title: 500nM Palbo-9

description:
Library name: S09
LT-PAL9
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 500 nM Palbociclib isethionate


title: snATAC-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB544UMZ)

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/ENCSR278XIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR278XIZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB544UMZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male adult (43 years) naive thymus-derived CD4-positive, alpha-beta T primary cell nuclear fraction

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 43 year

tag: lab

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

tag: source

value: AllCells

tag: link

value: ENCBS074GDS at ENCODE; https://www.encodeproject.org/ENCBS074GDS/

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


title: 500nM Palbo-8

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: S08
LT-PAL8
202507_InVitroCompiled_All_CPMTPM.xlsx

library_source: transcriptomic

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.

molecule: total RNA

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.

tag: tissue

tag: genotype

tag: treatment


title: F12 Pool 1

city: Rochester

first: Regina

middle: K

last: Rowe

state: NY

address: 601 Elmwood Ave, Box 850

institute: University of Rochester

description:
Library name: Sample22
1550 cells

library_source: transcriptomic single cell

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

organism: Mus musculus

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

value: female

value: HDM

tag: batch


title: total RNA-seq from T-cell (ENCLB774OFJ)

description:
https://www.encodeproject.org/experiments/ENCSR858IYV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR858IYV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB774OFJ

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

value: T-cell

tag: encode accession

value: 42 year

value: John Stamatoyannopoulos, UW

value: ENCBS042MRY at ENCODE; https://www.encodeproject.org/ENCBS042MRY/


title: snATAC-seq from heart left ventricle (ENCLB916BMF)

description:
https://www.encodeproject.org/experiments/ENCSR277LDY/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR277LDY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB916BMF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (73 years) heart left ventricle tissue nuclear fraction

value: heart left ventricle

value: tissue

tag: health state

value: ischemic (EF 35%, LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: 73 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS287BPI at ENCODE; https://www.encodeproject.org/ENCBS287BPI/

value: Derived from ENCODE donor ENCDO804CLC; https://www.encodeproject.org/ENCDO804CLC/


title: 500nM Palbo-7

description:
Library name: S07
LT-PAL7
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

tag: cell line

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 500 nM Palbociclib isethionate


title: F11 Pool 1

description:
Library name: Sample21
1502 cells

value: MOE

value: female


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB825LHV)

description:
https://www.encodeproject.org/experiments/ENCSR857LPX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR857LPX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB825LHV

source_name: Homo sapiens male adult (24 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 24 year

value: AllCells

value: ENCBS204VHT at ENCODE; https://www.encodeproject.org/ENCBS204VHT/


title: snATAC-seq from pancreas (ENCLB797XUY)

description:
https://www.encodeproject.org/experiments/ENCSR275TWX/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human pancreas
experiment encode accession: ENCSR275TWX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB797XUY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: pancreas

value: tissue

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

value: child

value: 16 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS074RKO at ENCODE; https://www.encodeproject.org/ENCBS074RKO/

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


title: 500nM Palbo-6

description:
Library name: S06
LT-PAL6
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 500 nM Palbociclib isethionate


title: F10 Pool 1

description:
Library name: Sample20
1577 cells

value: MOE

value: female


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB807KIC)

description:
https://www.encodeproject.org/experiments/ENCSR855QFJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR855QFJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB807KIC

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

tag: biosample encode accession

value: adult

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS043MIO at ENCODE; https://www.encodeproject.org/ENCBS043MIO/


title: 500nM Palbo-5

description:
Library name: S05
LT-PAL5
202507_InVitroCompiled_All_CPMTPM.xlsx


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB838QNF)

description:
https://www.encodeproject.org/experiments/ENCSR855NNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR855NNT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB838QNF

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

tag: Sex

value: male

value: 42 year

value: ENCBS080HJH at ENCODE; https://www.encodeproject.org/ENCBS080HJH/


title: F9 Pool 1

description:
Library name: Sample19
1568 cells

value: water


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB740ISP)

description:
https://www.encodeproject.org/experiments/ENCSR854HMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR854HMF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB740ISP

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

tag: dev stage

value: 33 year

value: ENCBS066LNB at ENCODE; https://www.encodeproject.org/ENCBS066LNB/


title: 500nM Palbo-4

description:
Library name: S04
LT-PAL4
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: WT


title: 500nM Palbo-3

description:
Library name: S03
LT-PAL3
202507_InVitroCompiled_All_CPMTPM.xlsx

value: 500 nM Palbociclib isethionate


title: M3 Pool 1B

description:
Library name: Sample17
1928 cells

value: MOE


title: total RNA-seq from suppressor macrophage (ENCLB140IRD)

description:
https://www.encodeproject.org/experiments/ENCSR852WOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR852WOP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB140IRD

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

value: suppressor macrophage

value: primary cell

tag: age

value: 24 year

value: Shelly Heimfeld

value: ENCBS115FLX at ENCODE; https://www.encodeproject.org/ENCBS115FLX/


title: snATAC-seq from pancreas (ENCLB687VXL)

description:
https://www.encodeproject.org/experiments/ENCSR268LMV/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human pancreas
experiment encode accession: ENCSR268LMV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB687VXL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (47 years) pancreas tissue, preserved by cryopreservation nuclear fraction

value: pancreas

value: tissue

value: female

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

value: adult

value: 47 year

tag: lab

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS945AOX at ENCODE; https://www.encodeproject.org/ENCBS945AOX/

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


title: 500nM Palbo-2

description:
Library name: S02
LT-PAL2
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 500 nM Palbociclib isethionate


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB068EHE)

description:
https://www.encodeproject.org/experiments/ENCSR852CMR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR852CMR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB068EHE

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS734PQL at ENCODE; https://www.encodeproject.org/ENCBS734PQL/


title: snATAC-seq from T-helper 1 cell (ENCLB836XNG)

description:
https://www.encodeproject.org/experiments/ENCSR251LFB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR251LFB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB836XNG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (35 years) T-helper 1 primary cell treated with 1 ug/mL Interleukin-4 antibody, 30 ng/mL Interleukin-12 subunit alpha, 30 ng/mL Interleukin-12 subunit beta nuclear fraction

value: T-helper 1 cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

tag: subcellular fraction term name

tag: treatments

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein;

value: ENCBS706WTS at ENCODE; https://www.encodeproject.org/ENCBS706WTS/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: 500nM Palbo-1

description:
Library name: S01
LT-PAL1
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer


title: M1 Pool 1B

description:
Library name: Sample15
1530 cells

value: MOE

value: WT

value: water


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB646FWC)

description:
https://www.encodeproject.org/experiments/ENCSR851VJK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR851VJK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB646FWC

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: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 40 year

tag: source

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

tag: link

value: ENCBS252DZZ at ENCODE; https://www.encodeproject.org/ENCBS252DZZ/


title: snATAC-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB836HVE)

description:
https://www.encodeproject.org/experiments/ENCSR242VMQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR242VMQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB836HVE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (30 years) CD8-positive naive resting alpha-beta T primary cell nuclear fraction

value: male

value: adult

value: 30 year

value: AllCells

value: nucleus

value: ENCBS276ZZS at ENCODE; https://www.encodeproject.org/ENCBS276ZZS/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: M4 Pool 1A

description:
Library name: Sample14
1790 cells

tag: tissue

tag: genotype

value: HDM


title: DZIAhom_EryD_rep2

city: Oxford

first: Siyu

last: Liu

state: England

address: John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: DZIAhom_EryD_rep2

data_processing:
bowtie2 -k 2 --maxins 1000 (align to mm10) or bowtie2 -k 2 --minins 300 --maxins 600 (align to custome genome DZIA)
samtools view, sort, index
bamCoverage --binSize 20 --smoothLength 60 --normalizeUsing RPKM
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Cultured fetal liver cells

growth_protocol: Fetal livers were dissected from E12.5 mouse embryos, and the dissociated cells were expanded for up to 7 days in StemPro-34 (Invitrogen, 10639011) supplemented with GlutaMAX (Gibco), 100 U/mL Penicillin-Streptomycin (Gibco), 50 ng/mL mouse SCF (PeproTech), 1 U/mL erythropoietin (OUH hospital pharmacy) and 0.4 μg/mL dexamethasone (OUH hospital pharmacy). HSPCs were isolated by positive selection for CD117 using CD117 microbeads (Miltenyi Biotec) and cultured for at least 24 hours to allow erythroid differentiation.

extract_protocol:
ATAC-seq was performed following a published protocol (Buenrostro, 2013) using the Illumina Tagment DNA Enzyme and Buffer Kit. 10,000-50,000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to tagment reaction for 30 minutes at 37℃. Transposed DNA fragments were purified using a MinElute Kit (Qiagen).
Libraries were amplified and indexed using the Illumina Nextera index primers by PCR. Profiles were assessed using D1000 ScreenTape Assays (Agilent) and quantified using NEBNext Library Quant Kit for Illumina (NEB).

tag: sample group

value: Cultured fetal liver cells


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB401KJE)

description:
https://www.encodeproject.org/experiments/ENCSR849CMG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR849CMG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB401KJE

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

value: John Stamatoyannopoulos, UW

value: ENCBS302WUK at ENCODE; https://www.encodeproject.org/ENCBS302WUK/


title: DZIAhom_EryD_rep1

description: Library name: DZIAhom_EryD_rep1


title: M3 Pool 1A

description:
Library name: Sample13
2080 cells

value: MOE

tag: strain

value: WT

tag: treatment

tag: batch


title: total RNA-seq from T-cell (ENCLB450ZWS)

description:
https://www.encodeproject.org/experiments/ENCSR844IHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR844IHN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB450ZWS

source_name: Homo sapiens female adult (33 years) T-cell primary cell

value: T-cell

value: primary cell

tag: encode accession

value: female

value: 33 year

value: ENCBS916DNB at ENCODE; https://www.encodeproject.org/ENCBS916DNB/


title: snATAC-seq from heart left ventricle (ENCLB156FRX)

description:
https://www.encodeproject.org/experiments/ENCSR233KYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR233KYH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB156FRX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 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: nonischemic (EF 18%, LVEDD 6.8)

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS372CQB at ENCODE; https://www.encodeproject.org/ENCBS372CQB/

value: Derived from ENCODE donor ENCDO650FUH; https://www.encodeproject.org/ENCDO650FUH/


title: DZIAhom_EryP_rep2

description: Library name: DZIAhom_EryP_rep2

source_name: E10.5 primitive erythroblasts

tag: cell type

value: E10.5 primitive erythroblasts


title: M2 Pool 1A

description:
Library name: Sample12
1964 cells

source_name: MOE

value: MOE

value: WT

tag: Sex

value: male


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB593KSP)

description:
https://www.encodeproject.org/experiments/ENCSR843USK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR843USK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB593KSP

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

tag: biosample encode accession

tag: dev stage

tag: age

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS946FTS at ENCODE; https://www.encodeproject.org/ENCBS946FTS/


title: DZIAhom_EryP_rep1

description: Library name: DZIAhom_EryP_rep1


title: snATAC-seq from mesothelial cell of epicardium (ENCLB753DQQ)

description:
https://www.encodeproject.org/experiments/ENCSR231GXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR231GXD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB753DQQ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells nuclear fraction

value: mesothelial cell of epicardium

value: in vitro differentiated cells

value: WA09 derived epicardium (mesothelium)

value: female

value: healthy

value: embryonic

value: 5 day

tag: lab

value: Bradley Bernstein, Broad

tag: subcellular fraction term name

value: nucleus

value: SESCC

value: ENCBS262AKB at ENCODE; https://www.encodeproject.org/ENCBS262AKB/

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB088OPP)

description:
https://www.encodeproject.org/experiments/ENCSR838MLG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR838MLG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB088OPP

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: adult

value: 42 year

tag: source

tag: link

value: ENCBS927VLY at ENCODE; https://www.encodeproject.org/ENCBS927VLY/


title: snATAC-seq from pancreas (ENCLB165VJX)

description:
https://www.encodeproject.org/experiments/ENCSR229VVY/
***************
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 (ENCSR472RRP).
experiment encode accession: ENCSR229VVY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB165VJX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: pancreas

value: tissue

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS828VFV at ENCODE; https://www.encodeproject.org/ENCBS828VFV/

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


title: DZIAhet_EryD_rep2

description: Library name: DZIAhet_EryD_rep2

value: Cultured fetal liver cells


title: M1 Pool 1A

description:
Library name: Sample11
1538 cells

tag: tissue

value: MOE

tag: genotype

value: WT

value: water


title: F8 Pool 2B

description:
Library name: Sample10
1827 cells

tag: strain

value: female

value: HDM


title: total RNA-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB680CXX)

description:
https://www.encodeproject.org/experiments/ENCSR837NVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR837NVN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB680CXX

source_name: Homo sapiens female adult (33 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS163PSM at ENCODE; https://www.encodeproject.org/ENCBS163PSM/


title: snATAC-seq from K562 (ENCLB417HJU)

description:
https://www.encodeproject.org/experiments/ENCSR217VXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR217VXJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB417HJU
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens K562 cell line nuclear fraction

tag: line

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Mats Ljungman, UMichigan

value: nucleus

value: ATCC

value: ENCBS249EEJ at ENCODE; https://www.encodeproject.org/ENCBS249EEJ/

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


title: DZIAhet_EryD_rep1

description: Library name: DZIAhet_EryD_rep1

tag: sample group

value: Cultured fetal liver cells


title: F7 Pool 2B

description:
Library name: Sample9
1851 cells

value: MOE

value: WT

value: female

tag: treatment

tag: batch


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB461HXM)

description:
https://www.encodeproject.org/experiments/ENCSR834LNO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR834LNO
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB461HXM

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

tag: encode accession

value: male

value: adult

value: 42 year

value: ENCBS363IYS at ENCODE; https://www.encodeproject.org/ENCBS363IYS/


title: snATAC-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB831WTS)

description:
https://www.encodeproject.org/experiments/ENCSR207HVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR207HVA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB831WTS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (35 years) naive thymus-derived CD4-positive, alpha-beta T primary cell nuclear fraction

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS402MIH at ENCODE; https://www.encodeproject.org/ENCBS402MIH/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: DZIAhet_EryP_rep2

description: Library name: DZIAhet_EryP_rep2

tag: cell type

value: E10.5 primitive erythroblasts


title: F6 pool 2B

description:
Library name: Sample8
2004 cells

tag: Sex


title: total RNA-seq from T-cell (ENCLB284FTR)

description:
https://www.encodeproject.org/experiments/ENCSR827SLT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR827SLT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB284FTR

value: T-cell

tag: biosample encode accession

value: 33 year

value: John Stamatoyannopoulos, UW

value: ENCBS142KWH at ENCODE; https://www.encodeproject.org/ENCBS142KWH/


title: snATAC-seq from heart left ventricle (ENCLB544PBL)

description:
https://www.encodeproject.org/experiments/ENCSR273DAC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273DAC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB544PBL
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: dev stage

value: 62 year

value: Michael Snyder, Stanford

value: Shin Lin

tag: health state

value: viral->sarcoid (EF 15%, LVEDD 5.8, LVPWd 0.79)

value: ENCBS315KVT at ENCODE; https://www.encodeproject.org/ENCBS315KVT/

value: Derived from ENCODE donor ENCDO768WUT; https://www.encodeproject.org/ENCDO768WUT/


title: snATAC-seq from HCT116 (ENCLB005XVF)

description:
https://www.encodeproject.org/experiments/ENCSR270OJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR270OJH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB005XVF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A

value: cell line

value: male

value: colorectal carcinoma

value: adult

tag: age

value: 48 year

tag: lab

value: Dr. Masato Kanemaki

value: ENCBS376DVU at ENCODE; https://www.encodeproject.org/ENCBS376DVU/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: snATAC-seq from heart left ventricle (ENCLB055BZP)

description:
https://www.encodeproject.org/experiments/ENCSR270CUT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR270CUT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB055BZP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (63 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: 63 year

tag: source

value: sarcoid (EF 23%, LVEDD 5.7, LVPWd:0.68)

tag: link

value: ENCBS853VCN at ENCODE; https://www.encodeproject.org/ENCBS853VCN/

value: Derived from ENCODE donor ENCDO208BPU; https://www.encodeproject.org/ENCDO208BPU/


title: M4 Pool 1B

description:
Library name: Sample18
1757 cells

tag: tissue

value: MOE

tag: genotype

value: WT

value: HDM


title: DZIAhet_EryP_rep1

description: Library name: DZIAhet_EryP_rep1

value: E10.5 primitive erythroblasts


title: F5 Pool 2B

description:
Library name: Sample7
1702 cells

tag: strain

value: female

value: water


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB865DLU)

description:
https://www.encodeproject.org/experiments/ENCSR827MSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR827MSR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865DLU

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: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS057VQF at ENCODE; https://www.encodeproject.org/ENCBS057VQF/


title: snATAC-seq from placenta (ENCLB590LMV)

description:
https://www.encodeproject.org/experiments/ENCSR207ABL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR207ABL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB590LMV
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male embryo placenta tissue nuclear fraction

value: placenta

value: tissue

value: embryonic

value: not collected

tag: subcellular fraction term name

value: nucleus

value: John Stamatoyannopoulos

value: ENCBS241ZXP at ENCODE; https://www.encodeproject.org/ENCBS241ZXP/

value: Derived from ENCODE donor ENCDO384FEJ; https://www.encodeproject.org/ENCDO384FEJ/


title: snATAC-seq from adrenal gland (ENCLB889TFP)

description:
https://www.encodeproject.org/experiments/ENCSR205VFW/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human adrenal gland
experiment encode accession: ENCSR205VFW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB889TFP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (41 years) adrenal gland tissue, preserved by cryopreservation nuclear fraction

value: adrenal gland

value: female

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

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS728YNG at ENCODE; https://www.encodeproject.org/ENCBS728YNG/

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


title: SEAhom_EryD_rep2

description: Library name: SEAhom_EryD_rep2

source_name: Cultured fetal liver cells

tag: sample group

value: Cultured fetal liver cells


title: M2 Pool 1B

description:
Library name: Sample16
1934 cells

value: MOE

value: WT

value: male

tag: treatment

tag: batch


title: total RNA-seq from T-cell (ENCLB691HCJ)

description:
https://www.encodeproject.org/experiments/ENCSR826BSW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR826BSW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB691HCJ

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

value: T-cell

value: primary cell

tag: encode accession

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS146RSI at ENCODE; https://www.encodeproject.org/ENCBS146RSI/


title: snATAC-seq from HepG2 (ENCLB660SYP)

description:
https://www.encodeproject.org/experiments/ENCSR198TTU/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line HepG2
experiment encode accession: ENCSR198TTU
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB660SYP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens HepG2 cell line nuclear fraction

tag: line

value: cell line

tag: Sex

value: hepatocellular carcinoma

value: child

value: 15 year

value: nucleus

value: ATCC

value: ENCBS300DUB at ENCODE; https://www.encodeproject.org/ENCBS300DUB/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: F8 Pool 2A

description:
Library name: Sample6
1754 cells

source_name: MOE

value: MOE

value: female

value: HDM


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB634EAI)

description:
https://www.encodeproject.org/experiments/ENCSR825GMS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR825GMS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB634EAI

value: CD4-positive, alpha-beta T cell

tag: biosample encode accession

value: male

value: adult

value: ENCBS260IWM at ENCODE; https://www.encodeproject.org/ENCBS260IWM/


title: F7 Pool 2A

description:
Library name: Sample5
1681 cells

value: WT


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB021ZWO)

description:
https://www.encodeproject.org/experiments/ENCSR824HJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR824HJH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB021ZWO

value: CD8-positive, alpha-beta T cell

value: primary cell

tag: dev stage

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS832JLL at ENCODE; https://www.encodeproject.org/ENCBS832JLL/


title: SEAhom_EryD_rep1

description: Library name: SEAhom_EryD_rep1

tag: cell type

value: Cultured fetal liver cells


title: snATAC-seq from ovary (ENCLB478DVD)

description:
https://www.encodeproject.org/experiments/ENCSR197GLE/
***************
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 (ENCSR938CZJ).
experiment encode accession: ENCSR197GLE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB478DVD
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female adult (46 years) ovary tissue, preserved by flash-freezing nuclear fraction

value: ovary

value: tissue

tag: health state

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

tag: age

value: 46 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS857ABX at ENCODE; https://www.encodeproject.org/ENCBS857ABX/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: F6 pool 2A

description:
Library name: Sample4
1856 cells

value: MOE

value: WT

value: female


title: WT_EryD_rep2

description: Library name: WT_EryD_rep2


title: snATAC-seq from adrenal gland (ENCLB659VUK)

description:
https://www.encodeproject.org/experiments/ENCSR194KHA/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on human adrenal gland. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR726IPC).
experiment encode accession: ENCSR194KHA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB659VUK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (59 years) adrenal gland tissue, preserved by flash-freezing nuclear fraction

value: adrenal gland

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

value: adult

value: 59 year

tag: lab

tag: source

value: ENCBS291MOC at ENCODE; https://www.encodeproject.org/ENCBS291MOC/

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


title: WT_EryD_rep1

description: Library name: WT_EryD_rep1

value: Cultured fetal liver cells


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB704PGQ)

description:
https://www.encodeproject.org/experiments/ENCSR823OVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR823OVQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB704PGQ

value: CD4-positive, alpha-beta T cell

value: primary cell

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS233ICQ at ENCODE; https://www.encodeproject.org/ENCBS233ICQ/


title: F5 Pool 2A

description:
Library name: Sample3
1666 cells

tag: tissue

value: MOE

tag: genotype

value: water


title: Control ChIP-seq from K562 (ENCLB845WBX)

description:
https://www.encodeproject.org/experiments/ENCSR194GTV/
***************
biological replicate number: 1
technical replicate number: 1
description: Input for K562 cells treated with sgRNA targeting CEBPB
experiment encode accession: ENCSR194GTV
assay title: Control ChIP-seq
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB845WBX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (deletion) using CRISPR targeting H. sapiens CEBPB

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS115SWR at ENCODE; https://www.encodeproject.org/ENCBS115SWR/


title: total RNA-seq from inflammatory macrophage (ENCLB830FJD)

description:
https://www.encodeproject.org/experiments/ENCSR951TBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR951TBV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB830FJD

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

value: inflammatory macrophage

value: adult

value: 24 year

value: Shelly Heimfeld

value: ENCBS321WJA at ENCODE; https://www.encodeproject.org/ENCBS321WJA/


title: snATAC-seq from A549 (ENCLB195FQY)

description:
https://www.encodeproject.org/experiments/ENCSR237BTV/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line A549
experiment encode accession: ENCSR237BTV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB195FQY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens A549 cell line nuclear fraction

value: male

value: 58 year

tag: subcellular fraction term name

value: nucleus

value: ENCBS361UYS at ENCODE; https://www.encodeproject.org/ENCBS361UYS/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: B1 Mouse2 left BC

description:
Library name: Sample2
3666 cells

value: MOE

tag: strain

value: WT

value: no exposure


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB886PEI)

description:
https://www.encodeproject.org/experiments/ENCSR821QTU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR821QTU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB886PEI

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: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS731BYN at ENCODE; https://www.encodeproject.org/ENCBS731BYN/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB860ALT)

description:
https://www.encodeproject.org/experiments/ENCSR819DXL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR819DXL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB860ALT

value: CD4-positive, alpha-beta T cell

value: adult

value: ENCBS402GZV at ENCODE; https://www.encodeproject.org/ENCBS402GZV/


title: snATAC-seq from spleen (ENCLB319VZW)

description:
https://www.encodeproject.org/experiments/ENCSR188TJX/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human spleen
experiment encode accession: ENCSR188TJX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB319VZW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (59 years) spleen tissue, preserved by cryopreservation nuclear fraction

value: spleen

value: tissue

value: female

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS815EBK at ENCODE; https://www.encodeproject.org/ENCBS815EBK/

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB836SNL)

description:
https://www.encodeproject.org/experiments/ENCSR635VLR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR635VLR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB836SNL

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

value: primary cell

value: 34 year

value: ENCBS856JQP at ENCODE; https://www.encodeproject.org/ENCBS856JQP/


title: total RNA-seq from suppressor macrophage (ENCLB651ENJ)

description:
https://www.encodeproject.org/experiments/ENCSR484FKM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR484FKM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB651ENJ
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens male adult (40 years) suppressor macrophage primary cell

value: suppressor macrophage

value: male

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS480GNW at ENCODE; https://www.encodeproject.org/ENCBS480GNW/


title: F-5

city: qingdao

first: shijie

last: bi

address: No. 23, Hong Kong East Road

country: China

institute: ouc

description:
Library name: sample30
Column name in counts_allsamples.txt: F-5

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples
Differential expression analysis was performed using the DESeq25
Assembly: NCBI_GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Tumor

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
First, use the Single Cell Full Length mRNA-Amplification Kit to reverse transcribe and amplify RNA. For the cDNA that passes the quality inspection, use the cDNATruePrep DNA Library Prep Kit V2 for Illumina to construct the library in accordance with the instructions.

value: Tumor

tag: cell line

value: melanoma cell

value: WT

tag: treatment

value: Day 10


title: MO100-CGND-HRA-02982-ATAC

city: New York

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: MO100-CGND-HRA-02982-ATAC

library_source: genomic single cell

data_processing:
Sequenced 10x libraries were aligned to a standard reference genome (hg38; GENCODE v32/Ensembl98) and counted (Cellranger-ARC v2.0.2). ATAC peaks were aligned between samples for quantification (Cellranger-ARC aggr v2.0.2)
Assembly: hg38
Supplementary files format and content: atac_fragments.tsv
Supplementary files format and content: gex_molecule_info.h5
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: per_barcode_metrics.csv

extract_protocol:
Nuclei isolation protocol was adapted from previously described methods (PMID: 31042697; PMID: 36385529). All procedures were carried out on ice unless otherwise stated. Frozen post-mortem brain tissue was retrieved from storage at -80 °C and equilibrated on dry ice for 20–30 minutes before being transferred to a cryostat at -18 °C. Tissue samples were left for 15–20 minutes inside the cryostat before sectioning. We collected 20-50 mg of tissue per preparation, taking care to avoid excessive sampling of white matter. Tissue cuts were placed in a pre-chilled Dounce homogenizer containing 700 µL of ice-cold homogenization buffer (320 mM sucrose, 5 mM CaCl2 [#21115; Millipore Sigma], 3 mM magnesium acetate [#63052; Millipore Sigma], 10 mM Tris HCl [pH 7.8; prepared from Thermo Fisher’s #AM9850G and #AM9855G], 0.1 mM EDTA [pH 8.0; Thermo Fisher #AM9260G], 0.1% IGEPAL CA-630 [#I8896; Millipore Sigma], 1 mM DTT [#646563, Millipore Sigma], and 0.4 U/µl Protector RNase inhibitor [#03335402001, Millipore Sigma]). Homogenization was performed with 10 strokes of the loose pestle followed by 10 strokes of the tight pestle. After a 5-minute incubation on ice, the homogenized tissue was passed through a 70-µm Flowmi Cell Strainer (Bel-Art; H13680-0070) and combined with an equal volume of a solution made of 50% OptiPrep (#07820, STEMCELL Technologies), 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), and 1 mM DTT. Using a 15-mL conical tube, this mixture was then layered onto a density gradient made up of 750 µL of a 30% OptiPrep solution supplemented with 134 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.04% IGEPAL CA-630, and 0.17 U µl−1 RNase inhibitor) over 300 µL of 40% OptiPrep solution supplemented with 96 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 10 mM Tris HCl (pH 7.8), 0.1 mM EDTA (pH 8.0), 1 mM DTT, 0.03% IGEPAL CA-630, and 0.12 U µl−1 RNase inhibitor. Nuclei were separated by centrifugation at 3,000 × g for 20 minutes at 4 °C using a pre-chilled swinging-bucket rotor with the brake off. Approximately 150 µL of nuclei were collected from the 30%/40% gradient interphase and subsequently washed in PBS containing 1% BSA and 1 U µl-1 RNase inhibitor. Following a 5-minute incubation on ice, the nuclei were centrifuged at 450 × g for 3 minutes at 4 °C, and the pellet resuspended in 15 µL of diluted 10X Genomics Nuclei Buffer. Nuclei counting was performed using a Countess II FL instrument (Thermo Fisher) by staining with SYTOX Green (ThermoFisher; S7020). Additional quality control measures included Trypan Blue staining (#EBT-001, NanoEntek) to evaluate adequate permeabilization (cutoff: >95% of ‘dead cells’) and the assessment of nuclear morphology before proceeding with transposition.
Matched snRNA-seq and snATAC-seq libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (#PN-1000283) according to the protocol provided by 10X Genomics. Nuclei (16,100 per reaction; targeted recovery: 10,000 nuclei) from a single donor were used for each library preparation. Partitioning of nuclei was performed on a Chromium X instrument (10X Genomics). Quality control of cDNAs and libraries was conducted using Agilent High Sensitivity DNA Kits and a BioAnalyzer instrument. Final library quantification prior to pooling utilized KAPA Biosystems’ Library Quantification Kit for Illumina Platforms (KK4824). Libraries were sequenced on a NovaSeq X system using a 2 × 100 bp configuration run on a 10B flow cell. BA44/45 and BA46 libraries (n = 48) were prepared and sequenced in independent batches.

value: ALS

tag: pmi

value: F

tag: age at_death

tag: age at_symptom_onset

tag: site of_motor_onset

value: Bulbar and Limb


title: MO111-CGND-HRA-02454-ATAC

description: Library name: MO111-CGND-HRA-02454-ATAC

tag: Sex

value: Bulbar


title: total RNA-seq from HG03470 (ENCLB548NQW)

description:
https://www.encodeproject.org/experiments/ENCSR318BOT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR318BOT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB548NQW
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03470 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: note

value: HG03470 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

tag: dev stage

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS590LWQ at ENCODE; https://www.encodeproject.org/ENCBS590LWQ/


title: snATAC-seq from heart left ventricle (ENCLB573PHN)

description:
https://www.encodeproject.org/experiments/ENCSR185NXG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR185NXG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB573PHN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (50 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: age

value: 50 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Shin Lin

tag: health state

value: healthy

tag: link

value: ENCBS966QMB at ENCODE; https://www.encodeproject.org/ENCBS966QMB/

value: Derived from ENCODE donor ENCDO166SII; https://www.encodeproject.org/ENCDO166SII/


title: total RNA-seq from HG03271 (ENCLB608ZAK)

description:
https://www.encodeproject.org/experiments/ENCSR306XSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306XSI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB608ZAK
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03271 cell line

value: HG03271 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: ENCBS854YGA at ENCODE; https://www.encodeproject.org/ENCBS854YGA/


title: total RNA-seq from GM19390 (ENCLB091UXX)

description:
https://www.encodeproject.org/experiments/ENCSR305RZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR305RZD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB091UXX
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19390 cell line

value: cell line

value: GM19390 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: ENCBS337PPJ at ENCODE; https://www.encodeproject.org/ENCBS337PPJ/


title: A1 Mouse1 left BC

description:
Library name: Sample1
3865 cells

tag: tissue

value: MOE

tag: strain

tag: genotype

value: WT

tag: treatment

value: no exposure

tag: batch


title: snATAC-seq from mucosa of descending colon (ENCLB961PDO)

description:
https://www.encodeproject.org/experiments/ENCSR181TLD/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR181TLD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB961PDO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (40 years) mucosa of descending colon tissue, preserved by cryopreservation nuclear fraction

value: mucosa of descending colon

value: tissue

tag: Sex

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

value: adult

value: 40 year

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS466ZEW at ENCODE; https://www.encodeproject.org/ENCBS466ZEW/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB225VHZ)

description:
https://www.encodeproject.org/experiments/ENCSR817PKK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR817PKK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB225VHZ

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

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS147RTQ at ENCODE; https://www.encodeproject.org/ENCBS147RTQ/


title: total RNA-seq from suppressor macrophage (ENCLB253WTR)

description:
https://www.encodeproject.org/experiments/ENCSR353EHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR353EHP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB253WTR

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

value: suppressor macrophage

tag: encode accession

value: 24 year

value: Shelly Heimfeld

value: ENCBS429QLK at ENCODE; https://www.encodeproject.org/ENCBS429QLK/


title: snATAC-seq from ovary (ENCLB006MFK)

description:
https://www.encodeproject.org/experiments/ENCSR180GUX/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human ovary
experiment encode accession: ENCSR180GUX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB006MFK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (46 years) ovary tissue, preserved by cryopreservation nuclear fraction

value: ovary

value: tissue

value: female

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

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: ENCBS510XFX at ENCODE; https://www.encodeproject.org/ENCBS510XFX/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB934XNX)

description:
https://www.encodeproject.org/experiments/ENCSR808TUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR808TUZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB934XNX

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

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 33 year

value: ENCBS313BQZ at ENCODE; https://www.encodeproject.org/ENCBS313BQZ/


title: F-4

description:
Library name: sample29
Column name in counts_allsamples.txt: F-4

value: Tumor

tag: cell line

tag: cell type

value: melanoma cell

value: WT

value: Day 10


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB887DUO)

description:
https://www.encodeproject.org/experiments/ENCSR341NVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341NVL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB887DUO

value: CD4-positive, alpha-beta T cell

tag: dev stage

value: 34 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS558YQN at ENCODE; https://www.encodeproject.org/ENCBS558YQN/


title: F-3

description:
Library name: sample28
Column name in counts_allsamples.txt: F-3


title: GATA1_DM_HDP2_day8

description: Library name: GATA1_DM_HDP2_day8

data_processing:
bowtie2 -k 2 --maxins 1000
samtools view, sort, index
bamCoverage --binSize 20 --smoothLength 60 --normalizeUsing RPKM
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: HUDEP-2 cells were maintained in the expansion phase using StemSpan SFEM medium (Stem Cell Technologies) supplemented with GlutaMAX (Gibco), 100 U/mL Penicillin-Streptomycin (Gibco), 3 U/mL erythropoietin (OUH hospital pharmacy), 0.4 μg/mL dexamethasone (OUH hospital pharmacy), 50 ng/mL human SCF (PeproTech) and 2 μg/mL doxycycline (Sigma-Aldrich) at 37 ℃ with 5% CO2 incubation. To induce erythroid differentiation, cells were transferred to IMDM with GlutaMAX (Gibco) supplemented with 3% human AB plasma (NHSBT), 2% fetal bovine serum (Gibco), 100 U/mL Penicillin-Streptomycin (Gibco), 200 μg/mL holo-transferrin (Sigma-Aldrich), 3 U/mL heparin (Sigma-Aldrich), 10 μg/mL insulin (Sigma-Aldrich), 3 U/mL erythropoietin (OUH hospital pharmacy), 10 ng/mL human SCF (PeproTech), 1 ng/mL human IL-3 (PeproTech) and 2 μg/mL doxycycline (Sigma-Aldrich). After 5 days, SCF, IL-3 and doxycycline were removed from the media, and cells were then cultured with a high holo-transferrin concentration (500 μg/mL) for a further 3 days prior to experiments.

extract_protocol:
ATAC-seq was performed following a published protocol (Buenrostro, 2013) using the Illumina Tagment DNA Enzyme and Buffer Kit. 10,000-50,000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to tagment reaction for 30 minutes at 37℃. Transposed DNA fragments were purified using a MinElute Kit (Qiagen). ChIPmentation experiments were performed as previously described (Schmidl, 2015) with modifications. On day 8 of erythroid differentiation, 100,000-1,000,000 HUDEP-2 cells were fixed with 2 mM disuccinimidyl glutarate (DSG) for 30 minutes, followed by 1% formaldehyde for 10 minutes, then quenched with 125 mM glycine. Fixed cell pellets were washed with PBS, then lysed in cold lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA and 0.5% SDS) for 30 minutes on ice. The lysate was sonicated with the Covaris ME220 Focused-ultrasonicator to shear the DNA into ~200-300 bp fragments. The sonicate was neutralised with 1% Triton X-100 and incubated overnight with Dynabeads protein A and G (Invitrogen) and 5 μg GATA1 antibody (Abcam, ab181544). Chromatin-bound beads were washed three times using a low salt, a high salt and a LiCl-containing wash buffer, followed by on-bead tagmentation of the immunoprecipitated chromatin using Tagment DNA enzyme (Illumina). Samples were washed with 10 mM Tris-HCl before library preparation.
Libraries were amplified and indexed using the Illumina Nextera index primers by PCR. Profiles were assessed using D1000 ScreenTape Assays (Agilent) and quantified using NEBNext Library Quant Kit for Illumina (NEB).

value: Erythroblasts

value: Double Mutant

tag: chip antibody


title: F-2

description:
Library name: sample27
Column name in counts_allsamples.txt: F-2


title: GATA1_WT_HDP2_day8

description: Library name: GATA1_WT_HDP2_day8


title: snATAC-seq from heart left ventricle (ENCLB986YTL)

description:
https://www.encodeproject.org/experiments/ENCSR175JHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR175JHG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB986YTL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (39 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: male

value: healthy

value: adult

tag: age

value: 39 year

tag: lab

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS671QYO at ENCODE; https://www.encodeproject.org/ENCBS671QYO/

value: Derived from ENCODE donor ENCDO266KDE; https://www.encodeproject.org/ENCDO266KDE/


title: snATAC-seq from heart left ventricle (ENCLB319DHL)

description:
https://www.encodeproject.org/experiments/ENCSR173UUN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR173UUN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB319DHL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (65 years) heart left ventricle tissue, preserved by flash-freezing

tag: health state

value: ischemic (EF 5%)

value: 65 year

tag: source

tag: link

value: ENCBS198GNK at ENCODE; https://www.encodeproject.org/ENCBS198GNK/

value: Derived from ENCODE donor ENCDO187SDN; https://www.encodeproject.org/ENCDO187SDN/


title: snATAC-seq from MCF-7 (ENCLB303YGG)

description:
https://www.encodeproject.org/experiments/ENCSR176EJL/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line MCF-7
experiment encode accession: ENCSR176EJL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB303YGG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens MCF-7 cell line nuclear fraction

tag: line

value: cell line

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: nucleus

value: ATCC

value: ENCBS060FMS at ENCODE; https://www.encodeproject.org/ENCBS060FMS/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB038OYY)

description:
https://www.encodeproject.org/experiments/ENCSR806QZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR806QZX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB038OYY

value: CD8-positive, alpha-beta T cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS521GXX at ENCODE; https://www.encodeproject.org/ENCBS521GXX/


title: F-1

description:
Library name: sample26
Column name in counts_allsamples.txt: F-1

tag: tissue

value: Tumor

value: melanoma cell

tag: genotype

value: WT

tag: treatment

value: Day 10


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB869LIY)

description:
https://www.encodeproject.org/experiments/ENCSR808PWT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR808PWT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB869LIY

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

value: CD4-positive, alpha-beta T cell

tag: Sex

value: male

value: 38 year

value: ENCBS838EGT at ENCODE; https://www.encodeproject.org/ENCBS838EGT/


title: total RNA-seq from T-cell (ENCLB401UVJ)

description:
https://www.encodeproject.org/experiments/ENCSR802LWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR802LWN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB401UVJ

source_name: Homo sapiens female adult (33 years) T-cell primary cell

value: T-cell

tag: biosample encode accession

value: female

value: ENCBS514AWC at ENCODE; https://www.encodeproject.org/ENCBS514AWC/


title: snATAC-seq from heart right ventricle (ENCLB499ZOK)

description:
https://www.encodeproject.org/experiments/ENCSR169BCG/
***************
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 (ENCSR426PDU).
experiment encode accession: ENCSR169BCG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB499ZOK
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: heart right ventricle

value: tissue

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

value: 41 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS735VCK at ENCODE; https://www.encodeproject.org/ENCBS735VCK/

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


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB015NPD)

description:
https://www.encodeproject.org/experiments/ENCSR794BSV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR794BSV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB015NPD

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

tag: encode accession

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS860GMX at ENCODE; https://www.encodeproject.org/ENCBS860GMX/


title: E-5

description:
Library name: sample25
Column name in counts_allsamples.txt: E-5

source_name: Tumor

value: Tumor

tag: cell line

tag: cell type

value: melanoma cell

value: WT

value: VPE-PTEN+RG-NPs

tag: batch

value: Day 10


title: SEAhom_DM_HDP2_day8

description: Library name: SEAhom_DM_HDP2_day8

value: Erythroblasts

value: SEAhom Double Mutant


title: SEAhom_HDP2_day8

description: Library name: SEAhom_HDP2_day8

value: SEAhom


title: E-4

description:
Library name: sample24
Column name in counts_allsamples.txt: E-4


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB438XZL)

description:
https://www.encodeproject.org/experiments/ENCSR791VCC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR791VCC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB438XZL

value: female

tag: dev stage

value: 33 year

value: ENCBS069TZS at ENCODE; https://www.encodeproject.org/ENCBS069TZS/


title: WT_HDP2_day8

description: Library name: WT_HDP2_day8


title: E-3

description:
Library name: sample23
Column name in counts_allsamples.txt: E-3


title: total RNA-seq from T-cell (ENCLB565WTN)

description:
https://www.encodeproject.org/experiments/ENCSR789XGM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR789XGM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB565WTN

source_name: Homo sapiens male adult (38 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours

value: T-cell

value: primary cell

value: male

tag: age

value: 38 year

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour;

value: ENCBS409UGA at ENCODE; https://www.encodeproject.org/ENCBS409UGA/


title: snATAC-seq from activated CD8-positive, alpha-beta T cell (ENCLB632KXR)

description:
https://www.encodeproject.org/experiments/ENCSR154JHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154JHG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB632KXR
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads nuclear fraction

value: adult

value: 21 year

tag: lab

value: Yijun Ruan, JAX

value: nucleus

value: AllCells

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

value: ENCBS309DKJ at ENCODE; https://www.encodeproject.org/ENCBS309DKJ/

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


title: total RNA-seq from T-cell (ENCLB148DAU)

description:
https://www.encodeproject.org/experiments/ENCSR789HHB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR789HHB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB148DAU

source_name: Homo sapiens male adult (42 years) T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours

value: 42 year

value: John Stamatoyannopoulos, UW

tag: source

value: ENCBS534ICV at ENCODE; https://www.encodeproject.org/ENCBS534ICV/


title: MCF7 500nM Senexin 631 and 500nM Palbociclib-3

description:
Library name: S96
ST-SNX3
202507_InVitroCompiled_All_CPMTPM.xlsx

source_name: Adherent epithelial cells

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 500 nM SNX631 + 500 nM Palbociclib isethionate


title: E-2

description:
Library name: sample22
Column name in counts_allsamples.txt: E-2

value: Tumor

value: melanoma cell

value: VPE-PTEN+RG-NPs

value: Day 10


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB067BZX)

description:
https://www.encodeproject.org/experiments/ENCSR789GYR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR789GYR
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB067BZX

value: CD8-positive, alpha-beta T cell

value: primary cell

value: female

value: adult

value: 33 year

tag: link

value: ENCBS123TTG at ENCODE; https://www.encodeproject.org/ENCBS123TTG/


title: snATAC-seq from osteocyte (ENCLB337SFT)

description:
https://www.encodeproject.org/experiments/ENCSR146VJA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146VJA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB337SFT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (5 days) osteocyte in vitro differentiated cells nuclear fraction

value: osteocyte

value: in vitro differentiated cells

tag: description

value: WA09 derived osteocytes

tag: health state

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: nucleus

value: SESCC

value: ENCBS552YWP at ENCODE; https://www.encodeproject.org/ENCBS552YWP/

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


title: MCF7 500nM Senexin 631 and 500nM Palbociclib-1

description:
Library name: S94
ST-SNX1
202507_InVitroCompiled_All_CPMTPM.xlsx

tag: tissue

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

tag: genotype

value: WT

value: 500 nM SNX631 + 500 nM Palbociclib isethionate


title: D-5

description:
Library name: sample20
Column name in counts_allsamples.txt: D-5

value: Tumor

value: melanoma cell

tag: treatment

value: RG-NPs

value: Day 10


title: MCF7 500nM Senexin 631 and 500nM Palbociclib-2

description:
Library name: S95
ST-SNX2
202507_InVitroCompiled_All_CPMTPM.xlsx


title: total RNA-seq from GM19403 (ENCLB640VTB)

description:
https://www.encodeproject.org/experiments/ENCSR295MME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR295MME
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB640VTB
nucleic acid starting quantity: 21
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19403 cell line

tag: line

value: cell line

tag: biosample encode accession

tag: note

value: GM19403 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: Sex

value: female

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS096OAZ at ENCODE; https://www.encodeproject.org/ENCBS096OAZ/


title: MO097-U54-HRA-138-ATAC

description: Library name: MO097-U54-HRA-138-ATAC

value: Control

tag: pmi

value: F

tag: age at_death


title: total RNA-seq from GM18507 (ENCLB504ICG)

description:
https://www.encodeproject.org/experiments/ENCSR284QGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR284QGB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB504ICG
nucleic acid starting quantity: 52
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18507 cell line

tag: encode accession

value: GM18507 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: male

tag: dev stage

value: ENCBS283XDW at ENCODE; https://www.encodeproject.org/ENCBS283XDW/


title: U54-HRA-135-A1-ATAC

description: Library name: U54-HRA-135-A1-ATAC

value: M


title: Control ChIP-seq from HepG2 (ENCLB265XRH)

description:
https://www.encodeproject.org/experiments/ENCSR142JFU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input for HepG2 cells treated with shRNA targeting FOXA3
experiment encode accession: ENCSR142JFU
assay title: Control ChIP-seq
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB265XRH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line expressing RNAi targeting H. sapiens FOXA3

value: hepatocellular carcinoma

value: child

tag: age

value: 15 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS781CUL at ENCODE; https://www.encodeproject.org/ENCBS781CUL/


title: MCF7 500nM Palbociclib-3

description:
Library name: S93
ST-SNXPAL3
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 500 nM Palbociclib isethionate


title: total RNA-seq from T-cell (ENCLB443VLF)

description:
https://www.encodeproject.org/experiments/ENCSR788RFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR788RFN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB443VLF

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

value: T-cell

value: primary cell

value: adult

value: 38 year

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: AllCells

tag: link

value: ENCBS688EZP at ENCODE; https://www.encodeproject.org/ENCBS688EZP/


title: total RNA-seq from HG03464 (ENCLB679HBJ)

description:
https://www.encodeproject.org/experiments/ENCSR283BQG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR283BQG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB679HBJ
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03464 cell line

value: cell line

value: HG03464 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS422LXN at ENCODE; https://www.encodeproject.org/ENCBS422LXN/


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB536ZOB)

description:
https://www.encodeproject.org/experiments/ENCSR787QLY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR787QLY
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB536ZOB

value: CD8-positive, alpha-beta T cell

value: male

value: 42 year

value: ENCBS556ZXP at ENCODE; https://www.encodeproject.org/ENCBS556ZXP/


title: snATAC-seq from left lobe of liver (ENCLB633SCX)

description:
https://www.encodeproject.org/experiments/ENCSR139ATR/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on left lobe of liver Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR369UFT).
experiment encode accession: ENCSR139ATR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB633SCX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (45 years) left lobe of liver tissue nuclear fraction

value: left lobe of liver

value: tissue

tag: health state

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

value: 45 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS344HUA at ENCODE; https://www.encodeproject.org/ENCBS344HUA/

value: Derived from ENCODE donor ENCDO757VPQ; https://www.encodeproject.org/ENCDO757VPQ/


title: MCF7 500nM Palbociclib-2

description:
Library name: S92
ST-SNXPAL2
202507_InVitroCompiled_All_CPMTPM.xlsx

tag: tissue

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

tag: genotype

value: WT

tag: treatment

value: 500 nM Palbociclib isethionate


title: snATAC-seq from pancreas (ENCLB788PNL)

description:
https://www.encodeproject.org/experiments/ENCSR137FPX/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human pancreas
experiment encode accession: ENCSR137FPX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB788PNL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (41 years) pancreas tissue, preserved by cryopreservation nuclear fraction

value: pancreas

tag: biosample encode accession

value: female

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

value: adult

value: 41 year

value: ENCBS604ZEW at ENCODE; https://www.encodeproject.org/ENCBS604ZEW/

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


title: D-2

description:
Library name: sample17
Column name in counts_allsamples.txt: D-2

value: Tumor

value: melanoma cell

value: RG-NPs

tag: batch

value: Day 10


title: total RNA-seq from T follicular helper cell (ENCLB241AEA)

description:
https://www.encodeproject.org/experiments/ENCSR783TPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR783TPV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB241AEA

source_name: Homo sapiens female adult (33 years) T follicular helper primary cell

value: T follicular helper cell

value: primary cell

tag: Sex

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS923HPG at ENCODE; https://www.encodeproject.org/ENCBS923HPG/


title: snATAC-seq from heart left ventricle (ENCLB084CIJ)

description:
https://www.encodeproject.org/experiments/ENCSR131DKN/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on human heart left ventricle. Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR481QQR)
experiment encode accession: ENCSR131DKN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB084CIJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (46 years) heart left ventricle tissue, preserved by flash-freezing nuclear fraction

value: heart left ventricle

value: tissue

value: 46 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS196UFN at ENCODE; https://www.encodeproject.org/ENCBS196UFN/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: D-3

description:
Library name: sample18
Column name in counts_allsamples.txt: D-3

value: Tumor

value: melanoma cell

value: WT


title: MCF7 500nM Palbociclib-1

description:
Library name: S91
ST-SNXPAL1
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: 500 nM Palbociclib isethionate


title: MCF7 500nM SNX631-3

description:
Library name: S90
ST-PAL3
202507_InVitroCompiled_All_CPMTPM.xlsx


title: snATAC-seq from right lobe of liver (ENCLB431YMH)

description:
https://www.encodeproject.org/experiments/ENCSR114OKU/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human right lobe of liver
experiment encode accession: ENCSR114OKU
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB431YMH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) right lobe of liver tissue, preserved by cryopreservation nuclear fraction

value: right lobe of liver

tag: description

value: Child biosample for Chang/Greenleaf lab

value: female

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

value: adult

value: 47 year

value: ENCBS842RMN at ENCODE; https://www.encodeproject.org/ENCBS842RMN/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: D-1

description:
Library name: sample16
Column name in counts_allsamples.txt: D-1

value: RG-NPs

value: Day 10


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB225LFC)

description:
https://www.encodeproject.org/experiments/ENCSR778BHT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR778BHT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB225LFC

source_name: Homo sapiens female adult (40 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: encode accession

value: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS764WJS at ENCODE; https://www.encodeproject.org/ENCBS764WJS/


title: snATAC-seq from right lobe of liver (ENCLB151GYX)

description:
https://www.encodeproject.org/experiments/ENCSR112UBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human right lobe of liver
experiment encode accession: ENCSR112UBQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB151GYX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (40 years) right lobe of liver tissue nuclear fraction

value: right lobe of liver

value: tissue

value: male

tag: dev stage

tag: age

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS183CVV at ENCODE; https://www.encodeproject.org/ENCBS183CVV/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB838EUZ)

description:
https://www.encodeproject.org/experiments/ENCSR779SWL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR779SWL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB838EUZ

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

value: female

value: adult

value: 34 year

value: ENCBS140KLU at ENCODE; https://www.encodeproject.org/ENCBS140KLU/


title: MCF7 500nM SNX631-1

description:
Library name: S88
ST-PAL1
202507_InVitroCompiled_All_CPMTPM.xlsx

value: Adherent epithelial cells

tag: cell line

tag: cell type

value: Estrogen Receptor-Positive Breast Cancer

value: WT


title: C-4

description:
Library name: sample14
Column name in counts_allsamples.txt: C-4

source_name: Tumor

value: Tumor

value: melanoma cell

value: VPE-PTEN

value: Day 10


title: snATAC-seq from ovary (ENCLB575RDD)

description:
https://www.encodeproject.org/experiments/ENCSR105VKN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105VKN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB575RDD
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: ovary

value: tissue

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

value: 47 year

tag: lab

tag: source

value: ENCBS980YMW at ENCODE; https://www.encodeproject.org/ENCBS980YMW/

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


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB073QAM)

description:
https://www.encodeproject.org/experiments/ENCSR772PIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR772PIV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB073QAM

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: 40 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: link

value: ENCBS113XQS at ENCODE; https://www.encodeproject.org/ENCBS113XQS/


title: MCF7 Vehicle DMSO 0.1%-3

description:
Library name: S87
ST-DMSO3
202507_InVitroCompiled_All_CPMTPM.xlsx

source_name: Adherent epithelial cells

value: Adherent epithelial cells

value: Estrogen Receptor-Positive Breast Cancer

value: WT

value: 0.1 % DMSO


title: snATAC-seq from CD4-positive, alpha-beta T cell (ENCLB759ULR)

description:
https://www.encodeproject.org/experiments/ENCSR102QKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR102QKY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB759ULR
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell nuclear fraction

value: male

value: adult

value: 20 year

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

value: ENCBS381RYP at ENCODE; https://www.encodeproject.org/ENCBS381RYP/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: MCF7 Vehicle DMSO 0.1%-2

description:
Library name: S86
ST-DMSO2
202507_InVitroCompiled_All_CPMTPM.xlsx

tag: tissue


title: total RNA-seq from T-cell (ENCLB720HXS)

description:
https://www.encodeproject.org/experiments/ENCSR769XYT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR769XYT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB720HXS

value: T-cell

value: primary cell

value: 38 year

value: ENCBS086WLP at ENCODE; https://www.encodeproject.org/ENCBS086WLP/


title: snATAC-seq from heart left ventricle (ENCLB327QFR)

description:
https://www.encodeproject.org/experiments/ENCSR101LQQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101LQQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB327QFR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (64 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: 64 year

value: Michael Snyder, Stanford

value: Shin Lin

tag: health state

value: nonischemic -> giant cell vs. sarcoid (EF 18%, LVEDD 5.9, LVPWd 0.65)

value: ENCBS667KWK at ENCODE; https://www.encodeproject.org/ENCBS667KWK/

value: Derived from ENCODE donor ENCDO446FXE; https://www.encodeproject.org/ENCDO446FXE/