title: snATAC-seq from heart left ventricle (ENCLB395WTN)

description:
https://www.encodeproject.org/experiments/ENCSR918VTH/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on left heart ventricle. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR755CIF).
experiment encode accession: ENCSR918VTH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB395WTN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: heart left ventricle

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

value: 47 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS580LUW at ENCODE; https://www.encodeproject.org/ENCBS580LUW/

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


title: snATAC-seq from left colon (ENCLB369FES)

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/ENCSR916RYB/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human left colon
experiment encode accession: ENCSR916RYB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB369FES
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

value: left colon

value: tissue

tag: biosample encode accession

tag: Sex

value: female

tag: health state

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

tag: dev stage

value: adult

tag: age

value: 46 year

tag: lab

value: Michael Snyder, Stanford

tag: subcellular fraction term name

tag: source

tag: link

value: ENCBS897EHA at ENCODE; https://www.encodeproject.org/ENCBS897EHA/

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


title: total RNA-seq from HG03160 (ENCLB163GRQ)

description:
https://www.encodeproject.org/experiments/ENCSR240BDA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR240BDA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB163GRQ
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens HG03160 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: encode accession

tag: note

value: HG03160 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS355JEK at ENCODE; https://www.encodeproject.org/ENCBS355JEK/


title: snATAC-seq from psoas muscle (ENCLB605GHO)

description:
https://www.encodeproject.org/experiments/ENCSR916EDP/
***************
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 (ENCSR203THX).
experiment encode accession: ENCSR916EDP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB605GHO
fragmentation methods: chemical (Tn5 transposase)
size range: 250-450

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

value: psoas muscle

value: 41 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS345CVS at ENCODE; https://www.encodeproject.org/ENCBS345CVS/

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


title: total RNA-seq from HG02947 (ENCLB814XZP)

description:
https://www.encodeproject.org/experiments/ENCSR238AZV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR238AZV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB814XZP
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02947 cell line

value: HG02947 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: ENCBS503UTR at ENCODE; https://www.encodeproject.org/ENCBS503UTR/


title: MO113-CGND-HRA-02907-ATAC

city: New York

first: Christopher

last: Jackson

state: NY

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

description: Library name: MO113-CGND-HRA-02907-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.

tag: tissue

tag: genotype

value: ALS

tag: pmi

value: F

tag: age at_death

tag: age at_symptom_onset

tag: site of_motor_onset

value: Limb


title: total RNA-seq from HG02643 (ENCLB203DJJ)

description:
https://www.encodeproject.org/experiments/ENCSR321NYJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR321NYJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB203DJJ
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02643 cell line

value: cell line

tag: biosample encode accession

value: HG02643 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

tag: Sex

value: female

value: ENCBS821ZEX at ENCODE; https://www.encodeproject.org/ENCBS821ZEX/


title: MO108-CGND-HRA-02472-ATAC

description: Library name: MO108-CGND-HRA-02472-ATAC

value: M

value: Bulbar


title: snATAC-seq from heart left ventricle (ENCLB319COO)

description:
https://www.encodeproject.org/experiments/ENCSR912XZH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR912XZH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB319COO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (51 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

tag: health state

value: nonischemic (EF 31%, LVEDD 7.0)

tag: dev stage

value: 51 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS371YBL at ENCODE; https://www.encodeproject.org/ENCBS371YBL/

value: Derived from ENCODE donor ENCDO580GZH; https://www.encodeproject.org/ENCDO580GZH/


title: total RNA-seq from GM21303 (ENCLB646DIU)

description:
https://www.encodeproject.org/experiments/ENCSR237NBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237NBV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB646DIU
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21303 cell line

value: GM21303 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

tag: lab

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS796GBK at ENCODE; https://www.encodeproject.org/ENCBS796GBK/


title: total RNA-seq from GM21402 (ENCLB712TFF)

description:
https://www.encodeproject.org/experiments/ENCSR232AIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR232AIN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB712TFF
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21402 cell line

value: cell line

value: GM21402 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: source

value: ENCBS826JKP at ENCODE; https://www.encodeproject.org/ENCBS826JKP/


title: total RNA-seq from HG02854 (ENCLB732PCX)

description:
https://www.encodeproject.org/experiments/ENCSR231JEO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR231JEO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB732PCX
nucleic acid starting quantity: 36
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02854 cell line

value: HG02854 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

tag: link

value: ENCBS485LGT at ENCODE; https://www.encodeproject.org/ENCBS485LGT/


title: snATAC-seq from mucosa of gallbladder (ENCLB216SPH)

description:
https://www.encodeproject.org/experiments/ENCSR908HQW/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human mucosa of gallbladder
experiment encode accession: ENCSR908HQW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB216SPH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female child (16 years) mucosa of gallbladder tissue, preserved by flash-freezing nuclear fraction

value: mucosa of gallbladder

value: tissue

value: female

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

value: child

tag: age

value: 16 year

tag: subcellular fraction term name

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS030TPH at ENCODE; https://www.encodeproject.org/ENCBS030TPH/

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


title: total RNA-seq from GM19035 (ENCLB094VGJ)

description:
https://www.encodeproject.org/experiments/ENCSR237TRX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237TRX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB094VGJ
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19035 cell line

tag: line

value: GM19035 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: adult

value: unknown

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS102BOL at ENCODE; https://www.encodeproject.org/ENCBS102BOL/

value: Derived from ENCODE donor ENCDO776KEU; https://www.encodeproject.org/ENCDO776KEU/


title: snATAC-seq from heart left ventricle (ENCLB457IXY)

description:
https://www.encodeproject.org/experiments/ENCSR895LPX/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR895LPX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB457IXY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (56 years) heart left ventricle tissue nuclear fraction

value: heart left ventricle

value: tissue

value: PGD

value: 56 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS233TJY at ENCODE; https://www.encodeproject.org/ENCBS233TJY/

value: Derived from ENCODE donor ENCDO907YUG; https://www.encodeproject.org/ENCDO907YUG/


title: snATAC-seq from heart left ventricle (ENCLB300ABY)

description:
https://www.encodeproject.org/experiments/ENCSR913OAS/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR913OAS
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB300ABY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (66 years) heart left ventricle tissue nuclear fraction

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: nucleus

value: ENCBS452XQC at ENCODE; https://www.encodeproject.org/ENCBS452XQC/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: total RNA-seq from HG03058 (ENCLB610SUV)

description:
https://www.encodeproject.org/experiments/ENCSR227XJB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR227XJB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB610SUV
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03058 cell line

value: cell line

tag: encode accession

tag: note

value: HG03058 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS861TRG at ENCODE; https://www.encodeproject.org/ENCBS861TRG/


title: snATAC-seq from heart left ventricle (ENCLB877ZYF)

description:
https://www.encodeproject.org/experiments/ENCSR886PUY/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR886PUY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB877ZYF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue nuclear fraction

value: heart left ventricle

value: tissue

value: male

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: 54 year

value: ENCBS292PGU at ENCODE; https://www.encodeproject.org/ENCBS292PGU/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: total RNA-seq from HG02667 (ENCLB700TCU)

description:
https://www.encodeproject.org/experiments/ENCSR227KXJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR227KXJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB700TCU
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02667 cell line

value: HG02667 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Coriell

value: ENCBS594RYF at ENCODE; https://www.encodeproject.org/ENCBS594RYF/


title: snATAC-seq from heart left ventricle (ENCLB413OEM)

description:
https://www.encodeproject.org/experiments/ENCSR878VJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR878VJS
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB413OEM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: ischemic

value: Michael Snyder, Stanford

value: nucleus

value: Shin Lin

value: ENCBS034WRO at ENCODE; https://www.encodeproject.org/ENCBS034WRO/

value: Derived from ENCODE donor ENCDO874YWU; https://www.encodeproject.org/ENCDO874YWU/


title: total RNA-seq from GM21388 (ENCLB357ZUP)

description:
https://www.encodeproject.org/experiments/ENCSR226WFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR226WFV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB357ZUP
nucleic acid starting quantity: 45
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21388 cell line

value: cell line

value: GM21388 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: ENCBS060AZS at ENCODE; https://www.encodeproject.org/ENCBS060AZS/


title: snATAC-seq from psoas muscle (ENCLB219RNK)

description:
https://www.encodeproject.org/experiments/ENCSR869LEV/
***************
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 (ENCSR281RIH).
experiment encode accession: ENCSR869LEV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB219RNK
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: psoas muscle

value: tissue

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

value: 59 year

value: Yiing Lin, MD, PhD

value: ENCBS865RKW at ENCODE; https://www.encodeproject.org/ENCBS865RKW/

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


title: total RNA-seq from HG02952 (ENCLB477IEF)

description:
https://www.encodeproject.org/experiments/ENCSR231FVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR231FVM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB477IEF
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02952 cell line

value: HG02952 LCLs; Donor from the Esan in Nigeria (ESN)

value: Coriell

value: ENCBS295GTS at ENCODE; https://www.encodeproject.org/ENCBS295GTS/


title: snATAC-seq from pancreas (ENCLB068HFY)

description:
https://www.encodeproject.org/experiments/ENCSR868CRK/
***************
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 (ENCSR281NBH).
experiment encode accession: ENCSR868CRK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB068HFY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: pancreas

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

value: child

value: 16 year

value: Michael Snyder, Stanford

value: nucleus

value: ENCBS928ZLX at ENCODE; https://www.encodeproject.org/ENCBS928ZLX/

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


title: snATAC-seq from pancreas (ENCLB589KPI)

description:
https://www.encodeproject.org/experiments/ENCSR862WHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human pancreas
experiment encode accession: ENCSR862WHQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB589KPI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: tissue

value: female

value: adult

value: ENCBS042PQQ at ENCODE; https://www.encodeproject.org/ENCBS042PQQ/


title: total RNA-seq from HG03460 (ENCLB228OVN)

description:
https://www.encodeproject.org/experiments/ENCSR223JWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR223JWC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB228OVN
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03460 cell line

value: cell line

value: HG03460 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: unknown

value: Stephen Montgomery, Stanford

value: ENCBS383WOD at ENCODE; https://www.encodeproject.org/ENCBS383WOD/

value: Derived from ENCODE donor ENCDO499MFJ; https://www.encodeproject.org/ENCDO499MFJ/


title: total RNA-seq from GM19475 (ENCLB745BPN)

description:
https://www.encodeproject.org/experiments/ENCSR221NQI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR221NQI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB745BPN
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19475 cell line

value: GM19475 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Coriell

value: ENCBS775RAX at ENCODE; https://www.encodeproject.org/ENCBS775RAX/


title: snATAC-seq from heart left ventricle (ENCLB785PTV)

description:
https://www.encodeproject.org/experiments/ENCSR862IWS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR862IWS
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB785PTV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (25 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: 25 year

value: Michael Snyder, Stanford

value: Shin Lin

value: healthy

value: ENCBS186SQI at ENCODE; https://www.encodeproject.org/ENCBS186SQI/

value: Derived from ENCODE donor ENCDO607DMC; https://www.encodeproject.org/ENCDO607DMC/


title: snATAC-seq from HCT116 (ENCLB505VPF)

description:
https://www.encodeproject.org/experiments/ENCSR840IWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR840IWM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB505VPF
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 RAD21 treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: colorectal carcinoma

value: adult

value: 48 year

value: Dr. Masato Kanemaki

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS150DIX at ENCODE; https://www.encodeproject.org/ENCBS150DIX/

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


title: total RNA-seq from GM19318 (ENCLB108APM)

description:
https://www.encodeproject.org/experiments/ENCSR218GPO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR218GPO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB108APM
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19318 cell line

value: GM19318 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS378VAM at ENCODE; https://www.encodeproject.org/ENCBS378VAM/


title: snATAC-seq from bile duct (ENCLB873GZW)

description:
https://www.encodeproject.org/experiments/ENCSR833BMK/
***************
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 (ENCSR060SEA).
experiment encode accession: ENCSR833BMK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB873GZW
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: bile duct

value: tissue

value: female

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

value: 41 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS423NLA at ENCODE; https://www.encodeproject.org/ENCBS423NLA/

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


title: snATAC-seq from left colon (ENCLB737UHD)

description:
https://www.encodeproject.org/experiments/ENCSR830FPR/
***************
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 (ENCSR289ANH).
experiment encode accession: ENCSR830FPR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB737UHD
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: left colon

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

value: adult

value: 59 year

value: ENCBS451VLL at ENCODE; https://www.encodeproject.org/ENCBS451VLL/

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


title: total RNA-seq from HG03258 (ENCLB733QDL)

description:
https://www.encodeproject.org/experiments/ENCSR217LLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR217LLB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB733QDL
nucleic acid starting quantity: 44
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03258 cell line

value: cell line

value: HG03258 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS355JXS at ENCODE; https://www.encodeproject.org/ENCBS355JXS/


title: snATAC-seq from lower lobe of right lung (ENCLB175KMK)

description:
https://www.encodeproject.org/experiments/ENCSR830CXR/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human lower lobe of right lung
experiment encode accession: ENCSR830CXR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB175KMK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (60 years) lower lobe of right lung tissue, preserved by cryopreservation nuclear fraction

value: lower lobe of right lung

value: tissue

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

value: 60 year

value: Michael Snyder, Stanford

value: ENCBS637ZUP at ENCODE; https://www.encodeproject.org/ENCBS637ZUP/

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


title: total RNA-seq from HG03558 (ENCLB432VYR)

description:
https://www.encodeproject.org/experiments/ENCSR213ZST/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR213ZST
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB432VYR
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03558 cell line

value: HG03558 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: adult

value: unknown

value: ENCBS689TLP at ENCODE; https://www.encodeproject.org/ENCBS689TLP/

value: Derived from ENCODE donor ENCDO087EDQ; https://www.encodeproject.org/ENCDO087EDQ/


title: snATAC-seq from uterus (ENCLB673HOE)

description:
https://www.encodeproject.org/experiments/ENCSR828HVB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR828HVB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB673HOE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: uterus

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

value: 59 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS067MIE at ENCODE; https://www.encodeproject.org/ENCBS067MIE/

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


title: snATAC-seq from left lung (ENCLB411WBB)

description:
https://www.encodeproject.org/experiments/ENCSR816NWE/
***************
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 (ENCSR966DDY).
experiment encode accession: ENCSR816NWE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB411WBB
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens female child (16 years) left lung tissue, preserved by flash-freezing nuclear fraction

value: left lung

value: tissue

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

value: child

value: 16 year

value: ENCBS517LMU at ENCODE; https://www.encodeproject.org/ENCBS517LMU/

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


title: total RNA-seq from HG03241 (ENCLB603GWU)

description:
https://www.encodeproject.org/experiments/ENCSR212UYG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR212UYG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB603GWU
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03241 cell line

value: cell line

value: HG03241 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS679UQH at ENCODE; https://www.encodeproject.org/ENCBS679UQH/


title: snATAC-seq from upper lobe of left lung (ENCLB584ZLB)

description:
https://www.encodeproject.org/experiments/ENCSR824OCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR824OCY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB584ZLB
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (60 years) upper lobe of left lung tissue, preserved by flash-freezing nuclear fraction

value: upper lobe of left lung

value: male

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

value: 60 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS396OIY at ENCODE; https://www.encodeproject.org/ENCBS396OIY/

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


title: total RNA-seq from HG03410 (ENCLB072TEE)

description:
https://www.encodeproject.org/experiments/ENCSR212TVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR212TVA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB072TEE
nucleic acid starting quantity: 3
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03410 cell line

value: HG03410 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: ENCBS110ACB at ENCODE; https://www.encodeproject.org/ENCBS110ACB/


title: snATAC-seq from fallopian tube (ENCLB757NCI)

description:
https://www.encodeproject.org/experiments/ENCSR815FGT/
***************
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 (ENCSR011EDH).
experiment encode accession: ENCSR815FGT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB757NCI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: fallopian tube

value: tissue

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

value: 59 year

value: ENCBS994MYO at ENCODE; https://www.encodeproject.org/ENCBS994MYO/

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


title: total RNA-seq from HG03538 (ENCLB291DDT)

description:
https://www.encodeproject.org/experiments/ENCSR212SSB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR212SSB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB291DDT
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03538 cell line

value: cell line

value: HG03538 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS936NZA at ENCODE; https://www.encodeproject.org/ENCBS936NZA/


title: total RNA-seq from GM19323 (ENCLB736WFR)

description:
https://www.encodeproject.org/experiments/ENCSR208KSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR208KSN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB736WFR
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19323 cell line

value: GM19323 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: ENCBS945IVF at ENCODE; https://www.encodeproject.org/ENCBS945IVF/


title: total RNA-seq from GM21453 (ENCLB262BZG)

description:
https://www.encodeproject.org/experiments/ENCSR211VEI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR211VEI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB262BZG
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21453 cell line

value: GM21453 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS062OEI at ENCODE; https://www.encodeproject.org/ENCBS062OEI/


title: snATAC-seq from type B pancreatic cell (ENCLB386KHN)

description:
https://www.encodeproject.org/experiments/ENCSR811SRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR811SRE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB386KHN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: nucleus

value: SESCC

value: ENCBS348DRN at ENCODE; https://www.encodeproject.org/ENCBS348DRN/

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


title: total RNA-seq from GM19239 (ENCLB668ZSD)

description:
https://www.encodeproject.org/experiments/ENCSR203WRA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR203WRA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB668ZSD
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19239 cell line

value: cell line

value: GM19239 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS338BSH at ENCODE; https://www.encodeproject.org/ENCBS338BSH/


title: snATAC-seq from glutamatergic neuron (ENCLB310KWY)

description:
https://www.encodeproject.org/experiments/ENCSR811QVW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR811QVW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB310KWY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells nuclear fraction

value: glutamatergic neuron

value: male

value: 53 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS761ZFJ at ENCODE; https://www.encodeproject.org/ENCBS761ZFJ/

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


title: total RNA-seq from GM21360 (ENCLB699XON)

description:
https://www.encodeproject.org/experiments/ENCSR203HJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR203HJG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB699XON
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21360 cell line

value: GM21360 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: unknown

value: ENCBS084XDW at ENCODE; https://www.encodeproject.org/ENCBS084XDW/

value: Derived from ENCODE donor ENCDO503BYG; https://www.encodeproject.org/ENCDO503BYG/


title: snATAC-seq from heart left ventricle (ENCLB806HGQ)

description:
https://www.encodeproject.org/experiments/ENCSR803QTN/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR803QTN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB806HGQ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (43 years) heart left ventricle tissue nuclear fraction

value: heart left ventricle

value: tissue

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: 43 year

value: Michael Snyder, Stanford

value: nucleus

value: Shin Lin

value: ENCBS066NWP at ENCODE; https://www.encodeproject.org/ENCBS066NWP/

value: Derived from ENCODE donor ENCDO967KID; https://www.encodeproject.org/ENCDO967KID/


title: total RNA-seq from HG03108 (ENCLB064FQX)

description:
https://www.encodeproject.org/experiments/ENCSR202FZX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR202FZX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB064FQX
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03108 cell line

value: cell line

value: HG03108 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS148ZWC at ENCODE; https://www.encodeproject.org/ENCBS148ZWC/

value: Derived from ENCODE donor ENCDO406PYC; https://www.encodeproject.org/ENCDO406PYC/


title: total RNA-seq from HG02798 (ENCLB003DPL)

description:
https://www.encodeproject.org/experiments/ENCSR225QLT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR225QLT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB003DPL
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02798 cell line

value: HG02798 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: unknown

value: ENCBS923TDZ at ENCODE; https://www.encodeproject.org/ENCBS923TDZ/

value: Derived from ENCODE donor ENCDO589DVM; https://www.encodeproject.org/ENCDO589DVM/


title: total RNA-seq from GM21301 (ENCLB437EAT)

description:
https://www.encodeproject.org/experiments/ENCSR223TPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR223TPI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB437EAT
nucleic acid starting quantity: 44
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21301 cell line

value: GM21301 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS087VPK at ENCODE; https://www.encodeproject.org/ENCBS087VPK/


title: snATAC-seq from lower lobe of left lung (ENCLB621OUW)

description:
https://www.encodeproject.org/experiments/ENCSR799NRE/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human lower lobe of left lung
experiment encode accession: ENCSR799NRE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB621OUW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (60 years) lower lobe of left lung tissue, preserved by cryopreservation nuclear fraction

value: lower lobe of left lung

value: tissue

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

value: 60 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS762UOX at ENCODE; https://www.encodeproject.org/ENCBS762UOX/

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


title: total RNA-seq from HG03120 (ENCLB362EHO)

description:
https://www.encodeproject.org/experiments/ENCSR197QHM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197QHM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB362EHO
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03120 cell line

value: cell line

value: HG03120 LCLs; Donor from the Esan in Nigeria (ESN)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS349PNN at ENCODE; https://www.encodeproject.org/ENCBS349PNN/


title: total RNA-seq from GM21344 (ENCLB354WMA)

description:
https://www.encodeproject.org/experiments/ENCSR196SAS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR196SAS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB354WMA
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21344 cell line

value: GM21344 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS153LCU at ENCODE; https://www.encodeproject.org/ENCBS153LCU/


title: Expt1_TMAO1

first: Meenakshi

last: Chakraborty

address: 269 Campus Drive

institute: Stanford University

description: Library name: Expt1_TMAO1

data_processing:
TrimGalore v0.6.10
kallisto v0.50.1
Assembly: GRCm39
Supplementary files format and content: h5 files are outputs from kallisto
Supplementary files format and content: tsv files are outputs from kallisto

organism: Mus musculus

source_name: brain

extract_protocol:
Left brain hemispheres were stored in 1ml RNAlater overnight at 4 degrees C, and then dabbed on a Kimwipe to remove excess RNAlater before transfer to a fresh tube for storage at -80 degrees C. RNA was extracted from frozen left hemispheres using a modified version of the protocol from the QIAWave RNA Mini Kit (Qiagen, Catalog #74536). See our preprint at https://doi.org/10.1101/2025.10.03.680371 for more details.
mRNA libraries were prepared by Novogene from the extracted RNA, using a polyA enrichment strategy.

tag: tissue

value: brain

tag: genotype

tag: treatment

value: TMAO


title: snATAC-seq from heart left ventricle (ENCLB323JZS)

description:
https://www.encodeproject.org/experiments/ENCSR785BSP/
***************
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 (ENCSR727OYO).
experiment encode accession: ENCSR785BSP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB323JZS
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: heart left ventricle

value: tissue

tag: biosample encode accession

value: female

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

value: 41 year

value: ENCBS103VRO at ENCODE; https://www.encodeproject.org/ENCBS103VRO/

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


title: total RNA-seq from GM21491 (ENCLB043ZSM)

description:
https://www.encodeproject.org/experiments/ENCSR219KEH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR219KEH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB043ZSM
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21491 cell line

value: cell line

value: GM21491 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: Sex

value: ENCBS110CFZ at ENCODE; https://www.encodeproject.org/ENCBS110CFZ/


title: total RNA-seq from GM19038 (ENCLB231DUA)

description:
https://www.encodeproject.org/experiments/ENCSR195NKT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR195NKT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB231DUA
nucleic acid starting quantity: 21
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19038 cell line

value: GM19038 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS659JXI at ENCODE; https://www.encodeproject.org/ENCBS659JXI/


title: snATAC-seq from IMR-90 (ENCLB619SDN)

description:
https://www.encodeproject.org/experiments/ENCSR778RZT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR778RZT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB619SDN
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens IMR-90 cell line

value: unknown

value: embryonic

value: 16 week

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS872CEV at ENCODE; https://www.encodeproject.org/ENCBS872CEV/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: total RNA-seq from GM21722 (ENCLB787CCN)

description:
https://www.encodeproject.org/experiments/ENCSR195EDC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR195EDC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB787CCN
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21722 cell line

value: GM21722 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS479VYI at ENCODE; https://www.encodeproject.org/ENCBS479VYI/


title: Expt1_TMAO2

description: Library name: Expt1_TMAO2

value: brain

value: TMAO


title: total RNA-seq from GM21318 (ENCLB004CJN)

description:
https://www.encodeproject.org/experiments/ENCSR195DEV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR195DEV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB004CJN
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21318 cell line

value: cell line

value: GM21318 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS292TUT at ENCODE; https://www.encodeproject.org/ENCBS292TUT/


title: snATAC-seq from left cardiac atrium (ENCLB318GKE)

description:
https://www.encodeproject.org/experiments/ENCSR777GVP/
***************
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 (ENCSR700UVN).
experiment encode accession: ENCSR777GVP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB318GKE
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (40 years) left cardiac atrium tissue, preserved by flash-freezing nuclear fraction

value: left cardiac atrium

value: tissue

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

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS772XDC at ENCODE; https://www.encodeproject.org/ENCBS772XDC/

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


title: total RNA-seq from GM21438 (ENCLB300WYS)

description:
https://www.encodeproject.org/experiments/ENCSR194AHO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR194AHO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB300WYS
nucleic acid starting quantity: 20
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21438 cell line

value: GM21438 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS280DNM at ENCODE; https://www.encodeproject.org/ENCBS280DNM/


title: Expt1_TMAO3

description: Library name: Expt1_TMAO3

value: brain

value: TMAO


title: total RNA-seq from HG03354 (ENCLB113URM)

description:
https://www.encodeproject.org/experiments/ENCSR190VMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR190VMF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB113URM
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03354 cell line

value: cell line

tag: description

value: HG03354 LCLs; Donor from the Esan in Nigeria (ESN)

value: unknown

value: ENCBS364CMI at ENCODE; https://www.encodeproject.org/ENCBS364CMI/

value: Derived from ENCODE donor ENCDO271ELE; https://www.encodeproject.org/ENCDO271ELE/


title: total RNA-seq from GM21575 (ENCLB182ESN)

description:
https://www.encodeproject.org/experiments/ENCSR192PWG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR192PWG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB182ESN
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21575 cell line

value: GM21575 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: ENCBS347CBI at ENCODE; https://www.encodeproject.org/ENCBS347CBI/


title: snATAC-seq from A673 (ENCLB091KIU)

description:
https://www.encodeproject.org/experiments/ENCSR773HYY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR773HYY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB091KIU
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens A673 cell line nuclear fraction

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: nucleus

value: ATCC

value: ENCBS841WGQ at ENCODE; https://www.encodeproject.org/ENCBS841WGQ/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: Expt1_TMAO4

description: Library name: Expt1_TMAO4

value: brain

value: TMAO


title: total RNA-seq from HG02882 (ENCLB726EQX)

description:
https://www.encodeproject.org/experiments/ENCSR190BVW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR190BVW
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB726EQX
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02882 cell line

value: cell line

value: HG02882 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS131QTH at ENCODE; https://www.encodeproject.org/ENCBS131QTH/


title: snATAC-seq from heart right ventricle (ENCLB641KOZ)

description:
https://www.encodeproject.org/experiments/ENCSR772BEX/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR772BEX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB641KOZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (69 years) heart right ventricle tissue nuclear fraction

value: heart right ventricle

value: tissue

value: male

tag: health state

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS955QMB at ENCODE; https://www.encodeproject.org/ENCBS955QMB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: total RNA-seq from HG03270 (ENCLB170IBQ)

description:
https://www.encodeproject.org/experiments/ENCSR189EAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189EAL
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB170IBQ
nucleic acid starting quantity: 18
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03270 cell line

value: HG03270 LCLs; Donor from the Esan in Nigeria (ESN)

tag: dev stage

value: ENCBS840UQC at ENCODE; https://www.encodeproject.org/ENCBS840UQC/


title: Expt2_S3

description: Library name: Expt2_S3

value: brain

value: S


title: total RNA-seq from GM19347 (ENCLB456IXW)

description:
https://www.encodeproject.org/experiments/ENCSR186FEP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR186FEP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB456IXW
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19347 cell line

value: cell line

value: GM19347 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

tag: lab

value: Stephen Montgomery, Stanford

value: ENCBS735OMR at ENCODE; https://www.encodeproject.org/ENCBS735OMR/


title: snATAC-seq from heart left ventricle (ENCLB305DHH)

description:
https://www.encodeproject.org/experiments/ENCSR769WLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR769WLL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB305DHH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (51 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: 51 year

tag: source

value: LMNA-related dilated cardiomyopathy (EF 27.9%, LVEDD 6.1, LVPWd 1.3)

value: ENCBS631QFV at ENCODE; https://www.encodeproject.org/ENCBS631QFV/

value: Derived from ENCODE donor ENCDO098ZMW; https://www.encodeproject.org/ENCDO098ZMW/


title: total RNA-seq from HG02568 (ENCLB050IVI)

description:
https://www.encodeproject.org/experiments/ENCSR188QRH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR188QRH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB050IVI
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02568 cell line

value: HG02568 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: adult

value: Coriell

tag: link

value: ENCBS983DNO at ENCODE; https://www.encodeproject.org/ENCBS983DNO/


title: Expt2_S4

description: Library name: Expt2_S4

source_name: brain

value: brain

value: S


title: total RNA-seq from HG03432 (ENCLB595COR)

description:
https://www.encodeproject.org/experiments/ENCSR185YKL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR185YKL
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB595COR
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03432 cell line

value: cell line

value: HG03432 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

tag: age

value: unknown

value: ENCBS218AUL at ENCODE; https://www.encodeproject.org/ENCBS218AUL/

value: Derived from ENCODE donor ENCDO967XPT; https://www.encodeproject.org/ENCDO967XPT/


title: snATAC-seq from HepG2 (ENCLB761HKI)

description:
https://www.encodeproject.org/experiments/ENCSR967HFR/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line HepG2
experiment encode accession: ENCSR967HFR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB761HKI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens HepG2 cell line nuclear fraction

value: hepatocellular carcinoma

value: child

value: 15 year

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: ATCC

value: ENCBS442HJI at ENCODE; https://www.encodeproject.org/ENCBS442HJI/

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


title: snATAC-seq from heart right ventricle (ENCLB392JKJ)

description:
https://www.encodeproject.org/experiments/ENCSR814OLA/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR814OLA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB392JKJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (43 years) heart right ventricle tissue nuclear fraction

value: heart right ventricle

value: tissue

value: nonischemic (EF 23%, LVEDD 6.1; RV moderate dilation, normal function)

value: adult

value: 43 year

value: Shin Lin

value: ENCBS720ANU at ENCODE; https://www.encodeproject.org/ENCBS720ANU/

value: Derived from ENCODE donor ENCDO967KID; https://www.encodeproject.org/ENCDO967KID/


title: snATAC-seq from activated T-helper 1 cell (ENCLB076PEI)

description:
https://www.encodeproject.org/experiments/ENCSR759OSE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR759OSE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB076PEI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (35 years) activated 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, anti-CD3 and anti-CD28 coated beads nuclear fraction

value: activated T-helper 1 cell

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS674FJZ at ENCODE; https://www.encodeproject.org/ENCBS674FJZ/

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


title: total RNA-seq from GM19385 (ENCLB981ASZ)

description:
https://www.encodeproject.org/experiments/ENCSR183UYO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR183UYO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB981ASZ
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19385 cell line

tag: line

value: cell line

value: GM19385 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS187KZM at ENCODE; https://www.encodeproject.org/ENCBS187KZM/


title: total RNA-seq from GM18877 (ENCLB817MNR)

description:
https://www.encodeproject.org/experiments/ENCSR183JRL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR183JRL
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB817MNR
nucleic acid starting quantity: 47
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18877 cell line

tag: encode accession

value: GM18877 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: adult

value: ENCBS423TWY at ENCODE; https://www.encodeproject.org/ENCBS423TWY/


title: total RNA-seq from HG03111 (ENCLB573YYK)

description:
https://www.encodeproject.org/experiments/ENCSR182ZQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR182ZQT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB573YYK
nucleic acid starting quantity: 27
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03111 cell line

tag: note

value: HG03111 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS226JMS at ENCODE; https://www.encodeproject.org/ENCBS226JMS/


title: snATAC-seq from PC-3 (ENCLB464AJI)

description:
https://www.encodeproject.org/experiments/ENCSR756HYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR756HYX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB464AJI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens PC-3 cell line nuclear fraction

value: male

value: grade IV, adenocarcinoma

value: 62 year

value: Mats Ljungman, UMichigan

value: nucleus

value: ATCC

value: ENCBS254TBU at ENCODE; https://www.encodeproject.org/ENCBS254TBU/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/


title: Expt2_S1

description: Library name: Expt2_S1

value: brain

value: S


title: total RNA-seq from GM19310 (ENCLB548IHP)

description:
https://www.encodeproject.org/experiments/ENCSR182MKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR182MKX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB548IHP
nucleic acid starting quantity: 40
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19310 cell line

value: cell line

value: GM19310 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS976PCN at ENCODE; https://www.encodeproject.org/ENCBS976PCN/


title: Expt2_S2

description: Library name: Expt2_S2


title: Expt1_S1

description: Library name: Expt1_S1


title: total RNA-seq from GM19031 (ENCLB930MYO)

description:
https://www.encodeproject.org/experiments/ENCSR179JFX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR179JFX
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB930MYO
nucleic acid starting quantity: 45
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19031 cell line

value: GM19031 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: ENCBS719BWY at ENCODE; https://www.encodeproject.org/ENCBS719BWY/


title: Control ChIP-seq from K562 (ENCLB462HHZ)

description:
https://www.encodeproject.org/experiments/ENCSR755HEN/
***************
biological replicate number: 1
technical replicate number: 1
description: TEAD4 ChIP-seq on K562 cells treated with vector control shRNA
experiment encode accession: ENCSR755HEN
assay title: Control ChIP-seq
possible controls: ENCSR402HVP
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB462HHZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: antibody

value: Homo sapiens K562 cell line transduced with doxycycline-inducible shRNA targeting MAFF. Cells were treated for 72 hours with 4ug/mL doxycycline prior to experiment harvest.

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS474MBZ at ENCODE; https://www.encodeproject.org/ENCBS474MBZ/


title: total RNA-seq from GM19456 cell (ENCLB030OVA)

description:
https://www.encodeproject.org/experiments/ENCSR178XBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR178XBV
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB030OVA
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19456 cell line

value: GM19456 cell

value: GM19456 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS818HIZ at ENCODE; https://www.encodeproject.org/ENCBS818HIZ/


title: snATAC-seq from MCF-7 (ENCLB822WQS)

description:
https://www.encodeproject.org/experiments/ENCSR754TFT/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human cell line MCF-7
experiment encode accession: ENCSR754TFT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB822WQS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens MCF-7 cell line nuclear fraction

value: cell line

value: breast cancer (adenocarcinoma)

value: 69 year

value: nucleus

value: ATCC

value: ENCBS468WBR at ENCODE; https://www.encodeproject.org/ENCBS468WBR/

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


title: total RNA-seq from GM21741 (ENCLB707HHM)

description:
https://www.encodeproject.org/experiments/ENCSR173BSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR173BSI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB707HHM
nucleic acid starting quantity: 30
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21741 cell line

value: GM21741 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS926KQF at ENCODE; https://www.encodeproject.org/ENCBS926KQF/


title: total RNA-seq from HG02610 (ENCLB188QID)

description:
https://www.encodeproject.org/experiments/ENCSR174DGO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR174DGO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB188QID
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02610 cell line

value: HG02610 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: unknown

value: ENCBS816ZDM at ENCODE; https://www.encodeproject.org/ENCBS816ZDM/

value: Derived from ENCODE donor ENCDO258VYL; https://www.encodeproject.org/ENCDO258VYL/


title: total RNA-seq from HG03202 (ENCLB826QPJ)

description:
https://www.encodeproject.org/experiments/ENCSR170LYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR170LYC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB826QPJ
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03202 cell line

value: cell line

value: HG03202 LCLs; Donor from the Esan in Nigeria (ESN)

value: ENCBS413ZRW at ENCODE; https://www.encodeproject.org/ENCBS413ZRW/


title: snATAC-seq from heart left ventricle (ENCLB921NSM)

description:
https://www.encodeproject.org/experiments/ENCSR750YRO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR750YRO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB921NSM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (53 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: female

value: ischemic (EF 29%, LVEDD 6.5)

value: 53 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS775ZAT at ENCODE; https://www.encodeproject.org/ENCBS775ZAT/

value: Derived from ENCODE donor ENCDO750LVJ; https://www.encodeproject.org/ENCDO750LVJ/


title: total RNA-seq from GM18876 (ENCLB213CCC)

description:
https://www.encodeproject.org/experiments/ENCSR167QKJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR167QKJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB213CCC
nucleic acid starting quantity: 20
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18876 cell line

value: GM18876 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS963FZX at ENCODE; https://www.encodeproject.org/ENCBS963FZX/


title: snATAC-seq from neural crest cell (ENCLB464MTL)

description:
https://www.encodeproject.org/experiments/ENCSR740EIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR740EIL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB464MTL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: neural crest cell

value: in vitro differentiated cells

value: WA09 derived neural crest cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: nucleus

value: SESCC

value: ENCBS725YKV at ENCODE; https://www.encodeproject.org/ENCBS725YKV/

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


title: Expt1_S2

description: Library name: Expt1_S2

source_name: brain

tag: tissue

value: brain

value: S


title: Expt1_S3

description: Library name: Expt1_S3

tag: genotype


title: total RNA-seq from HG03079 (ENCLB122SKB)

description:
https://www.encodeproject.org/experiments/ENCSR167QJU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR167QJU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB122SKB
nucleic acid starting quantity: 43
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03079 cell line

value: cell line

value: HG03079 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: adult

value: ENCBS032OWG at ENCODE; https://www.encodeproject.org/ENCBS032OWG/


title: Expt1_S4

description: Library name: Expt1_S4

tag: treatment


title: total RNA-seq from HG02624 (ENCLB421YGE)

description:
https://www.encodeproject.org/experiments/ENCSR166RJP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR166RJP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB421YGE
nucleic acid starting quantity: 53
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02624 cell line

tag: biosample encode accession

value: HG02624 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS781EDL at ENCODE; https://www.encodeproject.org/ENCBS781EDL/


title: total RNA-seq from GM21357 (ENCLB814DWF)

description:
https://www.encodeproject.org/experiments/ENCSR163ELK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR163ELK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB814DWF
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21357 cell line

value: GM21357 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

tag: Sex

value: ENCBS657RGZ at ENCODE; https://www.encodeproject.org/ENCBS657RGZ/


title: snATAC-seq from H9 (ENCLB281BMO)

description:
https://www.encodeproject.org/experiments/ENCSR737MVK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR737MVK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB281BMO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens H9 cell line nuclear fraction

tag: description

value: WA09 ES cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: nucleus

value: ENCBS727UDM at ENCODE; https://www.encodeproject.org/ENCBS727UDM/


title: total RNA-seq from suppressor macrophage (ENCLB760OBD)

description:
https://www.encodeproject.org/experiments/ENCSR160SIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR160SIL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB760OBD
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: suppressor macrophage

value: primary cell

value: male

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS764QJV at ENCODE; https://www.encodeproject.org/ENCBS764QJV/


title: Expt2_SD2

description: Library name: Expt2_SD2

value: brain

value: SD


title: snATAC-seq from CD4-positive, alpha-beta memory T cell (ENCLB657KSK)

description:
https://www.encodeproject.org/experiments/ENCSR737VYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR737VYM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB657KSK
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: CD4-positive, alpha-beta memory T cell

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS562QZY at ENCODE; https://www.encodeproject.org/ENCBS562QZY/

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


title: Expt2_SD1

description: Library name: Expt2_SD1


title: total RNA-seq from GM21423 (ENCLB588ESU)

description:
https://www.encodeproject.org/experiments/ENCSR164PHT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR164PHT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB588ESU
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21423 cell line

value: cell line

value: GM21423 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: unknown

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS421BIV at ENCODE; https://www.encodeproject.org/ENCBS421BIV/

value: Derived from ENCODE donor ENCDO635HMA; https://www.encodeproject.org/ENCDO635HMA/


title: total RNA-seq from HG02860 (ENCLB412BSX)

description:
https://www.encodeproject.org/experiments/ENCSR160KZU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR160KZU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB412BSX
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02860 cell line

value: HG02860 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: ENCBS121NNX at ENCODE; https://www.encodeproject.org/ENCBS121NNX/


title: total RNA-seq from GM19384 (ENCLB769KQZ)

description:
https://www.encodeproject.org/experiments/ENCSR159NRB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR159NRB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB769KQZ
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19384 cell line

value: GM19384 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: ENCBS967ZFI at ENCODE; https://www.encodeproject.org/ENCBS967ZFI/


title: Expt2_SD4

description: Library name: Expt2_SD4

value: brain

value: SD


title: PRO-cap from HEK293T (ENCLB152STL)

description:
https://www.encodeproject.org/experiments/ENCSR733DAS/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in ZNF143_T cells.
experiment encode accession: ENCSR733DAS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2026-01-16
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB152STL

source_name: Homo sapiens HEK293T cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF143 treated with 500 nM dTAGV-1 for 6 hours

value: female

tag: health state

value: embryonic

value: Haiyuan Yu, Cornell

value: Michael Guertin

tag: treatments

value: treatment_term_name:dTAGV-1; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS997DQU at ENCODE; https://www.encodeproject.org/ENCBS997DQU/


title: snATAC-seq from adrenal gland (ENCLB720FMG)

description:
https://www.encodeproject.org/experiments/ENCSR725OFZ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human adrenal gland
experiment encode accession: ENCSR725OFZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB720FMG
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 cryopreservation nuclear fraction

value: adrenal gland

value: tissue

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

tag: dev stage

value: adult

value: 59 year

tag: lab

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS563LOV at ENCODE; https://www.encodeproject.org/ENCBS563LOV/

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


title: total RNA-seq from GM21521 (ENCLB444PRB)

description:
https://www.encodeproject.org/experiments/ENCSR159HCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR159HCQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB444PRB
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21521 cell line

value: cell line

value: GM21521 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS499XYD at ENCODE; https://www.encodeproject.org/ENCBS499XYD/


title: total RNA-seq from CD14-positive monocyte (ENCLB179KWG)

description:
https://www.encodeproject.org/experiments/ENCSR158GGH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR158GGH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB179KWG
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens male adult (21 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

tag: age

value: 21 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS547NVW at ENCODE; https://www.encodeproject.org/ENCBS547NVW/


title: total RNA-seq from GM19436 (ENCLB163JFE)

description:
https://www.encodeproject.org/experiments/ENCSR160EEU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR160EEU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB163JFE
nucleic acid starting quantity: 48
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19436 cell line

tag: line

value: GM19436 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: female

value: adult

value: ENCBS563DXB at ENCODE; https://www.encodeproject.org/ENCBS563DXB/


title: Expt2_SD3

description: Library name: Expt2_SD3

value: brain

value: SD


title: PRO-cap from HEK293T (ENCLB911UAA)

description:
https://www.encodeproject.org/experiments/ENCSR733DAS/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in ZNF143_T cells.
experiment encode accession: ENCSR733DAS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2026-01-16
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB911UAA

value: cell line

tag: encode accession

value: unknown

value: embryonic

value: Haiyuan Yu, Cornell

value: Michael Guertin

value: treatment_term_name:dTAGV-1; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS868ZCQ at ENCODE; https://www.encodeproject.org/ENCBS868ZCQ/


title: total RNA-seq from HG03099 (ENCLB788XOC)

description:
https://www.encodeproject.org/experiments/ENCSR236JKN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR236JKN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB788XOC
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03099 cell line

tag: note

value: HG03099 LCLs; Donor from the Esan in Nigeria (ESN)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS771IEM at ENCODE; https://www.encodeproject.org/ENCBS771IEM/


title: snATAC-seq from Caco-2 (ENCLB242WXC)

description:
https://www.encodeproject.org/experiments/ENCSR908RCU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908RCU
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB242WXC
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens Caco-2 cell line nuclear fraction

value: male

value: colorectal adenocarcinoma

value: 72 year

value: Mats Ljungman, UMichigan

tag: subcellular fraction term name

value: nucleus

value: ATCC

value: ENCBS223KKT at ENCODE; https://www.encodeproject.org/ENCBS223KKT/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: total RNA-seq from GM18498 (ENCLB699TTR)

description:
https://www.encodeproject.org/experiments/ENCSR157QJQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157QJQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB699TTR
nucleic acid starting quantity: 25
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18498 cell line

value: cell line

value: GM18498 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: adult

value: unknown

value: ENCBS669DHV at ENCODE; https://www.encodeproject.org/ENCBS669DHV/

value: Derived from ENCODE donor ENCDO740YRZ; https://www.encodeproject.org/ENCDO740YRZ/


title: Expt2_PA1

description: Library name: Expt2_PA1

source_name: brain

tag: tissue

value: brain

value: PA


title: Expt2_PA2

description: Library name: Expt2_PA2

tag: genotype


title: snATAC-seq from heart left ventricle (ENCLB426BPP)

description:
https://www.encodeproject.org/experiments/ENCSR722PYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR722PYH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-09-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB426BPP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (69 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: female

value: 69 year

value: Michael Snyder, Stanford

value: Shin Lin

value: sarcoid (EF 24%, LVEDD 6.9, PWd 0.6)

value: ENCBS692UAY at ENCODE; https://www.encodeproject.org/ENCBS692UAY/

value: Derived from ENCODE donor ENCDO695LFW; https://www.encodeproject.org/ENCDO695LFW/


title: total RNA-seq from HG03458 (ENCLB630KPK)

description:
https://www.encodeproject.org/experiments/ENCSR156IFC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR156IFC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB630KPK
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03458 cell line

value: cell line

value: HG03458 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS556TLZ at ENCODE; https://www.encodeproject.org/ENCBS556TLZ/


title: snATAC-seq from left colon (ENCLB809AHD)

description:
https://www.encodeproject.org/experiments/ENCSR904WIW/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human left colon
experiment encode accession: ENCSR904WIW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB809AHD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: left colon

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

value: adult

value: 59 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS170SOC at ENCODE; https://www.encodeproject.org/ENCBS170SOC/

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


title: total RNA-seq from CD14-positive monocyte (ENCLB922UTX)

description:
https://www.encodeproject.org/experiments/ENCSR154CBP/
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biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154CBP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB922UTX

source_name: Homo sapiens male adult (24 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: male

value: 24 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS055HYQ at ENCODE; https://www.encodeproject.org/ENCBS055HYQ/


title: total RNA-seq from HG03123 (ENCLB980RJT)

description:
https://www.encodeproject.org/experiments/ENCSR156VTP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR156VTP
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB980RJT
nucleic acid starting quantity: 26
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03123 cell line

value: cell line

value: HG03123 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS605JLD at ENCODE; https://www.encodeproject.org/ENCBS605JLD/


title: snATAC-seq from heart left ventricle (ENCLB361LKO)

description:
https://www.encodeproject.org/experiments/ENCSR718YPN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718YPN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB361LKO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: non ischemic (EF 33%, LVEDD 6.8), familial

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS578OEH at ENCODE; https://www.encodeproject.org/ENCBS578OEH/

value: Derived from ENCODE donor ENCDO522PCG; https://www.encodeproject.org/ENCDO522PCG/