title: MPRA from HepG2 (ENCLB535UGZ)

description:
https://www.encodeproject.org/experiments/ENCSR080JVM/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR080JVM
assay title: MPRA
assembly: hg19
possible controls: ENCSR468WFP
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB535UGZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using transduction

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS980SUO at ENCODE; https://www.encodeproject.org/ENCBS980SUO/


title: MPRA from HepG2 (ENCLB048AJG)

status: Public on Mar 06 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/ENCSR080JVM/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR080JVM
assay title: MPRA
assembly: hg19
possible controls: ENCSR468WFP
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB048AJG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

tag: line

tag: biosample encode accession

tag: encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

value: ENCBS196LXN at ENCODE; https://www.encodeproject.org/ENCBS196LXN/


title: DNase-seq from caudate nucleus (ENCLB571AZD)

description:
https://www.encodeproject.org/experiments/ENCSR101FLG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101FLG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB571AZD

library_source: genomic

molecule: genomic DNA

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS679XAP at ENCODE; https://www.encodeproject.org/ENCBS679XAP/


title: DNase-seq from activated B cell (ENCLB140JFO)

description:
https://www.encodeproject.org/experiments/ENCSR992GTE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR992GTE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB140JFO

source_name: Homo sapiens male adult (21 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: primary cell

value: 21 year

value: AllCells

tag: treatments

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS643YRS at ENCODE; https://www.encodeproject.org/ENCBS643YRS/


title: DNase-seq from activated B cell (ENCLB149AZQ)

description:
https://www.encodeproject.org/experiments/ENCSR992GTE/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR992GTE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB149AZQ

value: male

value: ENCBS307WLM at ENCODE; https://www.encodeproject.org/ENCBS307WLM/


title: DNase-seq from activated T-cell (ENCLB592UEW)

description:
https://www.encodeproject.org/experiments/ENCSR523VDT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR523VDT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB592UEW

source_name: Homo sapiens female adult (22 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: activated T-cell

value: 22 year

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS820UKZ at ENCODE; https://www.encodeproject.org/ENCBS820UKZ/


title: DNase-seq from caudate nucleus (ENCLB116SOY)

description:
https://www.encodeproject.org/experiments/ENCSR103JDI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR103JDI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB116SOY

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: adult

value: unknown

value: ENCBS117KUP at ENCODE; https://www.encodeproject.org/ENCBS117KUP/


title: MPRA from HepG2 (ENCLB591QXR)

description:
https://www.encodeproject.org/experiments/ENCSR080JVM/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR080JVM
assay title: MPRA
assembly: hg19
possible controls: ENCSR468WFP
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB591QXR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS441GNQ at ENCODE; https://www.encodeproject.org/ENCBS441GNQ/


title: DNase-seq from cerebellum (ENCLB393ANG)

description:
https://www.encodeproject.org/experiments/ENCSR100EVG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR100EVG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393ANG

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS731MFK at ENCODE; https://www.encodeproject.org/ENCBS731MFK/


title: Sard (Rep2)

city: Cambridge

first: Pushkal

last: Sharma

address: 455 Main Street

institute: Whitehead Institute

description: Library name: PS8

data_processing:
Reads were aligned to the human reference genome (hg38) using STAR (version 2.7.1a) with default parameters.
Gene-level counts were generated based on GRCh38 annotation (GTF version 38.93).
Gene expression levels were calculated and reported as fragments per kilobase of transcript per million mapped reads (FPKM).
Differential expression analysis between experimental groups (e.g., control vs sardomozide) was performed using DESeq2. False discovery rate (FDR) was controlled using the Benjamini-Hochberg method.
Assembly: hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files containing gene-level expression values (FPKM) and differential expression statistics generated using DESeq2. Files include gene identifiers, normalized expression values, log2 fold change, p-values, and FDR-adjusted p-values.

molecule: polyA RNA

source_name: K562 cells

growth_protocol: Cells were cultured under standard conditions appropriate for the cell type as described in the manuscript. Cells were maintained in complete growth medium and incubated at 37°C with 5% CO₂ until experimental treatment.

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions. RNA quantity and quality were assessed prior to library preparation.
Poly(A)+ RNA selection and library preparation were performed by Novogene. RNA sequencing libraries were prepared using polyA enrichment and sequenced as 150 × 150 bp paired-end reads on an Illumina NovaSeq 6000 platform to a depth of ≥20 million reads per sample.

treatment_protocol: Cells were treated with sardomozide (5 uM) or DMSO control for 72h.

tag: tissue

value: K562 cells

tag: cell line

tag: treatment

value: Sard


title: Sard (Rep3)

description: Library name: PS9


title: DFMO (Rep2)

description: Library name: PS5

value: DFMO


title: snATAC-seq from activated naive CD8-positive, alpha-beta T cell (ENCLB539XVO)

description:
https://www.encodeproject.org/experiments/ENCSR110IID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR110IID
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB539XVO
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (30 years) activated CD8-positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads , 10 ng/mL Interleukin-2 nuclear fraction

value: primary cell

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

tag: subcellular fraction term name

value: nucleus

value: ENCBS488HSX at ENCODE; https://www.encodeproject.org/ENCBS488HSX/

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


title: snATAC-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB541LUH)

description:
https://www.encodeproject.org/experiments/ENCSR196EOO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR196EOO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB541LUH
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads , 10 ng/mL Interleukin-2 nuclear fraction

value: ENCBS603PFY at ENCODE; https://www.encodeproject.org/ENCBS603PFY/


title: MPRA from HepG2 (ENCLB827JVS)

description:
https://www.encodeproject.org/experiments/ENCSR069RCF/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR069RCF
assay title: MPRA
assembly: hg19
possible controls: ENCSR579XDB
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB827JVS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS881RLT at ENCODE; https://www.encodeproject.org/ENCBS881RLT/


title: DFMO (Rep1)

description: Library name: PS4

value: K562 cells

value: DFMO


title: MPRA from HepG2 (ENCLB297QGP)

description:
https://www.encodeproject.org/experiments/ENCSR069RCF/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR069RCF
assay title: MPRA
assembly: hg19
possible controls: ENCSR579XDB
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB297QGP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: ENCBS647QOM at ENCODE; https://www.encodeproject.org/ENCBS647QOM/


title: Control cells (Rep2)

description: Library name: PS2

value: Control


title: DNase-seq from cerebellum (ENCLB189GPS)

description:
https://www.encodeproject.org/experiments/ENCSR159GHL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR159GHL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB189GPS

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS391AXD at ENCODE; https://www.encodeproject.org/ENCBS391AXD/


title: MPRA from HepG2 (ENCLB487UVH)

description:
https://www.encodeproject.org/experiments/ENCSR069RCF/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR069RCF
assay title: MPRA
assembly: hg19
possible controls: ENCSR579XDB
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB487UVH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: ENCBS774KVJ at ENCODE; https://www.encodeproject.org/ENCBS774KVJ/


title: Control cells (Rep1)

description: Library name: PS1


title: DNase-seq from Ammon's horn (ENCLB655HMI)

description:
https://www.encodeproject.org/experiments/ENCSR087WQF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087WQF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB655HMI

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: female

value: ENCBS119VKV at ENCODE; https://www.encodeproject.org/ENCBS119VKV/


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB511PBL)

description:
https://www.encodeproject.org/experiments/ENCSR092LHI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092LHI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB511PBL

source_name: Homo sapiens female adult C1 segment of cervical spinal cord tissue

value: C1 segment of cervical spinal cord

value: ENCBS274EYR at ENCODE; https://www.encodeproject.org/ENCBS274EYR/


title: Control cells (Rep3)

description: Library name: PS3

value: K562 cells

value: Control


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB623JSC)

description:
https://www.encodeproject.org/experiments/ENCSR100JVV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR100JVV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB623JSC

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: male

value: ENCBS446XCO at ENCODE; https://www.encodeproject.org/ENCBS446XCO/


title: DNase-seq from Ammon's horn (ENCLB473CRT)

description:
https://www.encodeproject.org/experiments/ENCSR093HBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR093HBV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB473CRT

source_name: Homo sapiens male adult Ammon's horn tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS493BLL at ENCODE; https://www.encodeproject.org/ENCBS493BLL/


title: DFMO (Rep3)

description: Library name: PS6

value: DFMO


title: Sard (Rep1)

description: Library name: PS7

value: Sard


title: DNase-seq from hypothalamus (ENCLB198JCO)

description:
https://www.encodeproject.org/experiments/ENCSR092PYP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR092PYP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB198JCO

source_name: Homo sapiens female adult hypothalamus tissue

value: hypothalamus

value: female

value: ENCBS816XWN at ENCODE; https://www.encodeproject.org/ENCBS816XWN/


title: MPRA from HepG2 (ENCLB582OYQ)

description:
https://www.encodeproject.org/experiments/ENCSR058RIG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR058RIG
assay title: MPRA
possible controls: ENCSR366UIC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB582OYQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using transient transfection

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS087IVY at ENCODE; https://www.encodeproject.org/ENCBS087IVY/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB596QIO)

description:
https://www.encodeproject.org/experiments/ENCSR497BYS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR497BYS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB596QIO

source_name: Homo sapiens female adult (36 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: adult

value: 36 year

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS555ULI at ENCODE; https://www.encodeproject.org/ENCBS555ULI/


title: DNase-seq from activated B cell (ENCLB349KCS)

description:
https://www.encodeproject.org/experiments/ENCSR441WRS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR441WRS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB349KCS

source_name: Homo sapiens male adult (30 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: male

value: 30 year

value: John Stamatoyannopoulos, UW

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS321VXG at ENCODE; https://www.encodeproject.org/ENCBS321VXG/


title: DNase-seq from nucleus accumbens (ENCLB559YIY)

description:
https://www.encodeproject.org/experiments/ENCSR087VYL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087VYL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB559YIY

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: female

value: unknown

value: Kristin Ardlie

value: ENCBS279WTI at ENCODE; https://www.encodeproject.org/ENCBS279WTI/


title: DNase-seq from activated B cell (ENCLB220ABJ)

description:
https://www.encodeproject.org/experiments/ENCSR441WRS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR441WRS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB220ABJ

value: primary cell

value: adult

value: ENCBS707OZE at ENCODE; https://www.encodeproject.org/ENCBS707OZE/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB114RZE)

description:
https://www.encodeproject.org/experiments/ENCSR497BYS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR497BYS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB114RZE

value: 36 year

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS453ZSM at ENCODE; https://www.encodeproject.org/ENCBS453ZSM/


title: DNase-seq from nucleus accumbens (ENCLB260PZD)

description:
https://www.encodeproject.org/experiments/ENCSR087ASG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087ASG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB260PZD

source_name: Homo sapiens male adult nucleus accumbens tissue

value: male

value: ENCBS191OPQ at ENCODE; https://www.encodeproject.org/ENCBS191OPQ/


title: MPRA from HepG2 (ENCLB533MIZ)

description:
https://www.encodeproject.org/experiments/ENCSR049RIU/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.
experiment encode accession: ENCSR049RIU
assay title: MPRA
assembly: hg19
possible controls: ENCSR383FIW
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB533MIZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS930VCW at ENCODE; https://www.encodeproject.org/ENCBS930VCW/


title: DNase-seq from activated B cell (ENCLB508HRX)

description:
https://www.encodeproject.org/experiments/ENCSR418YUJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR418YUJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB508HRX

source_name: Homo sapiens female adult (36 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: female

value: John Stamatoyannopoulos, UW

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS785LOJ at ENCODE; https://www.encodeproject.org/ENCBS785LOJ/


title: DNase-seq from activated B cell (ENCLB246TBW)

description:
https://www.encodeproject.org/experiments/ENCSR418YUJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR418YUJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB246TBW

value: primary cell

value: adult

value: 36 year

value: Stemcell Technologies

value: ENCBS382XJK at ENCODE; https://www.encodeproject.org/ENCBS382XJK/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB853TGM)

description:
https://www.encodeproject.org/experiments/ENCSR383EMG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR383EMG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB853TGM

source_name: Homo sapiens male adult (26 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: male

value: 26 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS373GUT at ENCODE; https://www.encodeproject.org/ENCBS373GUT/


title: DNase-seq from nucleus accumbens (ENCLB098MOT)

description:
https://www.encodeproject.org/experiments/ENCSR085FYV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR085FYV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB098MOT

value: nucleus accumbens

value: tissue

value: unknown

value: Kristin Ardlie

value: ENCBS628SDB at ENCODE; https://www.encodeproject.org/ENCBS628SDB/


title: MPRA from HepG2 (ENCLB638EZJ)

description:
https://www.encodeproject.org/experiments/ENCSR049RIU/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.
experiment encode accession: ENCSR049RIU
assay title: MPRA
assembly: hg19
possible controls: ENCSR383FIW
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB638EZJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS628ZAS at ENCODE; https://www.encodeproject.org/ENCBS628ZAS/


title: DNase-seq from activated T-cell (ENCLB193NCK)

description:
https://www.encodeproject.org/experiments/ENCSR349UGM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR349UGM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB193NCK

source_name: Homo sapiens female adult (54 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: activated T-cell

value: primary cell

value: female

value: adult

value: 54 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS541WTC at ENCODE; https://www.encodeproject.org/ENCBS541WTC/


title: MPRA from HepG2 (ENCLB417DIG)

description:
https://www.encodeproject.org/experiments/ENCSR058RIG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR058RIG
assay title: MPRA
possible controls: ENCSR366UIC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB417DIG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: ENCBS370UNX at ENCODE; https://www.encodeproject.org/ENCBS370UNX/


title: MPRA from HepG2 (ENCLB888RRJ)

description:
https://www.encodeproject.org/experiments/ENCSR049RIU/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.
experiment encode accession: ENCSR049RIU
assay title: MPRA
assembly: hg19
possible controls: ENCSR383FIW
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB888RRJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: ENCBS143ZWN at ENCODE; https://www.encodeproject.org/ENCBS143ZWN/


title: DNase-seq from activated T-cell (ENCLB791VXD)

description:
https://www.encodeproject.org/experiments/ENCSR349UGM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR349UGM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB791VXD

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS366TNQ at ENCODE; https://www.encodeproject.org/ENCBS366TNQ/


title: DNase-seq from nucleus accumbens (ENCLB298ROU)

description:
https://www.encodeproject.org/experiments/ENCSR085FYV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR085FYV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB298ROU

value: nucleus accumbens

value: tissue

value: unknown

value: Kristin Ardlie

value: ENCBS816BED at ENCODE; https://www.encodeproject.org/ENCBS816BED/


title: MPRA from HepG2 (ENCLB960BVO)

description:
https://www.encodeproject.org/experiments/ENCSR022GQD/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR022GQD
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR721BJI
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB960BVO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using transduction

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS227PRD at ENCODE; https://www.encodeproject.org/ENCBS227PRD/


title: DNase-seq from putamen (ENCLB981SXX)

description:
https://www.encodeproject.org/experiments/ENCSR081PVE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR081PVE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB981SXX

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: female

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS629KCZ at ENCODE; https://www.encodeproject.org/ENCBS629KCZ/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB251RIT)

description:
https://www.encodeproject.org/experiments/ENCSR298SHM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR298SHM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB251RIT

source_name: Homo sapiens female adult (22 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: 22 year

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS688MGH at ENCODE; https://www.encodeproject.org/ENCBS688MGH/


title: DNase-seq from activated B cell (ENCLB763IFS)

description:
https://www.encodeproject.org/experiments/ENCSR321YPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR321YPI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB763IFS

source_name: Homo sapiens male adult (26 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: male

value: 26 year

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS226ZQN at ENCODE; https://www.encodeproject.org/ENCBS226ZQN/


title: DNase-seq from activated T-cell (ENCLB744ZIJ)

description:
https://www.encodeproject.org/experiments/ENCSR248LYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR248LYM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB744ZIJ

source_name: Homo sapiens female adult (51 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: activated T-cell

value: 51 year

value: AllCells

value: ENCBS582GUH at ENCODE; https://www.encodeproject.org/ENCBS582GUH/


title: DNase-seq from putamen (ENCLB560ACG)

description:
https://www.encodeproject.org/experiments/ENCSR080XGJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR080XGJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB560ACG

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: tissue

value: adult

value: unknown

value: Kristin Ardlie

value: ENCBS025DFE at ENCODE; https://www.encodeproject.org/ENCBS025DFE/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB468CZT)

description:
https://www.encodeproject.org/experiments/ENCSR298SHM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298SHM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB468CZT

value: primary cell

value: female

value: 22 year

value: John Stamatoyannopoulos, UW

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS911TRS at ENCODE; https://www.encodeproject.org/ENCBS911TRS/


title: MPRA from HepG2 (ENCLB703YQQ)

description:
https://www.encodeproject.org/experiments/ENCSR058RIG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR058RIG
assay title: MPRA
possible controls: ENCSR366UIC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB703YQQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS342QXA at ENCODE; https://www.encodeproject.org/ENCBS342QXA/


title: MPRA from HepG2 (ENCLB468THH)

description:
https://www.encodeproject.org/experiments/ENCSR022GQD/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR022GQD
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR721BJI
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB468THH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS415QKE at ENCODE; https://www.encodeproject.org/ENCBS415QKE/


title: MPRA from HepG2 (ENCLB642ONP)

description:
https://www.encodeproject.org/experiments/ENCSR022GQD/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR022GQD
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR721BJI
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB642ONP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS397WJZ at ENCODE; https://www.encodeproject.org/ENCBS397WJZ/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB913VXW)

description:
https://www.encodeproject.org/experiments/ENCSR182ZRL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR182ZRL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB913VXW

source_name: Homo sapiens female adult (26 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: adult

value: 26 year

value: ENCBS595KMU at ENCODE; https://www.encodeproject.org/ENCBS595KMU/


title: DNase-seq from activated B cell (ENCLB414ZUA)

description:
https://www.encodeproject.org/experiments/ENCSR161LOZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR161LOZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB414ZUA

source_name: Homo sapiens female adult (26 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: female

value: John Stamatoyannopoulos, UW

value: Stemcell Technologies

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS946THL at ENCODE; https://www.encodeproject.org/ENCBS946THL/


title: DNase-seq from anterior cingulate cortex (ENCLB091FVF)

description:
https://www.encodeproject.org/experiments/ENCSR079IAM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR079IAM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB091FVF

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: tissue

value: male

value: unknown

value: Kristin Ardlie

value: ENCBS500PHP at ENCODE; https://www.encodeproject.org/ENCBS500PHP/


title: DNase-seq from hypothalamus (ENCLB114BLK)

description:
https://www.encodeproject.org/experiments/ENCSR077DYH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR077DYH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB114BLK

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: ENCBS443MFL at ENCODE; https://www.encodeproject.org/ENCBS443MFL/


title: DNase-seq from activated B cell (ENCLB558DZH)

description:
https://www.encodeproject.org/experiments/ENCSR161LOZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR161LOZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB558DZH

value: primary cell

value: adult

value: ENCBS836ABO at ENCODE; https://www.encodeproject.org/ENCBS836ABO/


title: MPRA from SK-MEL-28 (ENCLB088KWT)

description:
https://www.encodeproject.org/experiments/ENCSR006GAG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.
experiment encode accession: ENCSR006GAG
assay title: MPRA
possible controls: ENCSR814CZJ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB088KWT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens SK-MEL-28 cell line genetically modified (insertion) using transient transfection

value: cell line

value: Malignant Melanoma, negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: 51 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS145FIB at ENCODE; https://www.encodeproject.org/ENCBS145FIB/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB109LOE)

description:
https://www.encodeproject.org/experiments/ENCSR105LXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105LXZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB109LOE

source_name: Homo sapiens male adult (30 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: 30 year

value: John Stamatoyannopoulos, UW

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS779ZCF at ENCODE; https://www.encodeproject.org/ENCBS779ZCF/


title: DNase-seq from activated T-cell (ENCLB963UMF)

description:
https://www.encodeproject.org/experiments/ENCSR130DGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR130DGG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB963UMF

source_name: Homo sapiens male adult (26 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: activated T-cell

value: male

value: 26 year

value: ENCBS283SHC at ENCODE; https://www.encodeproject.org/ENCBS283SHC/


title: MPRA from SK-MEL-28 (ENCLB240ROU)

description:
https://www.encodeproject.org/experiments/ENCSR006GAG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.
experiment encode accession: ENCSR006GAG
assay title: MPRA
possible controls: ENCSR814CZJ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB240ROU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: ENCBS365NJG at ENCODE; https://www.encodeproject.org/ENCBS365NJG/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB023QGQ)

description:
https://www.encodeproject.org/experiments/ENCSR101OTC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101OTC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB023QGQ

source_name: Homo sapiens female adult (23 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: female

value: 23 year

value: ENCBS837FRC at ENCODE; https://www.encodeproject.org/ENCBS837FRC/


title: DNase-seq from putamen (ENCLB401EPH)

description:
https://www.encodeproject.org/experiments/ENCSR075FRQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075FRQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB401EPH

value: putamen

value: tissue

value: unknown

value: Kristin Ardlie

value: ENCBS585UFH at ENCODE; https://www.encodeproject.org/ENCBS585UFH/


title: DNase-seq from hypothalamus (ENCLB253QGK)

description:
https://www.encodeproject.org/experiments/ENCSR073CUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR073CUH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB253QGK

value: hypothalamus

value: John Stamatoyannopoulos, UW

value: ENCBS919SGX at ENCODE; https://www.encodeproject.org/ENCBS919SGX/


title: DNase-seq from immature natural killer cell (ENCLB222HPH)

description:
https://www.encodeproject.org/experiments/ENCSR863HYZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR863HYZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB222HPH

source_name: Homo sapiens immature natural killer primary cell, preserved by cryopreservation

value: immature natural killer cell

tag: description

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS880JPN at ENCODE; https://www.encodeproject.org/ENCBS880JPN/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: DNase-seq from immature natural killer cell (ENCLB363QHI)

description:
https://www.encodeproject.org/experiments/ENCSR863HYZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR863HYZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB363QHI

source_name: Homo sapiens immature natural killer primary cell

value: primary cell

value: ENCBS099DKL at ENCODE; https://www.encodeproject.org/ENCBS099DKL/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB183YKY)

description:
https://www.encodeproject.org/experiments/ENCSR905BAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR905BAW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB183YKY

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: ENCBS488XUS at ENCODE; https://www.encodeproject.org/ENCBS488XUS/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: MPRA from HepG2 (ENCLB702DMD)

description:
https://www.encodeproject.org/experiments/ENCSR002UCW/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR002UCW
assay title: MPRA
assembly: hg19
possible controls: ENCSR547NTG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB702DMD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using transient transfection

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS022VSB at ENCODE; https://www.encodeproject.org/ENCBS022VSB/


title: MPRA from SK-MEL-28 (ENCLB339ERN)

description:
https://www.encodeproject.org/experiments/ENCSR006GAG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.
experiment encode accession: ENCSR006GAG
assay title: MPRA
possible controls: ENCSR814CZJ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB339ERN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Malignant Melanoma, negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: adult

value: 51 year

value: ENCBS475TBA at ENCODE; https://www.encodeproject.org/ENCBS475TBA/


title: DNase-seq from putamen (ENCLB060DCH)

description:
https://www.encodeproject.org/experiments/ENCSR072HSD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR072HSD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB060DCH

value: putamen

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS147DJK at ENCODE; https://www.encodeproject.org/ENCBS147DJK/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB347UGX)

description:
https://www.encodeproject.org/experiments/ENCSR905NAN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR905NAN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB347UGX

source_name: Homo sapiens naive thymus-derived CD8-positive, alpha-beta T primary cell, preserved by cryopreservation

value: primary cell

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS977UPT at ENCODE; https://www.encodeproject.org/ENCBS977UPT/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: MPRA from HepG2 (ENCLB379BSK)

description:
https://www.encodeproject.org/experiments/ENCSR002UCW/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR002UCW
assay title: MPRA
assembly: hg19
possible controls: ENCSR547NTG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB379BSK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS265GZC at ENCODE; https://www.encodeproject.org/ENCBS265GZC/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB675RDQ)

description:
https://www.encodeproject.org/experiments/ENCSR641HZO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR641HZO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB675RDQ

source_name: Homo sapiens with multiple sclerosis; naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: multiple sclerosis

value: ENCBS635DXW at ENCODE; https://www.encodeproject.org/ENCBS635DXW/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB257XJC)

description:
https://www.encodeproject.org/experiments/ENCSR719DJX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR719DJX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB257XJC

source_name: Homo sapiens with multiple sclerosis; naive thymus-derived CD8-positive, alpha-beta T primary cell, preserved by cryopreservation

value: primary cell

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: not collected

value: ENCBS840GDX at ENCODE; https://www.encodeproject.org/ENCBS840GDX/


title: DNase-seq from substantia nigra (ENCLB546WBT)

description:
https://www.encodeproject.org/experiments/ENCSR070SVO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR070SVO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB546WBT

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS255CNT at ENCODE; https://www.encodeproject.org/ENCBS255CNT/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB468DUG)

description:
https://www.encodeproject.org/experiments/ENCSR793FAY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793FAY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB468DUG

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS977UPT at ENCODE; https://www.encodeproject.org/ENCBS977UPT/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: DNase-seq from putamen (ENCLB439JES)

description:
https://www.encodeproject.org/experiments/ENCSR069WFA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR069WFA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB439JES

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: female

value: ENCBS510SGE at ENCODE; https://www.encodeproject.org/ENCBS510SGE/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB380UWB)

description:
https://www.encodeproject.org/experiments/ENCSR530ZCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR530ZCQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB380UWB

value: primary cell

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: multiple sclerosis

value: ENCBS462QFO at ENCODE; https://www.encodeproject.org/ENCBS462QFO/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB882TVS)

description:
https://www.encodeproject.org/experiments/ENCSR610YUT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR610YUT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB882TVS

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: ENCBS372AWJ at ENCODE; https://www.encodeproject.org/ENCBS372AWJ/


title: DNase-seq from K562 (ENCLB893WCA)

description:
https://www.encodeproject.org/experiments/ENCSR970WFK/
***************
biological replicate number: 7
technical replicate number: 1
description:
experiment encode accession: ENCSR970WFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB893WCA

source_name: Homo sapiens K562 cell line

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: John Stamatoyannopoulos, UW

value: ATCC

value: ENCBS804EAY at ENCODE; https://www.encodeproject.org/ENCBS804EAY/


title: DNase-seq from CD4-positive, alpha-beta memory T cell (ENCLB628ARD)

description:
https://www.encodeproject.org/experiments/ENCSR509BPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR509BPF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB628ARD

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, preserved by cryopreservation

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

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS224UJU at ENCODE; https://www.encodeproject.org/ENCBS224UJU/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB972CEM)

description:
https://www.encodeproject.org/experiments/ENCSR641HZO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR641HZO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB972CEM

value: primary cell

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: multiple sclerosis

value: ENCBS635DXW at ENCODE; https://www.encodeproject.org/ENCBS635DXW/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB935ALG)

description:
https://www.encodeproject.org/experiments/ENCSR453ZWK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR453ZWK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB935ALG

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: ENCBS938EKE at ENCODE; https://www.encodeproject.org/ENCBS938EKE/


title: DNase-seq from immature natural killer cell (ENCLB228CJA)

description:
https://www.encodeproject.org/experiments/ENCSR446BSR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR446BSR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB228CJA

value: immature natural killer cell

value: ENCBS021VJD at ENCODE; https://www.encodeproject.org/ENCBS021VJD/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: DNase-seq from cerebellum (ENCLB043KOC)

description:
https://www.encodeproject.org/experiments/ENCSR075VZR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075VZR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB043KOC

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS680PAU at ENCODE; https://www.encodeproject.org/ENCBS680PAU/


title: DNase-seq from anterior cingulate cortex (ENCLB391XST)

description:
https://www.encodeproject.org/experiments/ENCSR065USE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR065USE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB391XST

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: male

value: ENCBS816OIE at ENCODE; https://www.encodeproject.org/ENCBS816OIE/


title: DNase-seq from NCI-H2081 (ENCLB949OMC)

description:
https://www.encodeproject.org/experiments/ENCSR376MYJ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR376MYJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB949OMC
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

source_name: Homo sapiens NCI-H2081 cell line

value: cell line

value: 59 year

value: ATCC

value: ENCBS993DVL at ENCODE; https://www.encodeproject.org/ENCBS993DVL/


title: DNase-seq from immature natural killer cell (ENCLB942FYG)

description:
https://www.encodeproject.org/experiments/ENCSR446BSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR446BSR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB942FYG

value: immature natural killer cell

value: primary cell

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS021VJD at ENCODE; https://www.encodeproject.org/ENCBS021VJD/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB546NAT)

description:
https://www.encodeproject.org/experiments/ENCSR353SYG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR353SYG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB546NAT

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: ENCBS381JHZ at ENCODE; https://www.encodeproject.org/ENCBS381JHZ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: DNase-seq from nucleus accumbens (ENCLB532XGL)

description:
https://www.encodeproject.org/experiments/ENCSR063SNR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063SNR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB532XGL

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS723MPI at ENCODE; https://www.encodeproject.org/ENCBS723MPI/


title: DNase-seq from nucleus accumbens (ENCLB539QAD)

description:
https://www.encodeproject.org/experiments/ENCSR060WFE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR060WFE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB539QAD

source_name: Homo sapiens male adult nucleus accumbens tissue

value: male

value: ENCBS248ETR at ENCODE; https://www.encodeproject.org/ENCBS248ETR/


title: DNase-seq from K562 (ENCLB822UNO)

description:
https://www.encodeproject.org/experiments/ENCSR840YOF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR840YOF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB822UNO
instrument models: Illumina NextSeq 500,Illumina HiSeq 4000

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS802SEH at ENCODE; https://www.encodeproject.org/ENCBS802SEH/


title: Fresh-2-24hr

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

description: Library name: Fresh-2-24hr

data_processing:
Raw sequencing data quality control was performed using FastQC to assess read quality prior to trimming.
Adapter trimming and low-quality filtering were performed using Trim Galore! with parameters -q 25 --phred33 --length 35 --paired.
Clean reads were aligned to the hg38 reference genome using HISAT2 with default parameters and --dta-cufflinks for downstream compatibility.
Aligned SAM files were converted to BAM, sorted, and indexed using Samtools with quality filtering (-q 5).
Gene-level read counts were quantified using HTSeq-count with the GENCODE v47 annotation (gene_id, strandedness = no).
Gene expression levels (FPKM) were calculated across all samples using Cuffdiff with hg38 genome and GENCODE v47 GTF annotation.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include gene read counts and FPKM expression matrix.

source_name: ProliHH

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.
1ug of total RNA was used for the construction of sequencing libraries.

value: ProliHH


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB614UVT)

description:
https://www.encodeproject.org/experiments/ENCSR308XZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR308XZY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB614UVT

value: primary cell

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS170TKF at ENCODE; https://www.encodeproject.org/ENCBS170TKF/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: MPRA from HepG2 (ENCLB984DTO)

description:
https://www.encodeproject.org/experiments/ENCSR002UCW/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR002UCW
assay title: MPRA
assembly: hg19
possible controls: ENCSR547NTG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB984DTO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ENCBS236VIR at ENCODE; https://www.encodeproject.org/ENCBS236VIR/


title: DNase-seq from NCI-H2081 (ENCLB393ANE)

description:
https://www.encodeproject.org/experiments/ENCSR376MYJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR376MYJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393ANE
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: cell line

value: female

value: adult

value: 59 year

value: John Stamatoyannopoulos, UW

value: ENCBS265MCL at ENCODE; https://www.encodeproject.org/ENCBS265MCL/


title: DNase-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB051VXR)

description:
https://www.encodeproject.org/experiments/ENCSR436ASB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR436ASB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB051VXR

value: primary cell

value: CD8+ naive CD3+ CD4- CD8+ CD45RA+ CD45RO-

value: not collected

value: multiple sclerosis

value: ENCBS840GDX at ENCODE; https://www.encodeproject.org/ENCBS840GDX/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB332TTN)

description:
https://www.encodeproject.org/experiments/ENCSR353SYG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR353SYG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB332TTN

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS381JHZ at ENCODE; https://www.encodeproject.org/ENCBS381JHZ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Fresh-2-0hr

description: Library name: Fresh-2-0hr

value: ProliHH


title: DNase-seq from GF-D8 (ENCLB629DNI)

description:
https://www.encodeproject.org/experiments/ENCSR342FHH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR342FHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB629DNI

source_name: Homo sapiens GF-D8 cell line

value: cell line

value: male

value: adult

value: 82 year

value: DSMZ

value: ENCBS799QID at ENCODE; https://www.encodeproject.org/ENCBS799QID/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB277BUQ)

description:
https://www.encodeproject.org/experiments/ENCSR060QMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR060QMW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB277BUQ

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS094UBD at ENCODE; https://www.encodeproject.org/ENCBS094UBD/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB245AUI)

description:
https://www.encodeproject.org/experiments/ENCSR060QMW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR060QMW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB245AUI

value: ENCBS562VDE at ENCODE; https://www.encodeproject.org/ENCBS562VDE/


title: Fresh-1-0hr

description: Library name: Fresh-1-0hr


title: DNase-seq from NCI-H2081 (ENCLB172NFK)

description:
https://www.encodeproject.org/experiments/ENCSR376MYJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR376MYJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB172NFK
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: female

value: 59 year

value: ATCC

value: ENCBS358MBS at ENCODE; https://www.encodeproject.org/ENCBS358MBS/


title: cv-3-24hr

description: Library name: cv-3-24hr

value: ProliHH


title: cv-1-24hr

description: Library name: cv-1-24hr


title: DNase-seq from K562 (ENCLB787ASX)

description:
https://www.encodeproject.org/experiments/ENCSR335RHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335RHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB787ASX

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS083JRV at ENCODE; https://www.encodeproject.org/ENCBS083JRV/


title: Fresh-1-24hr

description: Library name: Fresh-1-24hr


title: PBMC, Day 84, ATAC-seq, Individual 09

city: Olsztyn

first: Maciej

last: Rybiński

state: Warmian-Masurian Voivodeship

address: Trylińskiego 18

country: Poland

institute: Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences.

description: Library name: Ind09

data_processing:
ATAC-seq: Paired-end reads were aligned using the STAR aligner. ENCODE-identified blacklisted regions and reads with mapping quality score < 2 were filtered out. Duplicates were identified and marked with samtools markdup. Peak calling done with MACS3 (version 3.0.1) utilizing callpeak function with the parameters --f BAMPE --verbose 3 --shift 0 -g hs -q 0.01 -B Consensus peak summits matrix generated with DiffBind utilizing dba.count function with summits parameter set to 75.
Assembly: GRCh38.p14
Supplementary files format and content: Consensus_ATAC-seq_Day 84.csv

source_name: peripheral blood

extract_protocol:
ATAC-seq: nuclei were isolated from 100,000 PBMCs by incubation in 50 µl lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20; 0.1% IGEPAL CA-630; 0.01% digitonin). After 3 minutes on ice, 1 ml wash buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 3 mM MgCl₂; 0.1% Tween-20) was added. Nuclei were pelleted and subjected to transposition using a Tn5 transposase reaction mix (Illumina), supplemented with 0.01% digitonin and 0.1% Tween-20. The transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer. Transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research), followed by PCR amplification, purification, and size selection with SPRISelect beads (Beckman Coulter). Library quality was assessed using an Agilent TapeStation. Indexed libraries were quantified, pooled, and prepared for sequencing.
ATAC-seq  libraries were sequenced on an Illumina NextSeq500 system (Illumina) at 75 bp read length using standard protocols at the Gene Core facility of the EMBL (Heidelberg, Germany).

treatment_protocol: Peripheral blood samples were obtained from a single healthy male participant (age 59) enrolled in the VitDHiD trial (ClinicalTrials.gov Identifier: NCT03537027). The study was approved by the Ethics Committee of the Northern Savo Hospital District (Approval No. 515/2018).

value: peripheral blood

value: PBMC

tag: cell type

value: monocytes, T and B cells


title: cv-3-0hr

description: Library name: cv-3-0hr


title: DNase-seq from nucleus accumbens (ENCLB615OKU)

description:
https://www.encodeproject.org/experiments/ENCSR057MAC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR057MAC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB615OKU

value: nucleus accumbens

value: tissue

value: male

value: adult

value: unknown

value: ENCBS863HYI at ENCODE; https://www.encodeproject.org/ENCBS863HYI/


title: DNase-seq from amygdala (ENCLB543RFW)

description:
https://www.encodeproject.org/experiments/ENCSR053GLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR053GLL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB543RFW

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS826ZFU at ENCODE; https://www.encodeproject.org/ENCBS826ZFU/


title: cv-1-0hr

description: Library name: cv-1-0hr

value: ProliHH


title: bag-2-24hr

description: Library name: bag-2-24hr


title: PBMC, Day 84, ATAC-seq, Individual 13

description: Library name: Ind13


title: bag-2-0hr

description: Library name: bag-2-0hr


title: bag-1-0hr

description: Library name: bag-1-0hr


title: PBMC, Day 84, ATAC-seq, Individual 26

description: Library name: Ind26


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB666EEB)

description:
https://www.encodeproject.org/experiments/ENCSR069LMC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR069LMC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB666EEB

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: ENCBS045TKH at ENCODE; https://www.encodeproject.org/ENCBS045TKH/


title: Colorectal Cancer_Patient-Derived Organoid_Patient05

first: Yu

last: Meng

address: Zhongke Road No.1

institute: ShanghaiTech University

description: Library name: 5

library_source: transcriptomic single cell

data_processing:
Initial analysis and generation of the expression matrix were performed via the official Cell Ranger pipeline. Subsequent downstream analyses, including clustering and differential expression analysis, were implemented using the R package Seurat (v4.3.0).
Assembly: GRCh38 (10x Genomics)
Supplementary files format and content: MTX and TSV (gzipped)

source_name: colorectal tumor

extract_protocol:
The organoid culture medium was removed, and 500 mL of organoid harvesting solution was added. The organoids were incubated on ice for 15 min, collected, and centrifuged at 400 ×g for 5 min at 4 °C. After discarding the supernatant, 200 mL of organoid digestion solution was added, followed by incubation at 37 °C for 5 min. Digestion progress was monitored to ensure dissociation into single cells; if necessary, the digestion time was extended. Once complete dissociation was achieved, digestion was terminated by the addition of 1 mL of advanced DMEM/F12  supplemented with 5 % FBS. The mixture was centrifuged at 400 ×g for 5 min at 4 °C. The pellet was resuspended in 5 mL of advanced DMEM/F12 and filtered through a 30 mm cell strainer. After centrifugation, the cells were washed twice with calcium- and magnesium-free DPBS. The resulting single-cell suspension was used for subsequent single-cell RNA sequencing. Within the Chromium instrument, barcoded Single Cell 3’ Gel Beads are mixed with cells or nuclei, enzymes, and partitioning oil to form tens of thousands of single cell emulsion droplets called “GEMs” (Gel Bead-in-emulsion). Immediately following GEM generation, the Gel Bead is dissolved and any co-partitioned cell is lysed. Oligonucleotides containing (i) an Illumina Read 1 (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 12 nt unique molecular identifier (UMI), and (iv) 30 nt poly(dT) sequence are released and mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces 10x Barcoded, fulllength cDNA from poly-adenylated mRNA. Then, the first-strand cDNA of 10X Barcoded was purified by silane magnetic beads, and sufficient mass was obtained by PCR amplification. The PCR products were clean up by SPRI beads, and double-stranded cDNA was obtained. Then quantify and qualify the dsDNA by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), so as to confirm the final PCR cycle number for library construction.
Library Construction : The 1/4 of the dsDNA was then treated with Fragmentation Mix to fragment cDNA, End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by double sided size selection to recover ~300 bp of the cDNA. Each sample was then added adaptors to both ends by a T-A ligation. The purified Ligation was amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform Illumina bridge PCR. And P7 primers are a mixture of four primers, each carrying a eight-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic, Taiwan, China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

value: colorectal tumor

value: patient-derived organoid cells


title: DNase-seq from amygdala (ENCLB424APY)

description:
https://www.encodeproject.org/experiments/ENCSR050QPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR050QPI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB424APY

value: ENCBS550CFL at ENCODE; https://www.encodeproject.org/ENCBS550CFL/


title: PBMC, Day 84, ATAC-seq, Individual 02

description: Library name: Ind02

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: DNase-seq from Ammon's horn (ENCLB466DGR)

description:
https://www.encodeproject.org/experiments/ENCSR050IGM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR050IGM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB466DGR

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: male

value: adult

value: ENCBS687PHK at ENCODE; https://www.encodeproject.org/ENCBS687PHK/


title: Colorectal Cancer_Patient-Derived Organoid_Patient04

description: Library name: 4


title: Colorectal Cancer_Patient-Derived Organoid_Patient02

description: Library name: 2


title: CD34+ JH4308, scMultiome ATAC

city: Baltimore

first: Andrew

middle: P

last: Feinberg

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

description: Library name: JH4308_scATACseq_multi

library_source: genomic single cell

data_processing:
Single-cell sequencing data were aligned to the hg38 human reference genome. Multiomic data were processed using Cell Ranger Arc (10x Genomics), and single-omic scATAC-seq data were processed using Cell Ranger ATAC.
Quality control filtering was applied as follows: For multiomic data, cells were retained if they met all of the following criteria: (i) 5,000–100,000 total reads in the scATAC-seq modality, (ii) 1,000–100,000 total reads and <30% mitochondrial reads in the scRNA-seq modality. For single-omic scATAC-seq data, cells with 2,000–100,000 total reads were retained.
For scATAC-seq data processing, we first generated a unified peak set by merging peaks from all samples (both single-omic and multiomic) using Cell Ranger ATAC and Cell Ranger Arc output peak files. Read counts within these unified peak regions were then quantified for each cell using the Signac R package. Peak-level read counts were normalized using term frequency–inverse document frequency (TF-IDF) via the RunTFIDF() function.
Cross-sample integration was performed using Harmony based on gene expression data to correct for batch effects between patients and technologies (single-omic vs. multiomic).
Assembly: hg38
Supplementary files format and content: Tab-separated files (tsv) containing log-normalized count data for each peak.

source_name: Bone marrow derived CD34+ Stem/Progenitor

extract_protocol:
Cryopreserved samples were used to generate a single cell suspension (for scATAC-seq, according to protocol Nuclei Isolation for Single Cell ATAC Sequencing [10x Genomics]) or a single nuclei suspension (for single-cell Multiome, according to protocol Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing [10x Genomics]). Single cells (for scATAC-seq) or nuclei (for scMultiome ATAC+Gene Expression) were captured on a 10x Chromium Controller instrument according to manufacturer instructions.
Single-cell ATAC libraries were constructed with Chromium Next GEM Single Cell ATAC reagents. Single-cell multiome ATAC libraries were generated using the Chromium Next GEM Single-cell Multiome ATAC + Gene Expression reagents and a 10x Chromium Controller instrument according to the manufacturer’s instructions. A spike-in of 1% PhiX control library (Illumina) was used as the technical control.

tag: genotype

value: Normal CD34+


title: DNase-seq from putamen (ENCLB418DTW)

description:
https://www.encodeproject.org/experiments/ENCSR048QZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR048QZY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB418DTW

source_name: Homo sapiens male adult putamen tissue

value: putamen

tag: biosample encode accession

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS954UXA at ENCODE; https://www.encodeproject.org/ENCBS954UXA/


title: AML SU758, scMultiome ATAC

description: Library name: SU758_scATACseq_multi

source_name: Primary acute myeloid leukemia

value: Primary acute myeloid leukemia

value: CEBPA mutation


title: AML SU504, scMultiome ATAC

description: Library name: SU504_scATACseq_multi


title: bag-1-24hr

description: Library name: bag-1-24hr

value: ProliHH


title: PBMC, Day 84, ATAC-seq, Individual 38

description: Library name: Ind38

value: peripheral blood


title: DNase-seq from cerebellum (ENCLB373OQA)

description:
https://www.encodeproject.org/experiments/ENCSR048PMY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR048PMY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB373OQA

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

tag: encode accession

value: ENCBS347RYS at ENCODE; https://www.encodeproject.org/ENCBS347RYS/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB667DKB)

description:
https://www.encodeproject.org/experiments/ENCSR048KUD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR048KUD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB667DKB

value: dorsolateral prefrontal cortex

tag: Sex

value: ENCBS809HLF at ENCODE; https://www.encodeproject.org/ENCBS809HLF/


title: PBMC, Day 84, ATAC-seq, Individual 45

description: Library name: Ind45

value: PBMC

value: monocytes, T and B cells


title: AML SU494, scMultiome ATAC

description: Library name: SU494_scATACseq_multi


title: AML SU227, scMultiome ATAC

description: Library name: SU227_scATACseq_multi


title: AML SU075, scMultiome ATAC

description: Library name: SU075_scATACseq_multi

value: IDH1/2 mutation


title: PBMC, Day 84, ATAC-seq, Individual 30

description: Library name: Ind30


title: PBMC, Day 84, ATAC-seq, Individual 04

description: Library name: Ind04


title: DNase-seq from substantia nigra (ENCLB407LSE)

description:
https://www.encodeproject.org/experiments/ENCSR051TPB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR051TPB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB407LSE

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: tissue

value: male

value: adult

value: ENCBS596SDC at ENCODE; https://www.encodeproject.org/ENCBS596SDC/


title: AML JH6048, scMultiome ATAC

description: Library name: JH6048_scATACseq_multi


title: AML JH5236, scATAC-seq

description: Library name: JH5236_scATACseq_single


title: DNase-seq from anterior cingulate cortex (ENCLB512ELT)

description:
https://www.encodeproject.org/experiments/ENCSR047WUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR047WUB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB512ELT

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS474JSE at ENCODE; https://www.encodeproject.org/ENCBS474JSE/


title: PBMC, Day 84, ATAC-seq, Individual 36

description: Library name: Ind36

value: peripheral blood


title: AML JH5205, scMultiome ATAC

description: Library name: JH5205_scATACseq_multi

value: Primary acute myeloid leukemia

value: DNMT3A mutation


title: AML JH4639, scMultiome ATAC

description: Library name: JH4639_scATACseq_multi


title: DNase-seq from substantia nigra (ENCLB605OKC)

description:
https://www.encodeproject.org/experiments/ENCSR047BGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR047BGB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB605OKC

value: ENCBS637FCU at ENCODE; https://www.encodeproject.org/ENCBS637FCU/


title: DNase-seq from anterior cingulate cortex (ENCLB730KCP)

description:
https://www.encodeproject.org/experiments/ENCSR047HME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR047HME
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB730KCP

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: female

value: ENCBS395DMD at ENCODE; https://www.encodeproject.org/ENCBS395DMD/


title: AML JH5034, scMultiome ATAC

description: Library name: JH5034_scATACseq_multi


title: AML SU214 Replicate 2, scMultiome ATAC

description:
Library name: SU214_scATACseq_multi
SU214 was sequenced with scATACseq single-omics and single-cell multiome sequencing (Biological replicates). This record contains the ATAC portion of the single-cell multiomics data.


title: PBMC, Day 84, ATAC-seq, Individual 16

description: Library name: Ind16

value: PBMC

value: monocytes, T and B cells


title: AML JH4198, scATAC-seq

description: Library name: JH4189_scATACseq_single

value: IDH1/2 mutation


title: AML JH4316, scMultiome ATAC

description: Library name: JH4316_scATACseq_multi

value: TET2 mutation


title: PBMC, Day 84, ATAC-seq, Individual 01

description: Library name: Ind01


title: CMP, WGBS

description: Library name: CMP_WGBS

data_processing:
Following DNA sequencing, fastq files were trimmed using TrimGalore. Trimmed reads were aligned to the hg19 genome using Bismark. Samtools was used to merge, sort, and deduplicate bam files. Finally, the informME analysis pipeline was applied to quantify methylation stochasticity within individual samples and to compare methylation stochasticity between samples.
Assembly: hg19
Supplementary files format and content: bigwig format. Tracks include mean methylation level (MML), normalized methylation entropy (NME), and Jensen Shannon Distance (JSD) to measure methylation stochasticity between samples.
Supplementary files format and content: Processed data for AML samples and normal CD34+ and GMP controls includes comparison to WGBS data from a previously published LMPP sample (GSM4036933).

source_name: Sorted normal CMP

extract_protocol:
Primary AML samples were collected from peripheral blood or bone marrow.
WGBS libraries for CMP and MEP normal controls were generated using the IDT Methyl-Seq Kit. For primary AML samples, and CD34+ and GMP normal controls, WGBS libraries were generated using NEBNext Ultra DNA library Prep kit for Illumina according to the manufacturer's instructions with modifications. Input gDNA was spiked with 1% unmethylated Lambda DNA (Promega) to monitor bisulfite conversion efficiency. Size selection was performed using SPRIselect beads and insert sizes of 300-400bp were isolated. Samples were bisulfite converted after size selection using EZ DNA Methylation-Lightning Kit (Zymo). Libraries were sequenced on an Illumina HiSeq4000 or NovaSeq6000 instruments.

value: Sorted normal CMP

value: Normal CMP


title: DNase-seq from hypothalamus (ENCLB663FRJ)

description:
https://www.encodeproject.org/experiments/ENCSR046VKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR046VKG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB663FRJ

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: tissue

value: male

value: adult

value: ENCBS886XVU at ENCODE; https://www.encodeproject.org/ENCBS886XVU/


title: DNase-seq from Ammon's horn (ENCLB973ILJ)

description:
https://www.encodeproject.org/experiments/ENCSR046VFU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR046VFU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB973ILJ

value: Ammon's horn

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS257RNF at ENCODE; https://www.encodeproject.org/ENCBS257RNF/


title: MEP, WGBS

description: Library name: MEP_WGBS

source_name: Sorted normal MEP

value: Sorted normal MEP

value: Normal MEP


title: DNase-seq from putamen (ENCLB481JEK)

description:
https://www.encodeproject.org/experiments/ENCSR046FVG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR046FVG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB481JEK

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: female

value: ENCBS920TZV at ENCODE; https://www.encodeproject.org/ENCBS920TZV/


title: PBMC, Day 84, ATAC-seq, Individual 29

description: Library name: Ind29

value: peripheral blood

value: PBMC

value: monocytes, T and B cells


title: AML JH5236, WGBS

description: Library name: JH5236_WGBS

value: Primary acute myeloid leukemia

value: IDH1/2 mutation


title: PBMC, Day 84, ATAC-seq, Individual 31

description: Library name: Ind31


title: PBMC, Day 84, ATAC-seq, Individual 12

description: Library name: Ind12


title: AML SU075, WGBS

description: Library name: SU075_WGBS