title: snATAC-seq from mucosa of descending colon (ENCLB585EGO)

description:
https://www.encodeproject.org/experiments/ENCSR605FGF/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR605FGF
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB585EGO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (61 years) mucosa of descending colon tissue, preserved by cryopreservation nuclear fraction

value: mucosa of descending colon

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

value: adult

value: 61 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS973WEQ at ENCODE; https://www.encodeproject.org/ENCBS973WEQ/

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


title: total RNA-seq from HG03212 (ENCLB049JXH)

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/ENCSR063HLA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063HLA
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB049JXH
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens HG03212 cell line

extract_protocol: not provided

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: note

value: HG03212 LCLs; Donor from the Mende in Sierra Leone (MSL)

tag: Sex

value: female

tag: dev stage

tag: lab

value: Stephen Montgomery, Stanford

tag: source

value: Coriell

tag: link

value: ENCBS894ASB at ENCODE; https://www.encodeproject.org/ENCBS894ASB/


title: snATAC-seq from gastrocnemius (ENCLB404GXH)

description:
https://www.encodeproject.org/experiments/ENCSR546WNG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR546WNG
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB404GXH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B6CASTF1/J gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

value: not collected

tag: age

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: The Jackson Laboratory

value: ENCBS911KWK at ENCODE; https://www.encodeproject.org/ENCBS911KWK/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snATAC-seq from gastrocnemius (ENCLB777IBZ)

description:
https://www.encodeproject.org/experiments/ENCSR531ZFB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR531ZFB
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB777IBZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: nucleus

value: ENCBS306WRP at ENCODE; https://www.encodeproject.org/ENCBS306WRP/


title: total RNA-seq from GM21341 (ENCLB809GBZ)

description:
https://www.encodeproject.org/experiments/ENCSR063GUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063GUM
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB809GBZ
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21341 cell line

value: GM21341 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: ENCBS582KAM at ENCODE; https://www.encodeproject.org/ENCBS582KAM/


title: total RNA-seq from GM21522 (ENCLB121WOK)

description:
https://www.encodeproject.org/experiments/ENCSR061IMG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR061IMG
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB121WOK
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21522 cell line

value: cell line

value: GM21522 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS496ZQW at ENCODE; https://www.encodeproject.org/ENCBS496ZQW/


title: snATAC-seq from heart right ventricle (ENCLB847JLV)

description:
https://www.encodeproject.org/experiments/ENCSR604PDO/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR604PDO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB847JLV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: heart right ventricle

value: female

tag: health state

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

value: 46 year

value: Yiing Lin, MD, PhD

value: ENCBS442ZGU at ENCODE; https://www.encodeproject.org/ENCBS442ZGU/

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


title: snATAC-seq from activated CD4-positive, alpha-beta T cell (ENCLB765OJP)

description:
https://www.encodeproject.org/experiments/ENCSR597YWW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR597YWW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB765OJP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (35 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads nuclear fraction

value: primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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

value: ENCBS755CSE at ENCODE; https://www.encodeproject.org/ENCBS755CSE/

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


title: total RNA-seq from GM19439 (ENCLB387SNL)

description:
https://www.encodeproject.org/experiments/ENCSR060QQK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR060QQK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB387SNL
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19439 cell line

value: cell line

value: GM19439 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS807GWB at ENCODE; https://www.encodeproject.org/ENCBS807GWB/


title: snATAC-seq from adrenal gland (ENCLB810QUN)

description:
https://www.encodeproject.org/experiments/ENCSR525WPH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR525WPH
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB810QUN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue nuclear fraction

value: adrenal gland

value: tissue

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS396SGF at ENCODE; https://www.encodeproject.org/ENCBS396SGF/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from HG03578 (ENCLB297FCO)

description:
https://www.encodeproject.org/experiments/ENCSR060KDT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR060KDT
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB297FCO
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03578 cell line

value: HG03578 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: ENCBS330NFA at ENCODE; https://www.encodeproject.org/ENCBS330NFA/


title: snATAC-seq from heart left ventricle (ENCLB079KRG)

description:
https://www.encodeproject.org/experiments/ENCSR594WKI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR594WKI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB079KRG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: heart left ventricle

tag: description

value: Homo sapiens heart left ventricle tissue

value: male

value: ischemic (EF 35%, LVEDD mild enlargement)

value: 68 year

value: Shin Lin

value: ENCBS519OPS at ENCODE; https://www.encodeproject.org/ENCBS519OPS/

value: Derived from ENCODE donor ENCDO076AMT; https://www.encodeproject.org/ENCDO076AMT/


title: total RNA-seq from HG03073 (ENCLB553GNC)

description:
https://www.encodeproject.org/experiments/ENCSR059RCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059RCN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB553GNC
nucleic acid starting quantity: 35
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03073 cell line

value: cell line

value: HG03073 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS331FII at ENCODE; https://www.encodeproject.org/ENCBS331FII/


title: snATAC-seq from left cerebral cortex (ENCLB576WBK)

description:
https://www.encodeproject.org/experiments/ENCSR521RLW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR521RLW
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB576WBK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: tissue

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS940SLP at ENCODE; https://www.encodeproject.org/ENCBS940SLP/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snATAC-seq from colonic mucosa (ENCLB791DXB)

description:
https://www.encodeproject.org/experiments/ENCSR593FCC/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human colonic mucosa
experiment encode accession: ENCSR593FCC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB791DXB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: colonic mucosa

value: female

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

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS354ZXK at ENCODE; https://www.encodeproject.org/ENCBS354ZXK/

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


title: total RNA-seq from HG02629 (ENCLB112RDM)

description:
https://www.encodeproject.org/experiments/ENCSR059GHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059GHC
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB112RDM
nucleic acid starting quantity: 52
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02629 cell line

value: cell line

value: HG02629 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS850LGX at ENCODE; https://www.encodeproject.org/ENCBS850LGX/


title: total RNA-seq from HG02813 (ENCLB839TBJ)

description:
https://www.encodeproject.org/experiments/ENCSR058EMK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR058EMK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB839TBJ
nucleic acid starting quantity: 42
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02813 cell line

value: HG02813 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: ENCBS683QFX at ENCODE; https://www.encodeproject.org/ENCBS683QFX/


title: snATAC-seq from left cerebral cortex (ENCLB613FCX)

description:
https://www.encodeproject.org/experiments/ENCSR502SUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR502SUM
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB613FCX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: left cerebral cortex

value: tissue

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS766VSB at ENCODE; https://www.encodeproject.org/ENCBS766VSB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from HG03452 (ENCLB587YFC)

description:
https://www.encodeproject.org/experiments/ENCSR055TOH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR055TOH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB587YFC
nucleic acid starting quantity: 40
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03452 cell line

value: cell line

value: HG03452 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: female

value: ENCBS747WUP at ENCODE; https://www.encodeproject.org/ENCBS747WUP/


title: total RNA-seq from HG02645 (ENCLB338OMJ)

description:
https://www.encodeproject.org/experiments/ENCSR055PWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR055PWN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB338OMJ
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02645 cell line

value: HG02645 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS273SKW at ENCODE; https://www.encodeproject.org/ENCBS273SKW/


title: snATAC-seq from lower lobe of left lung (ENCLB819AVA)

description:
https://www.encodeproject.org/experiments/ENCSR592WYM/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human lower lobe of left lung
experiment encode accession: ENCSR592WYM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB819AVA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: lower lobe of left lung

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

value: 59 year

value: Yiing Lin, MD, PhD

value: ENCBS274HRN at ENCODE; https://www.encodeproject.org/ENCBS274HRN/

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


title: snATAC-seq from layer of hippocampus (ENCLB044TOU)

description:
https://www.encodeproject.org/experiments/ENCSR482ORB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR482ORB
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB044TOU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: tissue

value: not collected

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS502QAA at ENCODE; https://www.encodeproject.org/ENCBS502QAA/


title: total RNA-seq from HG02887 (ENCLB140JYX)

description:
https://www.encodeproject.org/experiments/ENCSR046SVK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR046SVK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB140JYX
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02887 cell line

value: cell line

value: HG02887 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: male

value: adult

value: ENCBS097FAN at ENCODE; https://www.encodeproject.org/ENCBS097FAN/


title: snATAC-seq from heart right ventricle (ENCLB013VAY)

description:
https://www.encodeproject.org/experiments/ENCSR588PEE/
***************
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 (ENCSR060ZXZ).
experiment encode accession: ENCSR588PEE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB013VAY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: heart right ventricle

value: female

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

value: 46 year

value: ENCBS717WTC at ENCODE; https://www.encodeproject.org/ENCBS717WTC/

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


title: total RNA-seq from GM18486 (ENCLB708NXY)

description:
https://www.encodeproject.org/experiments/ENCSR045PFH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR045PFH
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB708NXY
nucleic acid starting quantity: 53
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18486 cell line

value: GM18486 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS633ZRB at ENCODE; https://www.encodeproject.org/ENCBS633ZRB/


title: total RNA-seq from suppressor macrophage (ENCLB003CAV)

description:
https://www.encodeproject.org/experiments/ENCSR040ZFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR040ZFV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB003CAV

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

value: suppressor macrophage

value: primary cell

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS972SPP at ENCODE; https://www.encodeproject.org/ENCBS972SPP/


title: snATAC-seq from gastrocnemius (ENCLB878EBG)

description:
https://www.encodeproject.org/experiments/ENCSR451PWE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR451PWE
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB878EBG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J female (2 months) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

value: Encode B6CastF1 2 months female #1 Gastroc.

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: nucleus

value: The Jackson Laboratory

value: ENCBS589EZL at ENCODE; https://www.encodeproject.org/ENCBS589EZL/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snATAC-seq from HCT116 (ENCLB006VYI)

description:
https://www.encodeproject.org/experiments/ENCSR587XSM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR587XSM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB006VYI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1 uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Michael Snyder, Stanford

value: Dr. Masato Kanemaki

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

value: ENCBS441NUR at ENCODE; https://www.encodeproject.org/ENCBS441NUR/

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


title: total RNA-seq from GM19346 (ENCLB943OLZ)

description:
https://www.encodeproject.org/experiments/ENCSR039KCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR039KCN
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB943OLZ
nucleic acid starting quantity: 38
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM19346 cell line

value: GM19346 LCLs; Donor from the Luhya in Webuye, Kenya (LWK)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS459IXM at ENCODE; https://www.encodeproject.org/ENCBS459IXM/


title: total RNA-seq from HG02820 (ENCLB794DLL)

description:
https://www.encodeproject.org/experiments/ENCSR038ZQK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR038ZQK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB794DLL
nucleic acid starting quantity: 42
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02820 cell line

value: HG02820 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: ENCBS491ZXF at ENCODE; https://www.encodeproject.org/ENCBS491ZXF/


title: snATAC-seq from layer of hippocampus (ENCLB496MUX)

description:
https://www.encodeproject.org/experiments/ENCSR425RRQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR425RRQ
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB496MUX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: layer of hippocampus

value: tissue

value: not collected

value: nucleus

value: The Jackson Laboratory

value: ENCBS282ICD at ENCODE; https://www.encodeproject.org/ENCBS282ICD/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from GM21517 (ENCLB447EFF)

description:
https://www.encodeproject.org/experiments/ENCSR038YSS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR038YSS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB447EFF
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21517 cell line

value: cell line

value: GM21517 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: adult

value: ENCBS259ZHJ at ENCODE; https://www.encodeproject.org/ENCBS259ZHJ/


title: snATAC-seq from heart right ventricle (ENCLB941SVG)

description:
https://www.encodeproject.org/experiments/ENCSR579TPC/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR579TPC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB941SVG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: heart right ventricle

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

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS158VHF at ENCODE; https://www.encodeproject.org/ENCBS158VHF/

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


title: snATAC-seq from layer of hippocampus (ENCLB172CBX)

description:
https://www.encodeproject.org/experiments/ENCSR401ARG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR401ARG
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB172CBX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue, preserved by flash-freezing nuclear fraction

value: layer of hippocampus

value: tissue

value: ENCBS749FCK at ENCODE; https://www.encodeproject.org/ENCBS749FCK/


title: total RNA-seq from GM18489 (ENCLB784FZF)

description:
https://www.encodeproject.org/experiments/ENCSR038NUI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR038NUI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB784FZF
nucleic acid starting quantity: 29
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18489 cell line

value: GM18489 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS796ULZ at ENCODE; https://www.encodeproject.org/ENCBS796ULZ/


title: snATAC-seq from chondrocyte (ENCLB770AYK)

description:
https://www.encodeproject.org/experiments/ENCSR575LID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR575LID
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB770AYK
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: nucleus

value: SESCC

value: ENCBS407ILA at ENCODE; https://www.encodeproject.org/ENCBS407ILA/

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


title: total RNA-seq from GM21443 (ENCLB171UXV)

description:
https://www.encodeproject.org/experiments/ENCSR029OEU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029OEU
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB171UXV
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21443 cell line

value: cell line

value: GM21443 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: ENCBS088KUU at ENCODE; https://www.encodeproject.org/ENCBS088KUU/


title: total RNA-seq from HG03078 (ENCLB345NXF)

description:
https://www.encodeproject.org/experiments/ENCSR029GJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029GJS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB345NXF
nucleic acid starting quantity: 28
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03078 cell line

value: HG03078 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS987GIH at ENCODE; https://www.encodeproject.org/ENCBS987GIH/


title: snATAC-seq from right lobe of liver (ENCLB059PMJ)

description:
https://www.encodeproject.org/experiments/ENCSR568XID/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human right lobe of liver
experiment encode accession: ENCSR568XID
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB059PMJ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (45 years) right lobe of liver tissue, preserved by cryopreservation nuclear fraction

value: right lobe of liver

value: tissue

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

value: 45 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS840ZJL at ENCODE; https://www.encodeproject.org/ENCBS840ZJL/

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


title: total RNA-seq from GM21352 (ENCLB528KQB)

description:
https://www.encodeproject.org/experiments/ENCSR028PMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR028PMB
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB528KQB
nucleic acid starting quantity: 23
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21352 cell line

value: cell line

value: GM21352 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS735KPB at ENCODE; https://www.encodeproject.org/ENCBS735KPB/


title: snATAC-seq from heart (ENCLB359PDJ)

description:
https://www.encodeproject.org/experiments/ENCSR376OIU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR376OIU
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB359PDJ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue nuclear fraction

value: heart

value: Encode B6CastF1 2 months male #2 Heart

value: male

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: nucleus

value: The Jackson Laboratory

value: ENCBS166CVE at ENCODE; https://www.encodeproject.org/ENCBS166CVE/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from GM21363 (ENCLB111CPO)

description:
https://www.encodeproject.org/experiments/ENCSR025LOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025LOD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB111CPO
nucleic acid starting quantity: 47
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21363 cell line

value: GM21363 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS893HRS at ENCODE; https://www.encodeproject.org/ENCBS893HRS/


title: Control ChIP-seq from K562 (ENCLB079VNZ)

description:
https://www.encodeproject.org/experiments/ENCSR562EHT/
***************
biological replicate number: 1
technical replicate number: 1
description: Input for K562 cells treated with shRNA targeting GATA1
experiment encode accession: ENCSR562EHT
assay title: Control ChIP-seq
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB079VNZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line expressing RNAi targeting H. sapiens GATA1

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS100YUF at ENCODE; https://www.encodeproject.org/ENCBS100YUF/


title: snATAC-seq from gastrocnemius (ENCLB538GYO)

description:
https://www.encodeproject.org/experiments/ENCSR334WIT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR334WIT
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB538GYO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: gastrocnemius

value: tissue

value: Encode B6CastF1 2 months female #2 Gastroc.

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: ENCBS455FAA at ENCODE; https://www.encodeproject.org/ENCBS455FAA/


title: total RNA-seq from GM21719 (ENCLB349CNE)

description:
https://www.encodeproject.org/experiments/ENCSR022BLY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR022BLY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB349CNE
nucleic acid starting quantity: 47
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21719 cell line

value: GM21719 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: adult

value: ENCBS345NEB at ENCODE; https://www.encodeproject.org/ENCBS345NEB/


title: total RNA-seq from GM21476 (ENCLB729GRC)

description:
https://www.encodeproject.org/experiments/ENCSR022CXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR022CXD
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB729GRC
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21476 cell line

value: cell line

value: GM21476 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS441IBB at ENCODE; https://www.encodeproject.org/ENCBS441IBB/


title: snATAC-seq from adrenal gland (ENCLB701VDT)

description:
https://www.encodeproject.org/experiments/ENCSR400PXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR400PXQ
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB701VDT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue nuclear fraction

value: adrenal gland

value: Michael Snyder, Stanford

value: nucleus

value: The Jackson Laboratory

value: ENCBS277UYJ at ENCODE; https://www.encodeproject.org/ENCBS277UYJ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snATAC-seq from gastrocnemius (ENCLB224KFY)

description:
https://www.encodeproject.org/experiments/ENCSR322HGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR322HGX
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB224KFY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: tissue

value: not collected

value: ENCBS234LLL at ENCODE; https://www.encodeproject.org/ENCBS234LLL/


title: snATAC-seq from heart left ventricle (ENCLB849SJA)

description:
https://www.encodeproject.org/experiments/ENCSR556UHL/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart left ventricle
experiment encode accession: ENCSR556UHL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB849SJA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: heart left ventricle

value: male

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

value: adult

value: 61 year

value: Shin Lin

value: ENCBS747KKI at ENCODE; https://www.encodeproject.org/ENCBS747KKI/

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


title: snATAC-seq from Right ventricle myocardium superior (ENCLB316WEN)

description:
https://www.encodeproject.org/experiments/ENCSR548IRG/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on human right ventricle myocardium superior. Please note that this experiment is part of 10x multiome and has a corresponding scRNA experiment (ENCSR813PWQ)
experiment encode accession: ENCSR548IRG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB316WEN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (60 years) Right ventricle myocardium superior tissue nuclear fraction

value: Right ventricle myocardium superior

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

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS296OWY at ENCODE; https://www.encodeproject.org/ENCBS296OWY/

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


title: total RNA-seq from HG03040 (ENCLB319UNW)

description:
https://www.encodeproject.org/experiments/ENCSR019NBI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR019NBI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB319UNW
nucleic acid starting quantity: 14
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03040 cell line

value: cell line

value: HG03040 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: female

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS548FOX at ENCODE; https://www.encodeproject.org/ENCBS548FOX/


title: total RNA-seq from suppressor macrophage (ENCLB701IVF)

description:
https://www.encodeproject.org/experiments/ENCSR019RPZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR019RPZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2026-01-26
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB701IVF

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

value: suppressor macrophage

value: primary cell

value: male

value: adult

value: 40 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS598XMI at ENCODE; https://www.encodeproject.org/ENCBS598XMI/


title: total RNA-seq from HG03139 (ENCLB575IAZ)

description:
https://www.encodeproject.org/experiments/ENCSR018OWO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018OWO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB575IAZ
nucleic acid starting quantity: 39
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03139 cell line

value: HG03139 LCLs; Donor from the Esan in Nigeria (ESN)

value: unknown

value: ENCBS174WCF at ENCODE; https://www.encodeproject.org/ENCBS174WCF/

value: Derived from ENCODE donor ENCDO021JCP; https://www.encodeproject.org/ENCDO021JCP/


title: snATAC-seq from heart (ENCLB309ESS)

description:
https://www.encodeproject.org/experiments/ENCSR300TZG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR300TZG
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB309ESS
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Mus musculus strain B6CASTF1/J female (2 months) heart tissue nuclear fraction

value: heart

value: tissue

value: Encode B6CastF1 2 months female #2 Heart

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: nucleus

value: The Jackson Laboratory

value: ENCBS019YAH at ENCODE; https://www.encodeproject.org/ENCBS019YAH/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: snATAC-seq from lower lobe of right lung (ENCLB170TGA)

description:
https://www.encodeproject.org/experiments/ENCSR548BXU/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human lower lobe of right lung
experiment encode accession: ENCSR548BXU
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB170TGA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens female adult (65 years) lower lobe of right lung tissue, preserved by cryopreservation nuclear fraction

value: lower lobe of right lung

value: female

value: lung transplant recipient with obliterative bronchiolitis; tissue sample from explanted lung

value: adult

value: 65 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS924OHQ at ENCODE; https://www.encodeproject.org/ENCBS924OHQ/

value: Derived from ENCODE donor ENCDO719GRD; https://www.encodeproject.org/ENCDO719GRD/


title: total RNA-seq from HG03517 (ENCLB406AJA)

description:
https://www.encodeproject.org/experiments/ENCSR014QPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR014QPI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB406AJA
nucleic acid starting quantity: 34
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03517 cell line

value: cell line

value: HG03517 LCLs; Donor from the Esan in Nigeria (ESN)

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS639RQV at ENCODE; https://www.encodeproject.org/ENCBS639RQV/


title: total RNA-seq from HG03343 (ENCLB916TID)

description:
https://www.encodeproject.org/experiments/ENCSR016KCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR016KCQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB916TID
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03343 cell line

value: HG03343 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: ENCBS606DTU at ENCODE; https://www.encodeproject.org/ENCBS606DTU/


title: snATAC-seq from left cerebral cortex (ENCLB308BXG)

description:
https://www.encodeproject.org/experiments/ENCSR265XVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR265XVL
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB308BXG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J female (2 months) left cerebral cortex tissue nuclear fraction

value: left cerebral cortex

value: tissue

value: Encode B6CastF1 2 months female #1 L. Cortex

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: nucleus

value: The Jackson Laboratory

value: ENCBS680HBI at ENCODE; https://www.encodeproject.org/ENCBS680HBI/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from GM21524 (ENCLB102YDR)

description:
https://www.encodeproject.org/experiments/ENCSR011CTI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR011CTI
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB102YDR
nucleic acid starting quantity: 32
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21524 cell line

value: cell line

value: GM21524 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: female

value: adult

value: ENCBS764GAN at ENCODE; https://www.encodeproject.org/ENCBS764GAN/


title: snATAC-seq from heart left ventricle (ENCLB717OWY)

description:
https://www.encodeproject.org/experiments/ENCSR546WZB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR546WZB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB717OWY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: 47 year

value: Michael Snyder, Stanford

value: Shin Lin

value: healthy

value: ENCBS546CBA at ENCODE; https://www.encodeproject.org/ENCBS546CBA/

value: Derived from ENCODE donor ENCDO280SCV; https://www.encodeproject.org/ENCDO280SCV/


title: total RNA-seq from HG03521 (ENCLB192LIG)

description:
https://www.encodeproject.org/experiments/ENCSR009PIF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR009PIF
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB192LIG
nucleic acid starting quantity: 33
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03521 cell line

value: HG03521 LCLs; Donor from the Esan in Nigeria (ESN)

value: male

value: unknown

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS053ERX at ENCODE; https://www.encodeproject.org/ENCBS053ERX/

value: Derived from ENCODE donor ENCDO992EYG; https://www.encodeproject.org/ENCDO992EYG/


title: snATAC-seq from left ventricle myocardium inferior (ENCLB124VNW)

description:
https://www.encodeproject.org/experiments/ENCSR541CKC/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human left ventricle myocardium inferior
experiment encode accession: ENCSR541CKC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB124VNW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue, preserved by cryopreservation nuclear fraction

value: left ventricle myocardium inferior

value: tissue

value: Inferior wall of left ventricle.

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

value: adult

value: 60 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS764NDF at ENCODE; https://www.encodeproject.org/ENCBS764NDF/

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


title: total RNA-seq from HG03372 (ENCLB335VAY)

description:
https://www.encodeproject.org/experiments/ENCSR008AAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR008AAJ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB335VAY
nucleic acid starting quantity: 31
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03372 cell line

value: cell line

value: HG03372 LCLs; Donor from the Esan in Nigeria (ESN)

value: female

value: ENCBS870JAT at ENCODE; https://www.encodeproject.org/ENCBS870JAT/


title: snATAC-seq from heart (ENCLB435KAM)

description:
https://www.encodeproject.org/experiments/ENCSR242ITJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR242ITJ
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB435KAM
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue nuclear fraction

value: heart

value: Encode B6CastF1 2 months male #1 Heart

value: male

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS405XFL at ENCODE; https://www.encodeproject.org/ENCBS405XFL/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from HG02613 (ENCLB026ZEF)

description:
https://www.encodeproject.org/experiments/ENCSR007NUY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007NUY
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB026ZEF
nucleic acid starting quantity: 37
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG02613 cell line

value: HG02613 LCLs; Donor from the Gambian in Western Divisions in the Gambia (GWD)

value: adult

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS656SCG at ENCODE; https://www.encodeproject.org/ENCBS656SCG/


title: snATAC-seq from adrenal gland (ENCLB361OIH)

description:
https://www.encodeproject.org/experiments/ENCSR024LKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR024LKR
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB361OIH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J adrenal gland tissue nuclear fraction

value: adrenal gland

value: tissue

value: Michael Snyder, Stanford

value: nucleus

value: ENCBS941IRK at ENCODE; https://www.encodeproject.org/ENCBS941IRK/


title: total RNA-seq from GM21351 (ENCLB023QRP)

description:
https://www.encodeproject.org/experiments/ENCSR006WEQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR006WEQ
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB023QRP
nucleic acid starting quantity: 24
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21351 cell line

value: cell line

value: GM21351 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: male

value: ENCBS293QOL at ENCODE; https://www.encodeproject.org/ENCBS293QOL/


title: total RNA-seq from GM21410 (ENCLB333UHA)

description:
https://www.encodeproject.org/experiments/ENCSR004YFS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004YFS
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB333UHA
nucleic acid starting quantity: 19
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM21410 cell line

value: GM21410 LCLs; Donor from the Maasai in Kinyawa, Kenya (MKK)

value: ENCBS929HLW at ENCODE; https://www.encodeproject.org/ENCBS929HLW/


title: total RNA-seq from GM18915 (ENCLB923AQN)

description:
https://www.encodeproject.org/experiments/ENCSR001WWO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR001WWO
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB923AQN
nucleic acid starting quantity: 22
nucleic acid starting quantity units: µg

source_name: Homo sapiens GM18915 cell line

value: GM18915 LCLs; Donor from the Yoruba in Ibadan, Nigeria (YRI)

value: ENCBS314VEV at ENCODE; https://www.encodeproject.org/ENCBS314VEV/


title: snATAC-seq from layer of hippocampus (ENCLB959NWW)

description:
https://www.encodeproject.org/experiments/ENCSR021UQR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR021UQR
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB959NWW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J layer of hippocampus tissue nuclear fraction

value: layer of hippocampus

value: not collected

value: The Jackson Laboratory

value: ENCBS432HEQ at ENCODE; https://www.encodeproject.org/ENCBS432HEQ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: Control ChIP-seq from K562 (ENCLB706JKG)

description:
https://www.encodeproject.org/experiments/ENCSR538UCE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input for K562 cells treated with shRNA targeting MAFF
experiment encode accession: ENCSR538UCE
assay title: Control ChIP-seq
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB706JKG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS785WKC at ENCODE; https://www.encodeproject.org/ENCBS785WKC/


title: total RNA-seq from HG03081 (ENCLB745NNS)

description:
https://www.encodeproject.org/experiments/ENCSR000VUK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000VUK
assay title: total RNA-seq
encode release date: 2026-05-12
lab: Stephen Montgomery, Stanford
library encode accession: ENCLB745NNS
nucleic acid starting quantity: 4
nucleic acid starting quantity units: µg

source_name: Homo sapiens HG03081 cell line

value: cell line

value: HG03081 LCLs; Donor from the Mende in Sierra Leone (MSL)

value: male

value: Stephen Montgomery, Stanford

value: Coriell

value: ENCBS269RKQ at ENCODE; https://www.encodeproject.org/ENCBS269RKQ/


title: snATAC-seq from heart right ventricle (ENCLB661MZC)

description:
https://www.encodeproject.org/experiments/ENCSR534KYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR534KYJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB661MZC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (46 years) heart right ventricle tissue, preserved by cryopreservation nuclear fraction

value: heart right ventricle

value: tissue

value: Arrhythmogenic right ventricular cardiomyopathy

value: 46 year

value: Michael Snyder, Stanford

value: nucleus

value: Shin Lin

value: ENCBS882TGY at ENCODE; https://www.encodeproject.org/ENCBS882TGY/

value: Derived from ENCODE donor ENCDO014LAW; https://www.encodeproject.org/ENCDO014LAW/


title: snATAC-seq from gastrocnemius (ENCLB045RZO)

description:
https://www.encodeproject.org/experiments/ENCSR012QUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR012QUJ
assay title: snATAC-seq
assembly: mm10
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB045RZO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Mus musculus strain B6CASTF1/J male (2 months) gastrocnemius tissue nuclear fraction

value: gastrocnemius

value: Encode B6CastF1 2 months male #1 Gastroc

value: not collected

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS618FPS at ENCODE; https://www.encodeproject.org/ENCBS618FPS/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: BMMC_Taxinine_3

city: Gangneung si

first: Wook-Bin

last: Lee

state: Gangwon do

address: 679 Saimdang-ro

department: Natural Product Efficacy Optimization Research Center

country: South Korea

institute: Korea Institute of Science and Technology

description:
Library name: Tax3
C57BL/6 mouse bone marrow-derived mast cells; IgE/DNP-BSA stimulated + taxinine treatment

data_processing:
Reads cleaned with HTStream v1.1.0.
Aligned with STAR v2.7.0f to the mouse reference genome, assembly mm10 (GRCm38).
Counts compiled with custom R scripts; transcripts with median CPM > 1 retained (15,109 transcripts).
Differential expression with limma v3.11 on TMM-normalized log2-CPM values.
Assembly: mm10 (GRCm38)
Supplementary files format and content: CSV; genes (rows) x samples (columns). TMM-normalized counts (GEO_processed_TMMnorm_counts_9samples.csv); log2-CPM version also provided (GEO_processed_log2CPM_9samples.csv).

molecule: polyA RNA

source_name: bone marrow-derived mast cell (BMMC)

growth_protocol: Bone-marrow cells from C57BL/6 mice cultured in DMEM with 30% WEHI-3-conditioned medium, 20% heat-inactivated FBS, and penicillin/streptomycin; medium changed twice weekly for >=4 weeks to obtain mature, high-purity BMMCs.

extract_protocol:
Total RNA isolated with HybridR kit (GeneAll); RNA quality assessed on a 2100 Bioanalyzer (Agilent) and NanoDrop 2000 (Thermo Fisher).
Libraries prepared with TruSeq Stranded mRNA (Illumina); polyA-selected cDNA; paired-end (2x101 bp).

treatment_protocol: BMMCs were sensitized with anti-DNP-IgE, pretreated with or without taxinine for 1 h, and stimulated with DNP-BSA.

tag: strain

tag: cell type

value: bone marrow-derived mast cell (BMMC)

tag: genotype

value: wild-type

tag: treatment


title: snATAC-seq from ovary (ENCLB368GMZ)

description:
https://www.encodeproject.org/experiments/ENCSR533CSY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR533CSY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB368GMZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: ovary

value: tissue

tag: biosample encode accession

value: female

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

value: child

value: 16 year

value: Yiing Lin, MD, PhD

value: ENCBS510IAV at ENCODE; https://www.encodeproject.org/ENCBS510IAV/

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


title: U87MG, Input

city: Providence

first: Abigail

middle: K

last: Brown

state: RI

address: 70 Ship Street

department: Molecular Biology, Cell Biology, Biochemistry

institute: Brown University

data_processing:
Sequences were trimmed for Illumina adaptors using Trimmomatic.
ChIP-seq reads were then aligned to the human geneome (hg19) using Hisat2. Quality filtering was performed and peaks were called using MACS2.
BedGraph track files were generated using UCSC utilities in order to display the coverage throughout the genome
Assembly: hg19
Supplementary files format and content: BedGraph
Supplementary files format and content: narrowPeak (Input data incorporated)

source_name: Cell line

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

extract_protocol:
Cells were fixed with 1% formaladehyde for 10 minutes and then quenched with 0.125M Glycine for 5 minutes. Chromatin was sonicated using Bioruptor for 10 minutes.
ChIP-seq libraries were prepared using Illumina's NEBNext Ultra II DNA library Prep Kit.

tag: tissue

value: Cell line

tag: cell line

value: Human Glioblastoma

value: WT


title: U87MG, FLAG, Sigma-Aldrich


title: U87MG cells, 14d Etoposide, rep3

description:
Senescence_gene_count_matrix.csv
ABW6

data_processing:
Sequences were trimmed for Illumina adaptors using Trimmomatic.
Reads were then aligned to the human geneome (hg19) using Hisat2
Aligned reads were assembled using StringTie and the expression levels of all transcripts were estimated.
Assembly: hg19
Supplementary files format and content: CSV file includes the raw gene counts for all the transcripts

source_name: cell line

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

extract_protocol:
Total RNA was extracted with the Qiagen Rneasy mini kit
Libraries were constructed using the NEB Next Ultra III library kit for Illumina

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

value: cell line

value: Glioblastoma

value: 10µM etoposide 14 days


title: snATAC-seq from heart left ventricle (ENCLB846KBC)

description:
https://www.encodeproject.org/experiments/ENCSR531ZKI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR531ZKI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB846KBC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

tag: Sex

value: male

value: nonischemic (EF 21%, LVEDD 7.5)

value: adult

value: 68 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS210THB at ENCODE; https://www.encodeproject.org/ENCBS210THB/

value: Derived from ENCODE donor ENCDO038QFX; https://www.encodeproject.org/ENCDO038QFX/


title: U87MG cells, 14d Etoposide, rep2

description:
Senescence_gene_count_matrix.csv
ABW5


title: U87MG cells, 14d Etoposide, rep1

description:
Senescence_gene_count_matrix.csv
ABW4


title: U87MG cells, 3d Etoposide, rep3

description:
Senescence_gene_count_matrix.csv
ABW3

value: 10µM etoposide 3 days


title: BMMC_Taxinine_1

description:
Library name: Tax1
C57BL/6 mouse bone marrow-derived mast cells; IgE/DNP-BSA stimulated + taxinine treatment

value: bone marrow-derived mast cell (BMMC)

value: wild-type


title: snATAC-seq from heart right ventricle (ENCLB928GNO)

description:
https://www.encodeproject.org/experiments/ENCSR520ZUD/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR520ZUD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB928GNO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: heart right ventricle

value: tissue

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

tag: dev stage

value: 73 year

value: nucleus

value: ENCBS779QVN at ENCODE; https://www.encodeproject.org/ENCBS779QVN/

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


title: U87MG cells, 3d Etoposide, rep2

description:
Senescence_gene_count_matrix.csv
ABW2

value: cell line

value: Glioblastoma

value: WT


title: U87MG cells, FOXO3 shRNA, rep3

description:
F3KD_gene_count_matrix.csv
AB6

value: FOXO3 knockdown


title: BMMC_Taxinine_2

description:
Library name: Tax2
C57BL/6 mouse bone marrow-derived mast cells; IgE/DNP-BSA stimulated + taxinine treatment


title: snATAC-seq from endothelial cell of umbilical vein (ENCLB258PWG)

description:
https://www.encodeproject.org/experiments/ENCSR516MHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR516MHK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB258PWG
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male newborn endothelial of umbilical vein primary cell nuclear fraction

value: endothelial cell of umbilical vein

value: primary cell

value: male

value: newborn

value: not collected

tag: lab

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS610TZC at ENCODE; https://www.encodeproject.org/ENCBS610TZC/

value: Derived from ENCODE donor ENCDO628LXZ; https://www.encodeproject.org/ENCDO628LXZ/


title: snATAC-seq from heart right ventricle (ENCLB362AUG)

description:
https://www.encodeproject.org/experiments/ENCSR517QNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR517QNQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB362AUG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: heart right ventricle

value: tissue

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

value: adult

value: 66 year

value: Michael Snyder, Stanford

tag: source

value: Shin Lin

value: ENCBS875SYA at ENCODE; https://www.encodeproject.org/ENCBS875SYA/

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


title: BMMC_BSA_3

description:
Library name: BSA3
C57BL/6 mouse bone marrow-derived mast cells; IgE-sensitized (anti-DNP-IgE) + DNP-BSA stimulated

value: bone marrow-derived mast cell (BMMC)

value: wild-type


title: U87MG cells, 3d Etoposide, rep1

description:
Senescence_gene_count_matrix.csv
ABW1

value: cell line

value: Glioblastoma

value: WT

value: 10µM etoposide 3 days


title: BMMC_BSA_2

description:
Library name: BSA2
C57BL/6 mouse bone marrow-derived mast cells; IgE-sensitized (anti-DNP-IgE) + DNP-BSA stimulated


title: U87MG cells, FOXO3 shRNA, rep2

description:
F3KD_gene_count_matrix.csv
AB5

value: FOXO3 knockdown


title: snATAC-seq from heart left ventricle (ENCLB175TKM)

description:
https://www.encodeproject.org/experiments/ENCSR511VYN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR511VYN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB175TKM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (48 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: Homo sapiens heart left ventricle tissue

value: female

value: 48 year

value: healthy

tag: link

value: ENCBS078WTV at ENCODE; https://www.encodeproject.org/ENCBS078WTV/

value: Derived from ENCODE donor ENCDO817MDD; https://www.encodeproject.org/ENCDO817MDD/


title: U87MG cells, FOXO3 shRNA, rep1

description:
F3KD_gene_count_matrix.csv
AB4


title: U87MG cells, shControl, rep3

description:
F3KD_gene_count_matrix.csv
AB3


title: BMMC_BSA_1

description:
Library name: BSA1
C57BL/6 mouse bone marrow-derived mast cells; IgE-sensitized (anti-DNP-IgE) + DNP-BSA stimulated


title: U87MG cells, shControl, rep2

description:
F3KD_gene_count_matrix.csv
AB2


title: Expt2_GDCA4

first: Meenakshi

last: Chakraborty

address: 269 Campus Drive

institute: Stanford University

description: Library name: Expt2_GDCA4

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

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.

value: brain

value: GDCA


title: U87MG cells, shControl, rep1

description:
F3KD_gene_count_matrix.csv
AB1


title: snATAC-seq from heart left ventricle (ENCLB746WVZ)

description:
https://www.encodeproject.org/experiments/ENCSR506ROZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR506ROZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB746WVZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (58 years) heart left ventricle tissue, preserved by flash-freezing

value: tissue

value: male

value: ischemic (EF 30%, LVEDD 5.8)

value: adult

tag: age

value: 58 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS352UMO at ENCODE; https://www.encodeproject.org/ENCBS352UMO/

value: Derived from ENCODE donor ENCDO545EJY; https://www.encodeproject.org/ENCDO545EJY/


title: U87MG cells, FOXO3 Act.8hrs, rep3

description:
FOXO3Act_gene_count_matrix.csv
ABR9

value: cell line

value: Glioblastoma

value: WT

value: FOXO3 activation


title: U87MG cells, FOXO3 Act.16hrs, rep3

description:
FOXO3Act_gene_count_matrix.csv
ABR8


title: snATAC-seq from dendritic cell (ENCLB601CIX)

description:
https://www.encodeproject.org/experiments/ENCSR507ZEN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR507ZEN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB601CIX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (51 years) dendritic primary cell treated with 50 ng/mL granulocyte-macrophage colony-stimulating factor for 4 days, 40 ng/mL Interleukin-4 for 4 days nuclear fraction

value: dendritic cell

value: primary cell

value: 51 year

value: Yijun Ruan, JAX

tag: subcellular fraction term name

value: nucleus

value: AllCells

value: treatment_term_id:UniProtKB:P04141; treatment_term_name:granulocyte-macrophage colony-stimulating factor; treatment_type:protein; duration:4; duration_units:day; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:4; duration_units:day;

value: ENCBS299GOH at ENCODE; https://www.encodeproject.org/ENCBS299GOH/

value: Derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: BMMC_Control_3

description:
Library name: No3
C57BL/6 mouse bone marrow-derived mast cells; untreated normal control

value: bone marrow-derived mast cell (BMMC)

value: wild-type

value: untreated normal control


title: BMMC_Control_2

description:
Library name: No2
C57BL/6 mouse bone marrow-derived mast cells; untreated normal control


title: U87MG cells, GFP control, rep3

description:
FOXO3Act_gene_count_matrix.csv
ABR7

value: GFP control


title: BMMC_Control_1

description:
Library name: No1
C57BL/6 mouse bone marrow-derived mast cells; untreated normal control


title: U87MG cells, GFP control, rep2

description:
FOXO3Act_gene_count_matrix.csv
ABR6

value: cell line


title: snATAC-seq from right cardiac atrium (ENCLB410SYY)

description:
https://www.encodeproject.org/experiments/ENCSR499VTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR499VTJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB410SYY
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: right cardiac atrium

value: tissue

value: female

tag: health state

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

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS757KBR at ENCODE; https://www.encodeproject.org/ENCBS757KBR/

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


title: U87MG cells, FOXO3 Act.16hrs, rep2

description:
FOXO3Act_gene_count_matrix.csv
ABR5

value: Glioblastoma

value: WT

value: FOXO3 activation


title: snATAC-seq from pancreas (ENCLB669MTO)

description:
https://www.encodeproject.org/experiments/ENCSR496XXB/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC on human pancreas. Please note that this experiment is part of 10x multiome and has a correspoding scRNA experiment (ENCSR261BXB).
experiment encode accession: ENCSR496XXB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB669MTO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: pancreas

value: male

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

value: 26 year

value: nucleus

value: ENCBS995XKZ at ENCODE; https://www.encodeproject.org/ENCBS995XKZ/

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


title: U87MG cells, FOXO3 Act.8hrs, rep2

description:
FOXO3Act_gene_count_matrix.csv
ABR4

value: cell line


title: U87MG cells, GFP control, rep1

description:
FOXO3Act_gene_count_matrix.csv
ABR3

value: GFP control


title: Library 6 CITE-seq CD8+ T cells, V(D)J TCR

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

description:
Library name: Library_6_TCR
10x Genomics Chromium Single Cell 5' V(D)J TCR library from lineage-traced CD8+ T cells.

library_source: other

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

molecule: other

source_name: Tumor and lymph node

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

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

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

value: Tumor and lymph node

value: Sorted CD8+ T cells

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

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

tag: batch


title: snATAC-seq from heart left ventricle (ENCLB286ZEY)

description:
https://www.encodeproject.org/experiments/ENCSR495SMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR495SMB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB286ZEY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (32 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

tag: description

value: Homo sapiens heart left ventricle tissue

value: female

value: nonischemic (EF 14%, LVEDD 8.8)

value: adult

value: 32 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS655FSH at ENCODE; https://www.encodeproject.org/ENCBS655FSH/

value: Derived from ENCODE donor ENCDO739PAW; https://www.encodeproject.org/ENCDO739PAW/


title: U87MG cells, FOXO3 Act.8hrs, rep1

description:
FOXO3Act_gene_count_matrix.csv
ABR1

value: cell line

value: Glioblastoma

value: WT

value: FOXO3 activation


title: Library 6 CITE-seq CD8+ T cells, Feature Barcode (HTO)

description:
Library name: Library_6_HTO
10x Genomics Chromium Feature Barcode hashing library from lineage-traced CD8+ T cells.

molecule: protein

value: Tumor and lymph node

value: Sorted CD8+ T cells

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


title: U87MG cells, FOXO3 Act.16hrs, rep1

description:
FOXO3Act_gene_count_matrix.csv
ABR2


title: U87MG cells, shControl, 14d etoposide, Rep3

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

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

value: shRNA control

value: Etoposide 14 days


title: snATAC-seq from heart left ventricle (ENCLB375QCC)

description:
https://www.encodeproject.org/experiments/ENCSR494FFG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494FFG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB375QCC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (42 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: nonischemic (EF 29%, LVEDD 7.2)

value: 42 year

value: ENCBS528MOI at ENCODE; https://www.encodeproject.org/ENCBS528MOI/

value: Derived from ENCODE donor ENCDO423HZU; https://www.encodeproject.org/ENCDO423HZU/


title: U87MG cells, shControl, 14d etoposide, Rep2

value: cell line


title: snATAC-seq from CD8-positive, alpha-beta memory T cell (ENCLB950HXC)

description:
https://www.encodeproject.org/experiments/ENCSR493QJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR493QJO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB950HXC
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: CD8-positive, alpha-beta memory T cell

value: primary cell

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: nucleus

value: AllCells

value: ENCBS631WEW at ENCODE; https://www.encodeproject.org/ENCBS631WEW/

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


title: U87MG cells, shControl, 14d etoposide, Rep1

value: Glioblastoma

value: shRNA control

value: Etoposide 14 days


title: Library 6 CITE-seq CD8+ T cells, Gene Expression

description:
Library name: Library_6_GEX
10x Genomics Chromium Single Cell 5' Gene Expression library from lineage-traced CD8+ T cells.

library_source: transcriptomic single cell

value: Tumor and lymph node

value: Sorted CD8+ T cells

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

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


title: Library 5 CITE-seq CD8+ T cells, V(D)J TCR

description:
Library name: Library_5_TCR
10x Genomics Chromium Single Cell 5' V(D)J TCR library from lineage-traced CD8+ T cells.


title: U87MG cells, shControl, 3d etoposide, Rep3

value: cell line

value: Etoposide 3 days


title: snATAC-seq from left cardiac atrium (ENCLB863LYA)

description:
https://www.encodeproject.org/experiments/ENCSR491LSZ/
***************
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 (ENCSR463EEP).
experiment encode accession: ENCSR491LSZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB863LYA
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: left cardiac atrium

value: tissue

value: male

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

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS491YLC at ENCODE; https://www.encodeproject.org/ENCBS491YLC/

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


title: U87MG cells, shControl, 3d etoposide, Rep2

value: Glioblastoma

value: shRNA control


title: Library 5 CITE-seq CD8+ T cells, Feature Barcode (HTO)

description:
Library name: Library_5_HTO
10x Genomics Chromium Feature Barcode hashing library from lineage-traced CD8+ T cells.

value: Tumor and lymph node


title: U87MG cells, shControl, 3d etoposide, Rep1


title: snATAC-seq from right cardiac atrium (ENCLB639SHW)

description:
https://www.encodeproject.org/experiments/ENCSR486KVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR486KVX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB639SHW
fragmentation methods: chemical (Tn5 transposase)
size range: 300-800

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

value: right cardiac atrium

value: female

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

value: adult

value: 46 year

value: nucleus

value: ENCBS925UFW at ENCODE; https://www.encodeproject.org/ENCBS925UFW/

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


title: Library 5 CITE-seq CD8+ T cells, Gene Expression

description:
Library name: Library_5_GEX
10x Genomics Chromium Single Cell 5' Gene Expression library from lineage-traced CD8+ T cells.

value: Sorted CD8+ T cells

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

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


title: U87MG cells, shFOXO3, 14d etoposide, Rep3

source_name: cell line

value: cell line

value: FOXO3 knockdown

value: Etoposide 14 days


title: U87MG cells, shFOXO3, 14d etoposide, Rep2

value: Glioblastoma


title: U87MG cells, shFOXO3, 14d etoposide, Rep1


title: Control ChIP-seq from HepG2 (ENCLB122PIB)

description:
https://www.encodeproject.org/experiments/ENCSR482BUK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input for HepG2 cells treated with vector control shRNA
experiment encode accession: ENCSR482BUK
assay title: Control ChIP-seq
encode release date: 2025-09-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB122PIB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line

tag: line

tag: encode accession

tag: note

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS433VOT at ENCODE; https://www.encodeproject.org/ENCBS433VOT/


title: Library 4 CITE-seq CD8+ T cells, V(D)J TCR

description:
Library name: Library_4_TCR
10x Genomics Chromium Single Cell 5' V(D)J TCR library from lineage-traced CD8+ T cells.

value: Tumor and lymph node

tag: cell type

tag: genotype

tag: treatment


title: U87MG cells, shFOXO3, 3d etoposide, Rep3

tag: tissue

tag: cell line

value: Etoposide 3 days


title: snATAC-seq from pancreas (ENCLB013URB)

description:
https://www.encodeproject.org/experiments/ENCSR481YWC/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human pancreas
experiment encode accession: ENCSR481YWC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB013URB
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

source_name: Homo sapiens male adult (26 years) pancreas tissue, preserved by cryopreservation nuclear fraction

value: pancreas

value: tissue

tag: biosample encode accession

tag: Sex

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

tag: dev stage

value: adult

value: 26 year

value: nucleus

value: Yiing Lin, MD, PhD

value: ENCBS161WZF at ENCODE; https://www.encodeproject.org/ENCBS161WZF/

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


title: U87MG cells, shFOXO3, 3d etoposide, Rep1

value: cell line

value: Glioblastoma

value: FOXO3 knockdown


title: U87MG cells, shFOXO3, 3d etoposide, Rep2


title: PRO-cap from HEK293T (ENCLB911DFB)

description:
https://www.encodeproject.org/experiments/ENCSR473KVF/
***************
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_U cells.
experiment encode accession: ENCSR473KVF
assay title: PRO-cap
assembly: GRCh38
encode release date: 2026-01-16
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB911DFB

source_name: Homo sapiens HEK293T cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF143

value: female

value: unknown

value: embryonic

tag: lab

value: Haiyuan Yu, Cornell

tag: source

value: Michael Guertin

tag: link

value: ENCBS707ZIE at ENCODE; https://www.encodeproject.org/ENCBS707ZIE/


title: Library 4 CITE-seq CD8+ T cells, Feature Barcode (HTO)

description:
Library name: Library_4_HTO
10x Genomics Chromium Feature Barcode hashing library from lineage-traced CD8+ T cells.

value: Tumor and lymph node

value: Sorted CD8+ T cells

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

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


title: Library 4 CITE-seq CD8+ T cells, Gene Expression

description:
Library name: Library_4_GEX
10x Genomics Chromium Single Cell 5' Gene Expression library from lineage-traced CD8+ T cells.


title: U87MG cells, shControl, Rep3

value: shRNA control


title: U87MG cells, shControl, Rep2


title: PRO-cap from HEK293T (ENCLB146MVO)

description:
https://www.encodeproject.org/experiments/ENCSR473KVF/
***************
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_U cells.
experiment encode accession: ENCSR473KVF
assay title: PRO-cap
assembly: GRCh38
encode release date: 2026-01-16
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB146MVO

tag: health state

value: ENCBS000SRU at ENCODE; https://www.encodeproject.org/ENCBS000SRU/


title: Library 3 CITE-seq CD8+ T cells, V(D)J TCR

description:
Library name: Library_3_TCR
10x Genomics Chromium Single Cell 5' V(D)J TCR library from lineage-traced CD8+ T cells.

tag: batch


title: U87MG cells, shControl, Rep1


title: snATAC-seq from endodermal cell (ENCLB127HCC)

description:
https://www.encodeproject.org/experiments/ENCSR470TKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR470TKG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB127HCC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

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

value: endodermal cell

value: in vitro differentiated cells

tag: description

value: WA09 derived endoderm cells

value: healthy

tag: age

value: 5 day

value: Bradley Bernstein, Broad

tag: subcellular fraction term name

value: nucleus

value: SESCC

value: ENCBS723XMK at ENCODE; https://www.encodeproject.org/ENCBS723XMK/

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


title: U87MG cells, shFOXO3, Rep3

value: cell line

value: Glioblastoma

value: FOXO3 knockdown


title: Library 3 CITE-seq CD8+ T cells, Feature Barcode (HTO)

description:
Library name: Library_3_HTO
10x Genomics Chromium Feature Barcode hashing library from lineage-traced CD8+ T cells.

value: Tumor and lymph node

value: Sorted CD8+ T cells

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


title: U87MG cells, shFOXO3, Rep2


title: U87MG cells, shFOXO3, Rep1


title: snATAC-seq from ureter (ENCLB611MSX)

description:
https://www.encodeproject.org/experiments/ENCSR465CKP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR465CKP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB611MSX
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: ureter

value: tissue

value: female

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

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS779XQT at ENCODE; https://www.encodeproject.org/ENCBS779XQT/

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


title: Library 3 CITE-seq CD8+ T cells, Gene Expression

description:
Library name: Library_3_GEX
10x Genomics Chromium Single Cell 5' Gene Expression library from lineage-traced CD8+ T cells.

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


title: snATAC-seq from heart right ventricle (ENCLB707ZPW)

description:
https://www.encodeproject.org/experiments/ENCSR454YDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: scATAC-seq on human heart right ventricle
experiment encode accession: ENCSR454YDZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB707ZPW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000
spikeins used: Illumina PhiX sequencing control

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

value: heart right ventricle

value: male

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

value: 54 year

value: nucleus

value: Shin Lin

value: ENCBS800BAZ at ENCODE; https://www.encodeproject.org/ENCBS800BAZ/

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


title: U87MG cells, 14d Etoposide, Rep3

value: cell line

value: Glioblastoma

value: Wildtype

value: Etoposide 14 days


title: U87MG cells, 14d Etoposide, Rep2


title: Library 2 CITE-seq CD8+ T cells, V(D)J TCR

description:
Library name: Library_2_TCR
10x Genomics Chromium Single Cell 5' V(D)J TCR library from lineage-traced CD8+ T cells.

value: Tumor and lymph node

value: Sorted CD8+ T cells

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


title: U87MG cells, 14d Etoposide, Rep1


title: snATAC-seq from heart left ventricle (ENCLB068FRA)

description:
https://www.encodeproject.org/experiments/ENCSR450VTB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR450VTB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-07-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB068FRA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (67 years) heart left ventricle tissue, preserved by flash-freezing

value: heart left ventricle

value: tissue

value: Homo sapiens heart left ventricle tissue

value: ischemic (EF 15%, LVEDD 5.9)

value: adult

value: 67 year

value: Michael Snyder, Stanford

value: ENCBS753VJH at ENCODE; https://www.encodeproject.org/ENCBS753VJH/

value: Derived from ENCODE donor ENCDO269PFV; https://www.encodeproject.org/ENCDO269PFV/


title: U87MG cells, 3d Etoposide, Rep3

value: Etoposide 3 days


title: U87MG cells, 3d Etoposide, Rep2

value: cell line