 weeks were kept in home cages with a reverse 12/12 hour light/dark cycle and had unlimited access to food and water. Prior to environmental olfactory exposure, mice were solo housed for 7 days. On day 0, mice were moved into a new home cage with a petri dish containing 8g of mouse bedding material (1/8" Performance Bedding, Biofresh) spiked with the treatment conditions.  Treatments were as follows: (A) water only (negative control), (B) 8g of soiled bedding material, (C) amyl acetate (0.5%) or (D) house dust mite (Dermatophagoides pteronyssinus extract, 2mg/mL). For aqueous solutions (water, amyl acetate, and HDM), 1mL was mixed with 8g of fresh mouse bedding. Soiled bedding used was from 8-week-old wild-type male and female BALB/cJ mice after 7 days of use and combined equally. For soiled bedding exposure, soiled bedding from 8-week-old wild-type male and female BALB/cJ (Strain #000651) mice was collected after 7 days and combined equally. For treatments using aqueous solutions, 1mL was mixed with the 8g of fresh mouse bedding. The mice underwent a cage change every two days (days 0, 2, 4, 6), accompanied with fresh stimulus material. The experiment was repeated in duplicate for a total of 16 mice (8 male, 8 female) with 4 per exposure condition.

value: MOE

tag: strain

tag: genotype

value: WT

tag: treatment

value: HDM

tag: batch


title: snATAC-seq from heart left ventricle (ENCLB492VHQ)

description:
https://www.encodeproject.org/experiments/ENCSR321AHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR321AHR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB492VHQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (62 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

tag: biosample encode accession

tag: Sex

tag: dev stage

value: 62 year

value: Michael Snyder, Stanford

value: Shin Lin

value: familial (EF 27%, LVEDD 6.5, LVPWd 0.85)

value: ENCBS878QCW at ENCODE; https://www.encodeproject.org/ENCBS878QCW/

value: Derived from ENCODE donor ENCDO110LFV; https://www.encodeproject.org/ENCDO110LFV/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB389HOD)

description:
https://www.encodeproject.org/experiments/ENCSR907DLX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR907DLX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB389HOD

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-15 for 24 hours

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

value: female

value: adult

tag: age

value: 34 year

tag: lab

tag: source

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS775DVO at ENCODE; https://www.encodeproject.org/ENCBS775DVO/


title: total RNA-seq from T-cell (ENCLB593XPX)

description:
https://www.encodeproject.org/experiments/ENCSR906TQE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906TQE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB593XPX

value: T-cell

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS199WNT at ENCODE; https://www.encodeproject.org/ENCBS199WNT/


title: M15 Pool 2

description:
Library name: Sample33
1542 cells

tag: tissue

value: MOE

value: WT


title: snATAC-seq from heart left ventricle (ENCLB359XOO)

description:
https://www.encodeproject.org/experiments/ENCSR320QOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR320QOP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB359XOO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (30 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

tag: health state

value: healthy

value: 30 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS117SFS at ENCODE; https://www.encodeproject.org/ENCBS117SFS/

value: Derived from ENCODE donor ENCDO377SFB; https://www.encodeproject.org/ENCDO377SFB/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB209LNZ)

description:
https://www.encodeproject.org/experiments/ENCSR905XYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR905XYH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB209LNZ

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 40 year

value: ENCBS064CPG at ENCODE; https://www.encodeproject.org/ENCBS064CPG/


title: M14 Pool 2

description:
Library name: Sample32
1628 cells

value: MOE

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB625BSE)

description:
https://www.encodeproject.org/experiments/ENCSR902DVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR902DVO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB625BSE

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-15 for 1 hour

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS924FMA at ENCODE; https://www.encodeproject.org/ENCBS924FMA/


title: snATAC-seq from heart left ventricle (ENCLB620MIY)

description:
https://www.encodeproject.org/experiments/ENCSR318ERF/
***************
biological replicate number: 1
technical replicate number: 1
description: Please note that this experiment is part of 10x multiome and has a corresponding snRNA experiment (ENCSR405YKM).
experiment encode accession: ENCSR318ERF
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB620MIY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (59 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: 59 year

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS544NEM at ENCODE; https://www.encodeproject.org/ENCBS544NEM/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB805THQ)

description:
https://www.encodeproject.org/experiments/ENCSR899YQW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR899YQW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB805THQ

source_name: Homo sapiens male adult (38 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: adult

value: 38 year

value: ENCBS483PIH at ENCODE; https://www.encodeproject.org/ENCBS483PIH/


title: M13 Pool 2

description:
Library name: Sample31
1457 cells

value: MOE

tag: strain

value: WT

value: male

value: water


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB466FBY)

description:
https://www.encodeproject.org/experiments/ENCSR898IYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR898IYQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB466FBY

value: CD4-positive, alpha-beta T cell

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS222KDV at ENCODE; https://www.encodeproject.org/ENCBS222KDV/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB122SCM)

description:
https://www.encodeproject.org/experiments/ENCSR887GNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR887GNN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB122SCM

value: ENCBS971IKR at ENCODE; https://www.encodeproject.org/ENCBS971IKR/


title: M16 Pool 1

description:
Library name: Sample30
1802 cells

tag: genotype

value: HDM


title: snATAC-seq from OCI-LY7 (ENCLB462AAA)

description:
https://www.encodeproject.org/experiments/ENCSR314WGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314WGW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB462AAA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens OCI-LY7 cell line nuclear fraction

tag: line

value: cell line

value: B cell lymphoma

value: 48 year

value: Mats Ljungman, UMichigan

value: nucleus

value: DSMZ

value: ENCBS895YOQ at ENCODE; https://www.encodeproject.org/ENCBS895YOQ/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: total RNA-seq from T-cell (ENCLB927MJJ)

description:
https://www.encodeproject.org/experiments/ENCSR872YOT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR872YOT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB927MJJ

source_name: Homo sapiens male adult (42 years) T-cell primary cell

value: T-cell

value: primary cell

value: adult

value: 42 year

value: ENCBS967LLK at ENCODE; https://www.encodeproject.org/ENCBS967LLK/


title: snATAC-seq from K562 (ENCLB662FMI)

description:
https://www.encodeproject.org/experiments/ENCSR308ZGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line K562
experiment encode accession: ENCSR308ZGJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB662FMI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS337EJK at ENCODE; https://www.encodeproject.org/ENCBS337EJK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: DMSO Vehicle-5

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
Library name: S15
LT-DMSO5
202507_InVitroCompiled_All_CPMTPM.xlsx

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Sequences were aligned to the GRCh38 using STAR v2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38 & GRCm39
Supplementary files format and content: 202507_InVitroCompiled_All_CPMTPM.xlsx file includes CPM/TPM values for each Samples, subsequent sheets include treatment group avarage CPM/TPM and DEG values.
Supplementary files format and content: 202507_InVivo_Human_genes_TPM file includes TPM values for each in vivo sample, subsequent sheets include treatment group avarage TPM and DEG values.

source_name: Adherent epithelial cells

extract_protocol:
Total RNA was extracted using  Qiagen RNeasy Kits for RNA Purification kit as per manufacturer recommendations (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent) / 5200 Fragment Analyzer.
S01~S15 and S65~84 sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit, S85~S96 sequencing libraries were generated using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD.

value: Adherent epithelial cells

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

tag: treatment

value: 0.1 % DMSO


title: M15 Pool 1

description:
Library name: Sample29
1765 cells

value: MOE

tag: Sex

value: male

tag: batch


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB714OSK)

description:
https://www.encodeproject.org/experiments/ENCSR872RMM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR872RMM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB714OSK

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-15 for 24 hours

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: dev stage

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS073UVV at ENCODE; https://www.encodeproject.org/ENCBS073UVV/


title: DMSO Vehicle-4

description:
Library name: S14
LT-DMSO4
202507_InVitroCompiled_All_CPMTPM.xlsx


title: snATAC-seq from ovary (ENCLB644QSO)

description:
https://www.encodeproject.org/experiments/ENCSR305VES/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR305VES
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB644QSO
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (41 years) ovary tissue, preserved by flash-freezing nuclear fraction

value: ovary

value: tissue

value: female

value: DM:no; HTN:no; CAD:no

value: adult

tag: age

value: 41 year

tag: lab

value: Michael Snyder, Stanford

value: nucleus

tag: source

value: Yiing Lin, MD, PhD

value: ENCBS034EPW at ENCODE; https://www.encodeproject.org/ENCBS034EPW/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: M14 Pool 1

description:
Library name: Sample28
1850 cells

tag: tissue

value: MOE

value: WT

value: male


title: total RNA-seq from T-cell (ENCLB407YOW)

description:
https://www.encodeproject.org/experiments/ENCSR869DEC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR869DEC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB407YOW

value: T-cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS319VEC at ENCODE; https://www.encodeproject.org/ENCBS319VEC/


title: snATAC-seq from heart left ventricle (ENCLB280ILV)

description:
https://www.encodeproject.org/experiments/ENCSR305KUV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR305KUV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB280ILV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (68 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: female

tag: health state

value: ischemic

value: 68 year

value: Shin Lin

value: ENCBS211LOV at ENCODE; https://www.encodeproject.org/ENCBS211LOV/

value: Derived from ENCODE donor ENCDO435KUZ; https://www.encodeproject.org/ENCDO435KUZ/


title: DMSO Vehicle-3

description:
Library name: S13
LT-DMSO3
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

tag: genotype

value: WT

value: 0.1 % DMSO


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB312IAL)

description:
https://www.encodeproject.org/experiments/ENCSR864ZKS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR864ZKS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB312IAL

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 34 year

value: ENCBS976JGC at ENCODE; https://www.encodeproject.org/ENCBS976JGC/


title: M13 Pool 1

description:
Library name: Sample27
1718 cells

value: MOE

tag: strain

value: male

value: water


title: snATAC-seq from GM23338 (ENCLB276RLS)

description:
https://www.encodeproject.org/experiments/ENCSR290IUT/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line PGP1
experiment encode accession: ENCSR290IUT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB276RLS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens GM23338 cell line nuclear fraction

tag: line

value: cell line

value: 53 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: George Church

value: ENCBS082FRV at ENCODE; https://www.encodeproject.org/ENCBS082FRV/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: DMSO Vehicle-2

description:
Library name: S12
LT-DMSO2
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

tag: treatment


title: F12 Pool 2

description:
Library name: Sample26
1378 cells

tag: Sex

value: female

value: HDM

tag: batch


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB238HWZ)

description:
https://www.encodeproject.org/experiments/ENCSR864XZO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR864XZO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB238HWZ

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: biosample encode accession

tag: encode accession

tag: dev stage

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS336ZNM at ENCODE; https://www.encodeproject.org/ENCBS336ZNM/


title: snATAC-seq from heart left ventricle (ENCLB357QOY)

description:
https://www.encodeproject.org/experiments/ENCSR288RQI/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR288RQI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB357QOY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (55 years) heart left ventricle tissue nuclear fraction

value: heart left ventricle

value: tissue

value: male

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

tag: age

value: 55 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Shin Lin

value: ENCBS381WWF at ENCODE; https://www.encodeproject.org/ENCBS381WWF/

value: Derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: DMSO Vehicle-1

description:
Library name: S11
LT-DMSO1
202507_InVitroCompiled_All_CPMTPM.xlsx

tag: tissue

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 0.1 % DMSO


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB912IOR)

description:
https://www.encodeproject.org/experiments/ENCSR864WDM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR864WDM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB912IOR

source_name: Homo sapiens male adult (38 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 38 year

tag: link

value: ENCBS642PZD at ENCODE; https://www.encodeproject.org/ENCBS642PZD/


title: F11 Pool 2

description:
Library name: Sample25
1450 cells

source_name: MOE

value: MOE

tag: genotype

value: female


title: 500nM Palbo-10

description:
Library name: S10
LT-PAL10
202507_InVitroCompiled_All_CPMTPM.xlsx

value: 500 nM Palbociclib isethionate


title: snATAC-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB015HPS)

description:
https://www.encodeproject.org/experiments/ENCSR287GYJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287GYJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB015HPS
fragmentation methods: sonication (Bioruptor Pico)
size range: 150-1000

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads nuclear fraction

value: male

value: 43 year

value: Yijun Ruan, JAX

value: nucleus

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS443FND at ENCODE; https://www.encodeproject.org/ENCBS443FND/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: F10 Pool 2

description:
Library name: Sample24
1425 cells

tag: strain

value: WT


title: total RNA-seq from T-helper 9 cell (ENCLB290CTB)

description:
https://www.encodeproject.org/experiments/ENCSR863GGC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863GGC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB290CTB

source_name: Homo sapiens female adult (25 years) T-helper 9 primary cell

value: T-helper 9 cell

value: 25 year

value: John Stamatoyannopoulos, UW

value: ENCBS668PLA at ENCODE; https://www.encodeproject.org/ENCBS668PLA/


title: snATAC-seq from heart left ventricle (ENCLB216SSF)

description:
https://www.encodeproject.org/experiments/ENCSR280RVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR280RVT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB216SSF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (43 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

tag: health state

value: healthy

value: adult

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS405VQS at ENCODE; https://www.encodeproject.org/ENCBS405VQS/

value: Derived from ENCODE donor ENCDO738SLM; https://www.encodeproject.org/ENCDO738SLM/


title: F9 Pool 2

description:
Library name: Sample23
1383 cells

value: MOE

value: female

value: water


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB507FXR)

description:
https://www.encodeproject.org/experiments/ENCSR859LMY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR859LMY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB507FXR

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 34 year

value: AllCells

value: ENCBS693CHX at ENCODE; https://www.encodeproject.org/ENCBS693CHX/