title: DNase-seq from anterior cingulate cortex (ENCLB955RAL)

description:
https://www.encodeproject.org/experiments/ENCSR639BIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639BIZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB955RAL

value: tissue

value: ENCBS354FDP at ENCODE; https://www.encodeproject.org/ENCBS354FDP/


title: FKBP-PKR Dimerizer (24hrs) Rep2

status: Public on Mar 06 2026

type: SRA

city: Redwood City

first: Altos Labs

last: Bioinformatics Hub

state: CA

address: 2600 Island Dr.

department: Institute of Technology

country: USA

institute: Altos Labs

description:
Library name: Sample 17
FZ_6B_T1

library_source: transcriptomic

data_processing:
Raw sequencing data were demultiplexed using bclconvert. RNA-seq FASTQ files were trimmed, aligned to the human reference genome (GRCh38, v108), and quantified using the nf-core/rnaseq pipeline with the star_salmon option (v3.12.0). Gene-level length-scaled counts were used for all downstream analyses.
Assembly: GRCh38 v108
Supplementary files format and content: salmon.merged.gene_counts_length_scaled.tsv contains gene-level length-scaled estimated counts from Salmon across all samples.
Supplementary files format and content: quant.sf files for each sample contain Salmon transcript-level quantification results.

molecule: polyA RNA

organism: Homo sapiens

source_name: Brain

growth_protocol: U-2 OS (ATCC HTB-96), H4 (ATCC HTB-148), and HEK-293 (ATCC CRL-1573) cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1X GlutaMax (Gibco). All cell lines used in the study tested negative for Mycoplasma contamination when assayed with the Universal Mycoplasma Detection Kit.

extract_protocol:
Total RNA was extracted from ~200K cells using the Promega Maxwell automated RNA extractor following the manufacturer’s recommendations.
Libraries were prepared according to the Illumina Stranded mRNA Library Prep Kits (Illumina #20040534) protocol, using 200 ng of RNA input, and sequenced on an Illumina NovaSeq X+.

tag: tissue

value: Brain

tag: Sex

value: Male

tag: cell line

tag: cell type

value: epithelial

tag: treatment

value: Dimerizer


title: FKBP-PKR 4u8C + Dimerizer (0hrs) Rep1

description:
Library name: Sample 19
FZ_7A_T1

value: 4u8C + Dimerizer


title: DNase-seq from substantia nigra (ENCLB859ZBN)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR639NAH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR639NAH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB859ZBN

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

tag: biosample encode accession

tag: encode accession

value: male

tag: dev stage

value: adult

tag: age

value: unknown

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS502QZV at ENCODE; https://www.encodeproject.org/ENCBS502QZV/


title: DNase-seq from amygdala (ENCLB690PWC)

description:
https://www.encodeproject.org/experiments/ENCSR631VBB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR631VBB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB690PWC

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: ENCBS977ZML at ENCODE; https://www.encodeproject.org/ENCBS977ZML/


title: FKBP-PKR Dimerizer (24hrs) Rep1

description:
Library name: Sample 16
FZ_6A_T1


title: FKBP-PKR Dimerizer (16hrs) Rep3

description:
Library name: Sample 15
FZ_5C_T1


title: DNase-seq from caudate nucleus (ENCLB975TDH)

description:
https://www.encodeproject.org/experiments/ENCSR637IXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR637IXV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB975TDH

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: female

value: ENCBS314NMF at ENCODE; https://www.encodeproject.org/ENCBS314NMF/


title: DNase-seq from amygdala (ENCLB180ZAN)

description:
https://www.encodeproject.org/experiments/ENCSR631VBB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR631VBB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB180ZAN

value: tissue

value: ENCBS056QPS at ENCODE; https://www.encodeproject.org/ENCBS056QPS/


title: DNase-seq from anterior cingulate cortex (ENCLB735EMM)

description:
https://www.encodeproject.org/experiments/ENCSR657SFP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR657SFP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB735EMM

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: ENCBS536DLK at ENCODE; https://www.encodeproject.org/ENCBS536DLK/


title: DNase-seq from substantia nigra (ENCLB006VVI)

description:
https://www.encodeproject.org/experiments/ENCSR626NGB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR626NGB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB006VVI

source_name: Homo sapiens female adult substantia nigra tissue

value: ENCBS874YCN at ENCODE; https://www.encodeproject.org/ENCBS874YCN/


title: FKBP-PKR Dimerizer (16hrs) Rep2

description:
Library name: Sample 14
FZ_5B_T1

value: Brain

value: Male

value: epithelial

value: Dimerizer


title: DNase-seq from putamen (ENCLB132FYF)

description:
https://www.encodeproject.org/experiments/ENCSR629ZDJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR629ZDJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB132FYF

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: male

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS476HFU at ENCODE; https://www.encodeproject.org/ENCBS476HFU/


title: DNase-seq from nucleus accumbens (ENCLB041FXR)

description:
https://www.encodeproject.org/experiments/ENCSR628ICO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR628ICO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB041FXR

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: Kristin Ardlie

value: ENCBS359IAD at ENCODE; https://www.encodeproject.org/ENCBS359IAD/


title: FKBP-PKR Dimerizer (8hrs) Rep2

description:
Library name: Sample 11
FZ_4B_T1


title: DNase-seq from nucleus accumbens (ENCLB312ZFT)

description:
https://www.encodeproject.org/experiments/ENCSR622YET/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR622YET
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB312ZFT

value: tissue

value: ENCBS306JFE at ENCODE; https://www.encodeproject.org/ENCBS306JFE/


title: FKBP-PKR Dimerizer (8hrs) Rep3

description:
Library name: Sample 12
FZ_4C_T1


title: DNase-seq from Ammon's horn (ENCLB507LBU)

description:
https://www.encodeproject.org/experiments/ENCSR625XKF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR625XKF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB507LBU

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: ENCBS846AOR at ENCODE; https://www.encodeproject.org/ENCBS846AOR/


title: FKBP-PKR Dimerizer (8hrs) Rep1

description:
Library name: Sample 10
FZ_4A_T1

value: Brain


title: DNase-seq from hypothalamus (ENCLB960RDV)

description:
https://www.encodeproject.org/experiments/ENCSR650FAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR650FAV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB960RDV

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: ENCBS937SFW at ENCODE; https://www.encodeproject.org/ENCBS937SFW/


title: FKBP-PKR Dimerizer (4hrs) Rep3

description:
Library name: Sample 9
FZ_3C_T1

value: Male

value: epithelial

value: Dimerizer


title: FKBP-PKR Dimerizer (2hrs) Rep3

description:
Library name: Sample 6
FZ_2C_T1


title: DNase-seq from hypothalamus (ENCLB886GZU)

description:
https://www.encodeproject.org/experiments/ENCSR612KFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR612KFD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB886GZU

value: male

value: adult

value: ENCBS912INQ at ENCODE; https://www.encodeproject.org/ENCBS912INQ/


title: DNase-seq from anterior cingulate cortex (ENCLB206UKZ)

description:
https://www.encodeproject.org/experiments/ENCSR614IPP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR614IPP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB206UKZ

value: anterior cingulate cortex

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS719HAR at ENCODE; https://www.encodeproject.org/ENCBS719HAR/


title: DNase-seq from anterior cingulate cortex (ENCLB134LLP)

description:
https://www.encodeproject.org/experiments/ENCSR616PKU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR616PKU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB134LLP

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: tissue

value: female

value: Kristin Ardlie

value: ENCBS403WTT at ENCODE; https://www.encodeproject.org/ENCBS403WTT/


title: FKBP-PKR Dimerizer (4hrs) Rep2

description:
Library name: Sample 8
FZ_3B_T1

value: Brain


title: DNase-seq from hypothalamus (ENCLB349FJS)

description:
https://www.encodeproject.org/experiments/ENCSR619OGY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR619OGY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB349FJS

value: hypothalamus

value: ENCBS437ZJF at ENCODE; https://www.encodeproject.org/ENCBS437ZJF/


title: FKBP-PKR Dimerizer (2hrs) Rep2

description:
Library name: Sample 5
FZ_2B_T1

value: Male


title: FKBP-PKR Dimerizer (4hrs) Rep1

description:
Library name: Sample 7
FZ_3A_T1

value: epithelial


title: FKBP-PKR Dimerizer (16hrs) Rep1

description:
Library name: Sample 13
FZ_5A_T1

value: Dimerizer


title: FKBP-PKR Dimerizer (0hrs) Rep3

description:
Library name: Sample 3
FZ_1C_T1


title: FKBP-PKR Dimerizer (0hrs) Rep2

description:
Library name: Sample 2
FZ_1B_T1


title: DNase-seq from Ammon's horn (ENCLB457DCA)

description:
https://www.encodeproject.org/experiments/ENCSR607MRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR607MRE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB457DCA

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: ENCBS905HSN at ENCODE; https://www.encodeproject.org/ENCBS905HSN/


title: DNase-seq from Ammon's horn (ENCLB958PEM)

description:
https://www.encodeproject.org/experiments/ENCSR607MRE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR607MRE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB958PEM

value: adult

value: ENCBS211MIY at ENCODE; https://www.encodeproject.org/ENCBS211MIY/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB509TXN)

description:
https://www.encodeproject.org/experiments/ENCSR610IKS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR610IKS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB509TXN

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: unknown

value: ENCBS910VZA at ENCODE; https://www.encodeproject.org/ENCBS910VZA/


title: DNase-seq from amygdala (ENCLB624KBM)

description:
https://www.encodeproject.org/experiments/ENCSR611NHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR611NHP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB624KBM

value: amygdala

value: tissue

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS987NQY at ENCODE; https://www.encodeproject.org/ENCBS987NQY/


title: FKBP-PKR Dimerizer (0hrs) Rep1

description:
Library name: Sample 1
FZ_1A_T1

value: Brain


title: DNase-seq from putamen (ENCLB586KSG)

description:
https://www.encodeproject.org/experiments/ENCSR605PMD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR605PMD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB586KSG

value: putamen

value: Kristin Ardlie

value: ENCBS965KPR at ENCODE; https://www.encodeproject.org/ENCBS965KPR/


title: DNase-seq from caudate nucleus (ENCLB304JPO)

description:
https://www.encodeproject.org/experiments/ENCSR616UDW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR616UDW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB304JPO

value: caudate nucleus

value: female

value: ENCBS527FMV at ENCODE; https://www.encodeproject.org/ENCBS527FMV/


title: DNase-seq from putamen (ENCLB723ILC)

description:
https://www.encodeproject.org/experiments/ENCSR605PMD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR605PMD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB723ILC

value: adult

value: ENCBS904KFL at ENCODE; https://www.encodeproject.org/ENCBS904KFL/


title: FKBP-PKR Dimerizer (2hrs) Rep1

description:
Library name: Sample 4
FZ_2A_T1

value: Male

value: epithelial

value: Dimerizer


title: TF-1 DMSO Rep 3, WGBS

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: TF-1_DMSO_Rep3

data_processing:
Following DNA sequencing, fastq files were trimmed using TrimGalore. Trimmed reads were aligned to the hg38 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: hg38
Supplementary files format and content: bed format. Tracks include mean methylation level (MML), normalized methylation entropy (NME), differential quantities of the above between samples (dMML, dNME), and Jensen Shannon Distance (JSD) to measure methylation stochasticity between samples.

source_name: TF-1 (ATCC CRL-2003)

growth_protocol: Cells were grown in RPMI (ATCC modification) with 10% FBS and 2 ng/mL human GM-CSF.

extract_protocol:
DNA was extracted from harvested cells using the MasterPure Complete DNA and RNA Purifiation kit.
WGBS libraries were generated using NEBNext Ultra DNA library Prep kit for Illumina (New England BioLabs) according to the manufacturer's instructions with modifications. Input gDNA was spiked with 1% unmethylated Lambda DNA (Promega, cat. # D1521) 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, cat. # D5030). Libraries were sequenced on Illumina NovaSeq X Plus instrument.

treatment_protocol: Cells were treated with 500 nM decitabine or DMSO control for 72 hours before harvesting.

value: TF-1 (ATCC CRL-2003)

value: Human erythroleukemia

value: DMSO


title: TF-1 DMSO Rep 1, WGBS

description: Library name: TF-1_DMSO_Rep1


title: TF-1 DMSO Rep 2, WGBS

description: Library name: TF-1_DMSO_Rep2


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB185EXP)

description:
https://www.encodeproject.org/experiments/ENCSR603VXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR603VXZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB185EXP

value: dorsolateral prefrontal cortex

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS661YDY at ENCODE; https://www.encodeproject.org/ENCBS661YDY/


title: DNase-seq from Ammon's horn (ENCLB139TQV)

description:
https://www.encodeproject.org/experiments/ENCSR604DFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR604DFY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB139TQV

value: Ammon's horn

value: Kristin Ardlie

value: ENCBS806JBG at ENCODE; https://www.encodeproject.org/ENCBS806JBG/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB738AAW)

description:
https://www.encodeproject.org/experiments/ENCSR596OSX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR596OSX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB738AAW

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: male

value: ENCBS640SQN at ENCODE; https://www.encodeproject.org/ENCBS640SQN/


title: DNase-seq from caudate nucleus (ENCLB991HBH)

description:
https://www.encodeproject.org/experiments/ENCSR591VFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR591VFR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB991HBH

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: adult

value: ENCBS145ONK at ENCODE; https://www.encodeproject.org/ENCBS145ONK/


title: TF-1 DAC Rep 1, WGBS

description: Library name: TF-1_DAC_Rep1

value: 500 nM DAC, 72 hours


title: TF-1 DAC Rep 2, WGBS

description: Library name: TF-1_DAC_Rep2

value: TF-1 (ATCC CRL-2003)


title: DNase-seq from anterior cingulate cortex (ENCLB375RKM)

description:
https://www.encodeproject.org/experiments/ENCSR586WGL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR586WGL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB375RKM

value: anterior cingulate cortex

value: ENCBS389IEE at ENCODE; https://www.encodeproject.org/ENCBS389IEE/


title: DNase-seq from hypothalamus (ENCLB220OFY)

description:
https://www.encodeproject.org/experiments/ENCSR585NVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR585NVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB220OFY

value: hypothalamus

value: ENCBS270PTB at ENCODE; https://www.encodeproject.org/ENCBS270PTB/


title: DNase-seq from amygdala (ENCLB127GZC)

description:
https://www.encodeproject.org/experiments/ENCSR590CBB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR590CBB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB127GZC

value: amygdala

value: tissue

value: unknown

value: ENCBS272TKS at ENCODE; https://www.encodeproject.org/ENCBS272TKS/


title: IDH2-mutant isogenic TF-1 DAC Rep 3, WGBS

description: Library name: IDH2m_TF-1_DAC_Rep3

source_name: IDH2-mutant isogenic TF-1 (ATCC CRL-2003IG)

value: Human erythroleukemia

tag: genotype

value: IDH2R140Q mutation


title: TF-1 DAC Rep 3, WGBS

description: Library name: TF-1_DAC_Rep3


title: DNase-seq from Ammon's horn (ENCLB695BKF)

description:
https://www.encodeproject.org/experiments/ENCSR586NBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR586NBV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB695BKF

value: Ammon's horn

value: male

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS553WYK at ENCODE; https://www.encodeproject.org/ENCBS553WYK/


title: DNase-seq from nucleus accumbens (ENCLB210LMZ)

description:
https://www.encodeproject.org/experiments/ENCSR582LVC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR582LVC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB210LMZ

value: nucleus accumbens

value: adult

value: ENCBS269MQX at ENCODE; https://www.encodeproject.org/ENCBS269MQX/


title: DNase-seq from nucleus accumbens (ENCLB484RDB)

description:
https://www.encodeproject.org/experiments/ENCSR582LVC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR582LVC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB484RDB

value: ENCBS364OSH at ENCODE; https://www.encodeproject.org/ENCBS364OSH/


title: IDH2-mutant isogenic TF-1 DMSO Rep 3, WGBS

description: Library name: IDH2m_TF-1_DMSO_Rep3

value: IDH2-mutant isogenic TF-1 (ATCC CRL-2003IG)

value: DMSO


title: IDH2-mutant isogenic TF-1 DMSO Rep 1, WGBS

description: Library name: IDH2m_TF-1_DMSO_Rep1


title: long read RNA-seq from technical sample (ENCLB131TFM)

description:
https://www.encodeproject.org/experiments/ENCSR731MFY/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP H1 mix
experiment encode accession: ENCSR731MFY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB131TFM
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

molecule: total RNA

organism: synthetic construct

source_name: control

value: technical sample

tag: biosample term name

value: synthetic construct


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB604PJX)

description:
https://www.encodeproject.org/experiments/ENCSR680JGE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR680JGE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB604PJX

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

value: C1 segment of cervical spinal cord

value: tissue

value: female

value: unknown

value: ENCBS254QIX at ENCODE; https://www.encodeproject.org/ENCBS254QIX/


title: IDH2-mutant isogenic TF-1 DAC Rep 1, WGBS

description: Library name: IDH2m_TF-1_DAC_Rep1

value: Human erythroleukemia

value: IDH2R140Q mutation

value: 500 nM DAC, 72 hours


title: DNase-seq from caudate nucleus (ENCLB121JTD)

description:
https://www.encodeproject.org/experiments/ENCSR577BCI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR577BCI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB121JTD

value: caudate nucleus

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS510BVU at ENCODE; https://www.encodeproject.org/ENCBS510BVU/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB285GVE)

description:
https://www.encodeproject.org/experiments/ENCSR575UNV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR575UNV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB285GVE

value: dorsolateral prefrontal cortex

value: adult

value: ENCBS703OUT at ENCODE; https://www.encodeproject.org/ENCBS703OUT/


title: IDH2-mutant isogenic TF-1 DAC Rep 2, WGBS

description: Library name: IDH2m_TF-1_DAC_Rep2

value: IDH2-mutant isogenic TF-1 (ATCC CRL-2003IG)


title: long read RNA-seq from technical sample (ENCLB052XIG)

description:
https://www.encodeproject.org/experiments/ENCSR731MFY/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP H1 mix
experiment encode accession: ENCSR731MFY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB052XIG
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).

value: technical sample

value: synthetic construct


title: IDH2-mutant isogenic TF-1 DMSO Rep 2, WGBS

description: Library name: IDH2m_TF-1_DMSO_Rep2

value: DMSO


title: long read RNA-seq from technical sample (ENCLB939VOK)

description:
https://www.encodeproject.org/experiments/ENCSR731MFY/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP H1 mix
experiment encode accession: ENCSR731MFY
assay title: long read RNA-seq
assembly: GRCh38
encode release date: 2021-05-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB939VOK
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix., ERCC reference spike-ins used for LRGASP. Note that this does NOT contain the SIRVs that are a part of this mix (found in ENCSR759PLA).


title: DNase-seq from amygdala (ENCLB310XVS)

description:
https://www.encodeproject.org/experiments/ENCSR571XNF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR571XNF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB310XVS

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: tissue

value: male

value: ENCBS063NMN at ENCODE; https://www.encodeproject.org/ENCBS063NMN/


title: adult sample 4

city: Duarte

first: Sangeeta

last: Dhawan

address: 1500 E Duarte Rd

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: F194s_A

data_processing:
Paired-end RNA-Seq reads were processed by removing sequencing adapters and polyA tails, followed by alignment to the mouse genome (mm10) using STAR V2.6a.
The gene-level read counts per sample were generated using HTSeq v0.11.1.
Differential expression analysis was conducted using edgeR.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing normalized gene counts, log fold changes (neonatal vs adult) and Pvalues

organism: Mus musculus

source_name: Pancreatic islet

extract_protocol:
Total RNA was extracted from 30-50 hand-picked islets isolated from C57BL/6J mice at P5 (neonatal) and 2.5 months (adult) using the RNeasy Micro Kit (Qiagen).
cDNA libraries were prepared from 250 ng total RNA using the KAPA HyperPrep Kit with RiboErase (HMR) (Kapa Biosystems) using manufacturer’s instructions. Libraries were validated using the Agilent Bioanalyzer and quantified with the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).

value: Pancreatic islet

tag: batch

value: Batch 2


title: adult sample 5

description: Library name: mm14A

value: Batch 3


title: adult sample 6

description: Library name: mm15A


title: DNase-seq from hypothalamus (ENCLB170CQY)

description:
https://www.encodeproject.org/experiments/ENCSR568ZVZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR568ZVZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB170CQY

source_name: Homo sapiens female adult hypothalamus tissue

value: hypothalamus

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS539IXH at ENCODE; https://www.encodeproject.org/ENCBS539IXH/


title: DNase-seq from Ammon's horn (ENCLB691GHC)

description:
https://www.encodeproject.org/experiments/ENCSR565QNJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR565QNJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB691GHC

value: Ammon's horn

value: adult

value: Kristin Ardlie

value: ENCBS745TKN at ENCODE; https://www.encodeproject.org/ENCBS745TKN/


title: adult sample 3

description: Library name: F192s_A


title: DNase-seq from nucleus accumbens (ENCLB134HSO)

description:
https://www.encodeproject.org/experiments/ENCSR571EDT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR571EDT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB134HSO

value: nucleus accumbens

value: ENCBS011LRD at ENCODE; https://www.encodeproject.org/ENCBS011LRD/


title: DNase-seq from cerebellum (ENCLB709ORU)

description:
https://www.encodeproject.org/experiments/ENCSR564YDM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR564YDM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB709ORU

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: ENCBS531LTO at ENCODE; https://www.encodeproject.org/ENCBS531LTO/


title: adult sample 2

description: Library name: M191s_A

value: Pancreatic islet


title: neonatal sample large 19

description: Library name: L9s_M

value: Batch 2


title: DNase-seq from cerebellum (ENCLB097JWH)

description:
https://www.encodeproject.org/experiments/ENCSR564YDM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR564YDM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB097JWH

value: ENCBS299TYZ at ENCODE; https://www.encodeproject.org/ENCBS299TYZ/


title: adult sample 1

description: Library name: M190s_A


title: neonatal sample large 18

description: Library name: L8s_M


title: neonatal sample large 20

description: Library name: L10s_M


title: DNase-seq from caudate nucleus (ENCLB741RML)

description:
https://www.encodeproject.org/experiments/ENCSR561DSZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR561DSZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB741RML

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS154ZFH at ENCODE; https://www.encodeproject.org/ENCBS154ZFH/


title: DNase-seq from anterior cingulate cortex (ENCLB793OXW)

description:
https://www.encodeproject.org/experiments/ENCSR558JMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR558JMZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB793OXW

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: male

value: unknown

value: ENCBS860UDD at ENCODE; https://www.encodeproject.org/ENCBS860UDD/


title: DNase-seq from nucleus accumbens (ENCLB178LRF)

description:
https://www.encodeproject.org/experiments/ENCSR571EDT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR571EDT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB178LRF

source_name: Homo sapiens male adult nucleus accumbens tissue

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS977IGV at ENCODE; https://www.encodeproject.org/ENCBS977IGV/


title: neonatal sample large 17

description: Library name: L7s_M


title: DNase-seq from Ammon's horn (ENCLB147PFL)

description:
https://www.encodeproject.org/experiments/ENCSR556AOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR556AOQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB147PFL

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: Kristin Ardlie

value: ENCBS335OXB at ENCODE; https://www.encodeproject.org/ENCBS335OXB/


title: DNase-seq from amygdala (ENCLB669XXR)

description:
https://www.encodeproject.org/experiments/ENCSR551KJH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR551KJH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB669XXR

value: amygdala

value: tissue

value: ENCBS653XXN at ENCODE; https://www.encodeproject.org/ENCBS653XXN/


title: neonatal sample large 15

description: Library name: mm4M

value: Pancreatic islet

value: Batch 3


title: neonatal sample large 14

description: Library name: mm2M


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB640MGM)

description:
https://www.encodeproject.org/experiments/ENCSR554EZP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR554EZP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB640MGM

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

value: C1 segment of cervical spinal cord

value: ENCBS203AJI at ENCODE; https://www.encodeproject.org/ENCBS203AJI/


title: DNase-seq from cerebellum (ENCLB730JBV)

description:
https://www.encodeproject.org/experiments/ENCSR564YDM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR564YDM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB730JBV

value: cerebellum

value: female

value: ENCBS650XMB at ENCODE; https://www.encodeproject.org/ENCBS650XMB/


title: DNase-seq from Ammon's horn (ENCLB100YHM)

description:
https://www.encodeproject.org/experiments/ENCSR547QPY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR547QPY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB100YHM

source_name: Homo sapiens female adult Ammon's horn tissue

value: unknown

value: ENCBS349CJG at ENCODE; https://www.encodeproject.org/ENCBS349CJG/


title: DNase-seq from Ammon's horn (ENCLB318QKN)

description:
https://www.encodeproject.org/experiments/ENCSR543GPI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR543GPI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB318QKN

value: male

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS317TPC at ENCODE; https://www.encodeproject.org/ENCBS317TPC/


title: neonatal sample large 12

description: Library name: M4_M

value: Batch 1


title: neonatal sample large 10

description: Library name: M2_M


title: neonatal sample large 13

description: Library name: M5_M


title: DNase-seq from putamen (ENCLB642XZT)

description:
https://www.encodeproject.org/experiments/ENCSR542LBV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR542LBV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB642XZT

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: Kristin Ardlie

value: ENCBS363RRZ at ENCODE; https://www.encodeproject.org/ENCBS363RRZ/


title: DNase-seq from putamen (ENCLB370OUT)

description:
https://www.encodeproject.org/experiments/ENCSR542LBV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR542LBV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB370OUT

value: tissue

value: ENCBS186JVP at ENCODE; https://www.encodeproject.org/ENCBS186JVP/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB609QUJ)

description:
https://www.encodeproject.org/experiments/ENCSR537KZC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR537KZC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB609QUJ

value: dorsolateral prefrontal cortex

value: ENCBS307LKC at ENCODE; https://www.encodeproject.org/ENCBS307LKC/


title: neonatal sample large 16

description: Library name: mm7L

value: Pancreatic islet

value: Batch 3


title: neonatal sample small 9

description: Library name: S9s_S

value: Batch 2


title: neonatal sample small 7

description: Library name: S6s_S


title: neonatal sample small 6

description: Library name: mm7S


title: neonatal sample small 8

description: Library name: S7s_S


title: DNase-seq from anterior cingulate cortex (ENCLB430UIN)

description:
https://www.encodeproject.org/experiments/ENCSR530AUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR530AUB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB430UIN

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: female

value: unknown

value: ENCBS856KZK at ENCODE; https://www.encodeproject.org/ENCBS856KZK/


title: neonatal sample small 4

description: Library name: S5_S


title: DNase-seq from Ammon's horn (ENCLB482CFG)

description:
https://www.encodeproject.org/experiments/ENCSR543GPI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR543GPI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB482CFG

value: Ammon's horn

value: male

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS251IVL at ENCODE; https://www.encodeproject.org/ENCBS251IVL/


title: DNase-seq from cerebellum (ENCLB155NHR)

description:
https://www.encodeproject.org/experiments/ENCSR523PNS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR523PNS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB155NHR

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: Kristin Ardlie

value: ENCBS890KJE at ENCODE; https://www.encodeproject.org/ENCBS890KJE/


title: neonatal sample small 2

description: Library name: S2_S

value: Batch 1


title: DNase-seq from caudate nucleus (ENCLB641BWM)

description:
https://www.encodeproject.org/experiments/ENCSR523IBJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR523IBJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB641BWM

value: caudate nucleus

value: tissue

value: ENCBS699PHP at ENCODE; https://www.encodeproject.org/ENCBS699PHP/


title: DNase-seq from substantia nigra (ENCLB881QYH)

description:
https://www.encodeproject.org/experiments/ENCSR536OWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR536OWC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB881QYH

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: ENCBS837LKO at ENCODE; https://www.encodeproject.org/ENCBS837LKO/


title: neonatal sample small 5

description: Library name: mm2S

value: Pancreatic islet

value: Batch 3


title: DNase-seq from putamen (ENCLB564LHD)

description:
https://www.encodeproject.org/experiments/ENCSR522VCX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR522VCX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB564LHD

value: putamen

value: female

value: unknown

value: ENCBS053TSE at ENCODE; https://www.encodeproject.org/ENCBS053TSE/


title: hippocampus microglia, Het, 1619

city: Beijing

first: Ya Bin

last: Wei

state: Beijing

address: 38 Xueyuan load

country: China

institute: Peking University

description:
P17-21 male mouse
1619

data_processing:
1.mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data；2. mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database；3.mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: mm39
Supplementary files format and content: gene_count_matrix.txt

source_name: hippocampus

extract_protocol:
Total RNA was extracted from sorted microglia of hippocampus of P17-21 mice using a TRIzol reagent (Thermo Fisher).
mRNA was reverse transcribed and amplified using the SMART-seq method. RNA-seq libraries for were prepared using TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's protocols.

value: hippocampus

value: microglia


title: DNase-seq from caudate nucleus (ENCLB059YYQ)

description:
https://www.encodeproject.org/experiments/ENCSR523IBJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR523IBJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB059YYQ

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS139BLS at ENCODE; https://www.encodeproject.org/ENCBS139BLS/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB064OTE)

description:
https://www.encodeproject.org/experiments/ENCSR523WWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR523WWM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB064OTE

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: male

value: Kristin Ardlie

value: ENCBS083RVL at ENCODE; https://www.encodeproject.org/ENCBS083RVL/


title: DNase-seq from hypothalamus (ENCLB986UPC)

description:
https://www.encodeproject.org/experiments/ENCSR529OUT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR529OUT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB986UPC

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: tissue

value: ENCBS915CUI at ENCODE; https://www.encodeproject.org/ENCBS915CUI/


title: neonatal sample small 3

description: Library name: S4_S

value: Pancreatic islet

value: Batch 1


title: hippocampus microglia, Het, 1615

description:
P17-21 male mouse
1615


title: hippocampus microglia, WT, 1613

description:
P17-21 male mouse
1613

value: WT


title: DNase-seq from Ammon's horn (ENCLB636WAN)

description:
https://www.encodeproject.org/experiments/ENCSR515QIF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515QIF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB636WAN

value: Ammon's horn

value: female

value: unknown

value: ENCBS094SYI at ENCODE; https://www.encodeproject.org/ENCBS094SYI/


title: hippocampus microglia, Het, 1604

description:
P17-21 male mouse
1604

value: hippocampus

value: microglia


title: neonatal sample small 1

description: Library name: S1_S


title: DNase-seq from anterior cingulate cortex (ENCLB294VWZ)

description:
https://www.encodeproject.org/experiments/ENCSR514WFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR514WFN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB294VWZ

value: anterior cingulate cortex

value: adult

value: John Stamatoyannopoulos, UW

value: ENCBS721ZYR at ENCODE; https://www.encodeproject.org/ENCBS721ZYR/


title: DNase-seq from substantia nigra (ENCLB368CNX)

description:
https://www.encodeproject.org/experiments/ENCSR510DSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR510DSI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB368CNX

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: Kristin Ardlie

value: ENCBS794REV at ENCODE; https://www.encodeproject.org/ENCBS794REV/


title: DNase-seq from cerebellum (ENCLB416BQR)

description:
https://www.encodeproject.org/experiments/ENCSR513GQE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR513GQE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB416BQR

value: cerebellum

value: tissue

value: ENCBS892GXI at ENCODE; https://www.encodeproject.org/ENCBS892GXI/


title: hippocampus microglia, WT, 1602

description:
P17-21 male mouse
1602

value: WT


title: DNase-seq from anterior cingulate cortex (ENCLB773UHY)

description:
https://www.encodeproject.org/experiments/ENCSR512GOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR512GOI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB773UHY

value: male

value: ENCBS584OHJ at ENCODE; https://www.encodeproject.org/ENCBS584OHJ/


title: DNase-seq from caudate nucleus (ENCLB129OIJ)

description:
https://www.encodeproject.org/experiments/ENCSR518OUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR518OUF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB129OIJ

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: unknown

value: ENCBS597CEK at ENCODE; https://www.encodeproject.org/ENCBS597CEK/


title: DNase-seq from hypothalamus (ENCLB301DIF)

description:
https://www.encodeproject.org/experiments/ENCSR508UEW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR508UEW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB301DIF

value: hypothalamus

value: ENCBS817IDC at ENCODE; https://www.encodeproject.org/ENCBS817IDC/


title: DNase-seq from anterior cingulate cortex (ENCLB062QSU)

description:
https://www.encodeproject.org/experiments/ENCSR507RDH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR507RDH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB062QSU

value: anterior cingulate cortex

value: female

value: adult

value: ENCBS488AWC at ENCODE; https://www.encodeproject.org/ENCBS488AWC/


title: C3H_4d

city: 成都

first: Lu

last: He

address: WUHAN

institute: TONGJI

data_processing:
CLC Genomics Workbench v 11.0.1
sequence  reads were trimmed for adaptor sequence/low-quality sequcence using CLCgenomic benchwork(parameter-Quanlity limit:0.05)
trimmed sequence reads were mapped to GrCM38/MM10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost: 3 length fraction:0.8 similarity fraction:0.8)
read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: heart

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for  the construction of sequencing libraries
RNA libraries for RNA-seq were prepares using SMARTER mRNA-seq library prep kit following manufacture's protocols

value: heart

value: ICR

value: citric acid is injected intraperitoneally during pregnancy


title: D2H_4d

value: STZ  is injected intraperitoneally during pregnancy


title: D1H_4d


title: C2H_4d


title: hippocampus microglia, WT, 1608

description:
P17-21 male mouse
1608

value: hippocampus

value: microglia


title: DNase-seq from Ammon's horn (ENCLB483IRM)

description:
https://www.encodeproject.org/experiments/ENCSR508MTS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR508MTS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB483IRM

value: Ammon's horn

value: tissue

value: male

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS063NYE at ENCODE; https://www.encodeproject.org/ENCBS063NYE/


title: DNase-seq from amygdala (ENCLB435ASC)

description:
https://www.encodeproject.org/experiments/ENCSR507HVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR507HVU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB435ASC

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: unknown

value: ENCBS524FPS at ENCODE; https://www.encodeproject.org/ENCBS524FPS/


title: D3H_4d

value: WT


title: DNase-seq from amygdala (ENCLB781CLK)

description:
https://www.encodeproject.org/experiments/ENCSR507HVU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR507HVU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB781CLK

value: adult

value: ENCBS121BKP at ENCODE; https://www.encodeproject.org/ENCBS121BKP/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB034PDC)

description:
https://www.encodeproject.org/experiments/ENCSR504BVS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR504BVS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034PDC

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: female

value: ENCBS520XSD at ENCODE; https://www.encodeproject.org/ENCBS520XSD/


title: Control MPRA from HepG2 (ENCLB716CRI)

description:
https://www.encodeproject.org/experiments/ENCSR990ZAU/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' 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: ENCSR990ZAU
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB716CRI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

tag: line

value: cell line

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS757FXZ at ENCODE; https://www.encodeproject.org/ENCBS757FXZ/


title: DNase-seq from Ammon's horn (ENCLB060SQQ)

description:
https://www.encodeproject.org/experiments/ENCSR508MTS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR508MTS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB060SQQ

value: Ammon's horn

value: tissue

value: male

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS636IHD at ENCODE; https://www.encodeproject.org/ENCBS636IHD/


title: Control MPRA from HepG2 (ENCLB620JFU)

description:
https://www.encodeproject.org/experiments/ENCSR990ZAU/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' 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: ENCSR990ZAU
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB620JFU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS865RQK at ENCODE; https://www.encodeproject.org/ENCBS865RQK/


title: DNase-seq from caudate nucleus (ENCLB036PLK)

description:
https://www.encodeproject.org/experiments/ENCSR502ZRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR502ZRV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB036PLK

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: adult

value: unknown

value: ENCBS649CZO at ENCODE; https://www.encodeproject.org/ENCBS649CZO/


title: DNase-seq from putamen (ENCLB853AHH)

description:
https://www.encodeproject.org/experiments/ENCSR503IRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR503IRE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB853AHH

value: putamen

value: female

value: ENCBS638WRQ at ENCODE; https://www.encodeproject.org/ENCBS638WRQ/


title: Control MPRA from HepG2 (ENCLB528TDT)

description:
https://www.encodeproject.org/experiments/ENCSR990ZAU/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' 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: ENCSR990ZAU
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB528TDT
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: ENCBS837XYC at ENCODE; https://www.encodeproject.org/ENCBS837XYC/


title: MPRA from glial cell (ENCLB099NSO)

description:
https://www.encodeproject.org/experiments/ENCSR976YTH/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR976YTH
assay title: MPRA
possible controls: ENCSR772XSY
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB099NSO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens male adult glial primary cell expressing RNAi, genetically modified (insertion) using transient transfection

value: glial cell

value: primary cell

value: male

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

value: ATCC

value: ENCBS897HTS at ENCODE; https://www.encodeproject.org/ENCBS897HTS/


title: C1H_4d

tag: tissue

value: heart

value: ICR

value: WT

value: citric acid is injected intraperitoneally during pregnancy


title: DNase-seq from amygdala (ENCLB082UGI)

description:
https://www.encodeproject.org/experiments/ENCSR502XLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR502XLP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB082UGI

value: amygdala

value: tissue

tag: Sex

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS149KGN at ENCODE; https://www.encodeproject.org/ENCBS149KGN/


title: MPRA from glial cell (ENCLB541IES)

description:
https://www.encodeproject.org/experiments/ENCSR976YTH/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR976YTH
assay title: MPRA
possible controls: ENCSR772XSY
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB541IES
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: Nadav Ahituv, UCSF

value: ENCBS929LBB at ENCODE; https://www.encodeproject.org/ENCBS929LBB/


title: DNase-seq from Ammon's horn (ENCLB709IKW)

description:
https://www.encodeproject.org/experiments/ENCSR498IFE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR498IFE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB709IKW

value: Ammon's horn

value: female

value: ENCBS445DLL at ENCODE; https://www.encodeproject.org/ENCBS445DLL/


title: MPRA from K562 (ENCLB795IFE)

description:
https://www.encodeproject.org/experiments/ENCSR987WTK/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.
experiment encode accession: ENCSR987WTK
assay title: MPRA
possible controls: ENCSR540PAH
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB795IFE
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens K562 cell line genetically modified (insertion) using transient transfection

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ATCC

value: ENCBS449YMQ at ENCODE; https://www.encodeproject.org/ENCBS449YMQ/


title: MPRA from K562 (ENCLB093YNB)

description:
https://www.encodeproject.org/experiments/ENCSR987WTK/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.
experiment encode accession: ENCSR987WTK
assay title: MPRA
possible controls: ENCSR540PAH
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB093YNB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS702DCE at ENCODE; https://www.encodeproject.org/ENCBS702DCE/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB213RXG)

description:
https://www.encodeproject.org/experiments/ENCSR494YNX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494YNX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB213RXG

value: dorsolateral prefrontal cortex

value: tissue

value: male

value: adult

value: ENCBS382YYG at ENCODE; https://www.encodeproject.org/ENCBS382YYG/


title: MPRA from K562 (ENCLB803LNL)

description:
https://www.encodeproject.org/experiments/ENCSR987WTK/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.
experiment encode accession: ENCSR987WTK
assay title: MPRA
possible controls: ENCSR540PAH
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB803LNL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS892VEN at ENCODE; https://www.encodeproject.org/ENCBS892VEN/


title: DNase-seq from cerebellum (ENCLB226ZHF)

description:
https://www.encodeproject.org/experiments/ENCSR494WPH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494WPH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB226ZHF

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS081FTK at ENCODE; https://www.encodeproject.org/ENCBS081FTK/


title: DNase-seq from nucleus accumbens (ENCLB328FOK)

description:
https://www.encodeproject.org/experiments/ENCSR499FBT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR499FBT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB328FOK

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: female

value: ENCBS293NVZ at ENCODE; https://www.encodeproject.org/ENCBS293NVZ/


title: MPRA from glial cell (ENCLB178JZA)

description:
https://www.encodeproject.org/experiments/ENCSR976YTH/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR976YTH
assay title: MPRA
possible controls: ENCSR772XSY
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB178JZA
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: primary cell

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

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS606CLZ at ENCODE; https://www.encodeproject.org/ENCBS606CLZ/


title: DNase-seq from Ammon's horn (ENCLB564OSE)

description:
https://www.encodeproject.org/experiments/ENCSR497WDC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR497WDC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB564OSE

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: male

value: adult

value: ENCBS987RVD at ENCODE; https://www.encodeproject.org/ENCBS987RVD/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB135KWP)

description:
https://www.encodeproject.org/experiments/ENCSR497GVB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR497GVB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB135KWP

value: dorsolateral prefrontal cortex

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS016OLB at ENCODE; https://www.encodeproject.org/ENCBS016OLB/


title: Control MPRA from HepG2 (ENCLB636DGW)

description:
https://www.encodeproject.org/experiments/ENCSR974CHK/
***************
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. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR974CHK
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB636DGW
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: ENCBS625PMB at ENCODE; https://www.encodeproject.org/ENCBS625PMB/


title: Control MPRA from HepG2 (ENCLB253ICP)

description:
https://www.encodeproject.org/experiments/ENCSR974CHK/
***************
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. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR974CHK
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB253ICP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ENCBS773ZYY at ENCODE; https://www.encodeproject.org/ENCBS773ZYY/


title: DNase-seq from putamen (ENCLB545GOC)

description:
https://www.encodeproject.org/experiments/ENCSR494EIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494EIL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB545GOC

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: female

value: Kristin Ardlie

value: ENCBS090UHG at ENCODE; https://www.encodeproject.org/ENCBS090UHG/


title: FKBP-PKR 4u8C + Dimerizer (4hrs) Rep3

description:
Library name: Sample 27
FZ_9C_T1

source_name: Brain

value: Brain

value: Male

tag: cell line

value: epithelial

value: 4u8C + Dimerizer


title: Control MPRA from HepG2 (ENCLB854NWQ)

description:
https://www.encodeproject.org/experiments/ENCSR974CHK/
***************
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. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR974CHK
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB854NWQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: ATCC

value: ENCBS259UPA at ENCODE; https://www.encodeproject.org/ENCBS259UPA/


title: Control MPRA from glial cell (ENCLB391JBS)

description:
https://www.encodeproject.org/experiments/ENCSR958QFH/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR958QFH
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB391JBS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens male adult glial primary cell genetically modified (insertion) using transient transfection

value: glial cell

value: primary cell

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

value: adult

value: unknown

value: ENCBS186BRY at ENCODE; https://www.encodeproject.org/ENCBS186BRY/


title: DNase-seq from amygdala (ENCLB137ZIP)

description:
https://www.encodeproject.org/experiments/ENCSR491HOK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR491HOK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB137ZIP

value: amygdala

value: tissue

value: John Stamatoyannopoulos, UW

value: ENCBS194EQW at ENCODE; https://www.encodeproject.org/ENCBS194EQW/


title: DNase-seq from substantia nigra (ENCLB510CHQ)

description:
https://www.encodeproject.org/experiments/ENCSR492XAM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR492XAM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB510CHQ

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: Kristin Ardlie

value: ENCBS593YIX at ENCODE; https://www.encodeproject.org/ENCBS593YIX/


title: Control MPRA from glial cell (ENCLB387MJY)

description:
https://www.encodeproject.org/experiments/ENCSR958QFH/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR958QFH
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB387MJY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ENCBS617EVF at ENCODE; https://www.encodeproject.org/ENCBS617EVF/


title: DNase-seq from putamen (ENCLB278AXK)

description:
https://www.encodeproject.org/experiments/ENCSR493EKM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR493EKM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB278AXK

value: putamen

value: female

value: ENCBS807HYY at ENCODE; https://www.encodeproject.org/ENCBS807HYY/


title: Control MPRA from glial cell (ENCLB007KZF)

description:
https://www.encodeproject.org/experiments/ENCSR958QFH/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR958QFH
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB007KZF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: primary cell

value: male

value: ATCC

value: ENCBS663ZQG at ENCODE; https://www.encodeproject.org/ENCBS663ZQG/


title: DNase-seq from hypothalamus (ENCLB533YXE)

description:
https://www.encodeproject.org/experiments/ENCSR487OSU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR487OSU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB533YXE

source_name: Homo sapiens female adult hypothalamus tissue

value: hypothalamus

value: adult

value: unknown

value: ENCBS457UMF at ENCODE; https://www.encodeproject.org/ENCBS457UMF/


title: MPRA from HEK293T (ENCLB746FKH)

description:
https://www.encodeproject.org/experiments/ENCSR934HHR/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
experiment encode accession: ENCSR934HHR
assay title: MPRA
possible controls: ENCSR484ECL
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB746FKH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens HEK293T cell line genetically modified (insertion) using transient transfection

value: cell line

value: embryonic

value: ENCBS247JRR at ENCODE; https://www.encodeproject.org/ENCBS247JRR/


title: Control MPRA from HepG2 (ENCLB415KSB)

description:
https://www.encodeproject.org/experiments/ENCSR932ZCL/
***************
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 mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR932ZCL
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB415KSB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ENCBS237BOI at ENCODE; https://www.encodeproject.org/ENCBS237BOI/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB121JDP)

description:
https://www.encodeproject.org/experiments/ENCSR485PFX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR485PFX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB121JDP

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS509PED at ENCODE; https://www.encodeproject.org/ENCBS509PED/


title: MPRA from HEK293T (ENCLB305ZNT)

description:
https://www.encodeproject.org/experiments/ENCSR934HHR/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
experiment encode accession: ENCSR934HHR
assay title: MPRA
possible controls: ENCSR484ECL
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB305ZNT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: ATCC

value: ENCBS545RRN at ENCODE; https://www.encodeproject.org/ENCBS545RRN/


title: MPRA from HEK293T (ENCLB558BEZ)

description:
https://www.encodeproject.org/experiments/ENCSR934HHR/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
experiment encode accession: ENCSR934HHR
assay title: MPRA
possible controls: ENCSR484ECL
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB558BEZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: unknown

value: ENCBS087PQP at ENCODE; https://www.encodeproject.org/ENCBS087PQP/


title: Control MPRA from HepG2 (ENCLB899NVE)

description:
https://www.encodeproject.org/experiments/ENCSR932ZCL/
***************
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 mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR932ZCL
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB899NVE
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: ENCBS251MKX at ENCODE; https://www.encodeproject.org/ENCBS251MKX/


title: DNase-seq from cerebellum (ENCLB536TJG)

description:
https://www.encodeproject.org/experiments/ENCSR483LYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR483LYC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB536TJG

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: adult

value: ENCBS179OWW at ENCODE; https://www.encodeproject.org/ENCBS179OWW/


title: Control MPRA from HEK293T (ENCLB298VIB)

description:
https://www.encodeproject.org/experiments/ENCSR916DHS/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR916DHS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB298VIB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: embryonic

value: Nadav Ahituv, UCSF

value: ENCBS932UYH at ENCODE; https://www.encodeproject.org/ENCBS932UYH/


title: Control MPRA from HEK293T (ENCLB166EQO)

description:
https://www.encodeproject.org/experiments/ENCSR916DHS/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR916DHS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB166EQO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS455ZEF at ENCODE; https://www.encodeproject.org/ENCBS455ZEF/


title: DNase-seq from Ammon's horn (ENCLB233YAD)

description:
https://www.encodeproject.org/experiments/ENCSR479AHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR479AHN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB233YAD

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS966ASJ at ENCODE; https://www.encodeproject.org/ENCBS966ASJ/


title: Control MPRA from HEK293T (ENCLB597REM)

description:
https://www.encodeproject.org/experiments/ENCSR916DHS/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR916DHS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB597REM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: unknown

value: ATCC

value: ENCBS986CSF at ENCODE; https://www.encodeproject.org/ENCBS986CSF/


title: DNase-seq from cerebellum (ENCLB262ZCY)

description:
https://www.encodeproject.org/experiments/ENCSR474DCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR474DCY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB262ZCY

value: male

value: ENCBS551BBE at ENCODE; https://www.encodeproject.org/ENCBS551BBE/


title: DNase-seq from hypothalamus (ENCLB056FHR)

description:
https://www.encodeproject.org/experiments/ENCSR473PBZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR473PBZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB056FHR

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: adult

value: ENCBS674ZLV at ENCODE; https://www.encodeproject.org/ENCBS674ZLV/


title: DNase-seq from caudate nucleus (ENCLB742IYC)

description:
https://www.encodeproject.org/experiments/ENCSR485IIT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR485IIT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB742IYC

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS308KGV at ENCODE; https://www.encodeproject.org/ENCBS308KGV/


title: DNase-seq from cerebellum (ENCLB879RBM)

description:
https://www.encodeproject.org/experiments/ENCSR477LTA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR477LTA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB879RBM

value: cerebellum

value: ENCBS684JQQ at ENCODE; https://www.encodeproject.org/ENCBS684JQQ/


title: MPRA from HepG2 (ENCLB474MYT)

description:
https://www.encodeproject.org/experiments/ENCSR912KDN/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR912KDN
assay title: MPRA
possible controls: ENCSR092XKS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB474MYT
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: ENCBS533EDQ at ENCODE; https://www.encodeproject.org/ENCBS533EDQ/


title: MPRA from HepG2 (ENCLB536GTF)

description:
https://www.encodeproject.org/experiments/ENCSR912KDN/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR912KDN
assay title: MPRA
possible controls: ENCSR092XKS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB536GTF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ATCC

value: ENCBS352KMY at ENCODE; https://www.encodeproject.org/ENCBS352KMY/


title: DNase-seq from hypothalamus (ENCLB965ITA)

description:
https://www.encodeproject.org/experiments/ENCSR472JUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR472JUH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB965ITA

value: tissue

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS666RSA at ENCODE; https://www.encodeproject.org/ENCBS666RSA/


title: DNase-seq from anterior cingulate cortex (ENCLB897ZTF)

description:
https://www.encodeproject.org/experiments/ENCSR479HTJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR479HTJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB897ZTF

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: female

value: adult

value: ENCBS821XFF at ENCODE; https://www.encodeproject.org/ENCBS821XFF/


title: Control MPRA from HepG2 (ENCLB010AGQ)

description:
https://www.encodeproject.org/experiments/ENCSR932ZCL/
***************
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 mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR932ZCL
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB010AGQ
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: hepatocellular carcinoma

value: ENCBS582VKB at ENCODE; https://www.encodeproject.org/ENCBS582VKB/


title: MPRA from HepG2 (ENCLB264ILB)

description:
https://www.encodeproject.org/experiments/ENCSR912KDN/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR912KDN
assay title: MPRA
possible controls: ENCSR092XKS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB264ILB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ENCBS063PSC at ENCODE; https://www.encodeproject.org/ENCBS063PSC/


title: DNase-seq from Ammon's horn (ENCLB650KBW)

description:
https://www.encodeproject.org/experiments/ENCSR468VXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR468VXW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB650KBW

value: Ammon's horn

value: tissue

value: ENCBS436FWW at ENCODE; https://www.encodeproject.org/ENCBS436FWW/


title: Control MPRA from LNCAP (ENCLB468FMU)

description:
https://www.encodeproject.org/experiments/ENCSR905UEC/
***************
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 MYC enhancer around SNP rs11986220.
experiment encode accession: ENCSR905UEC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB468FMU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: LNCAP

value: male

value: prostate adenocarcinoma

value: 50 year

value: ATCC

value: ENCBS582LUS at ENCODE; https://www.encodeproject.org/ENCBS582LUS/


title: Control MPRA from LNCAP (ENCLB272KSX)

description:
https://www.encodeproject.org/experiments/ENCSR905UEC/
***************
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 MYC enhancer around SNP rs11986220.
experiment encode accession: ENCSR905UEC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB272KSX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: ENCBS501KGT at ENCODE; https://www.encodeproject.org/ENCBS501KGT/


title: DNase-seq from nucleus accumbens (ENCLB860JWJ)

description:
https://www.encodeproject.org/experiments/ENCSR467ZWA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR467ZWA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB860JWJ

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS567AMV at ENCODE; https://www.encodeproject.org/ENCBS567AMV/


title: DNase-seq from putamen (ENCLB980CCX)

description:
https://www.encodeproject.org/experiments/ENCSR477VYA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477VYA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB980CCX

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: ENCBS832TIA at ENCODE; https://www.encodeproject.org/ENCBS832TIA/


title: Control MPRA from LNCAP (ENCLB897USR)

description:
https://www.encodeproject.org/experiments/ENCSR905UEC/
***************
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 MYC enhancer around SNP rs11986220.
experiment encode accession: ENCSR905UEC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB897USR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ENCBS499OIW at ENCODE; https://www.encodeproject.org/ENCBS499OIW/


title: DNase-seq from anterior cingulate cortex (ENCLB326ZVW)

description:
https://www.encodeproject.org/experiments/ENCSR466LWQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR466LWQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB326ZVW

value: anterior cingulate cortex

value: tissue

value: female

value: ENCBS345UJD at ENCODE; https://www.encodeproject.org/ENCBS345UJD/


title: Control MPRA from HepG2 (ENCLB702BAS)

description:
https://www.encodeproject.org/experiments/ENCSR902NRZ/
***************
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 wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR902NRZ
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB702BAS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

value: ENCBS821BCX at ENCODE; https://www.encodeproject.org/ENCBS821BCX/


title: DNase-seq from cerebellum (ENCLB511UST)

description:
https://www.encodeproject.org/experiments/ENCSR477LTA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477LTA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB511UST

value: cerebellum

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS265TYM at ENCODE; https://www.encodeproject.org/ENCBS265TYM/


title: DNase-seq from amygdala (ENCLB559LAQ)

description:
https://www.encodeproject.org/experiments/ENCSR458UNC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR458UNC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB559LAQ

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: ENCBS474AIK at ENCODE; https://www.encodeproject.org/ENCBS474AIK/


title: Control MPRA from HepG2 (ENCLB722GOV)

description:
https://www.encodeproject.org/experiments/ENCSR902NRZ/
***************
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 wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR902NRZ
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB722GOV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ENCBS390OEW at ENCODE; https://www.encodeproject.org/ENCBS390OEW/


title: DNase-seq from amygdala (ENCLB198BUQ)

description:
https://www.encodeproject.org/experiments/ENCSR458UNC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR458UNC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB198BUQ

value: tissue

value: male

value: ENCBS782CDI at ENCODE; https://www.encodeproject.org/ENCBS782CDI/