title: Control MPRA from HepG2 (ENCLB374JUO)

description:
https://www.encodeproject.org/experiments/ENCSR468WFP/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR468WFP
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB374JUO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HepG2 (ENCLB042ZCV)

status: Public on Mar 06 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR478ESZ/
***************
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 wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR478ESZ
assay title: MPRA
assembly: hg19
possible controls: ENCSR742NIM
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB042ZCV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

tag: health state

tag: dev stage

tag: age

tag: lab

tag: source

tag: link

value: ENCBS637OCX at ENCODE; https://www.encodeproject.org/ENCBS637OCX/


title: PUMCH tumor 145

type: genomic

city: Nanjing

first: Yifan

last: Wu

state: Jiangsu

address: Xianlin Road

department: School of Lif Sciences

country: China

institute: Nanjing University

description: genomic DNA from LUAD

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Infinium MethylationEPIC BeadChip.

scan_protocol: Methylation assays were conducted according to the instructions for the Infinium MethylationEPIC BeadChip Kit (Illumina, WG-317-1002) by Sinotech Genomics and Genergy using the Illumina iScan System.

data_processing:
IDAT data were filtered, quality controlled, and beta converted using the R package 'ChAMP' (version 2.21.1).
Average Beta

label: Cy3 and Cy149

molecule: genomic DNA

source_name: lung adenocarcinoma

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from FFPE samples using the QIAamp DNA FFPE Tissue Kit (Qiagen, #56404) according to the manufacturer's instructions.

tag: tissue

value: lung adenocarcinoma

tag: tumor stage

value: II

tag: age at diagnosis

value: Male


title: PUMCH tumor 146

description: genomic DNA from LUAD

label: Cy3 and Cy150

value: I

value: Female


title: Control MPRA from HepG2 (ENCLB646LLB)

description:
https://www.encodeproject.org/experiments/ENCSR468WFP/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR468WFP
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB646LLB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: genomic

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


title: DNase-seq from cerebellum (ENCLB010MTX)

description:
https://www.encodeproject.org/experiments/ENCSR283EEG/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR283EEG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB010MTX

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS883BYQ at ENCODE; https://www.encodeproject.org/ENCBS883BYQ/


title: DNase-seq from anterior cingulate cortex (ENCLB032HEO)

description:
https://www.encodeproject.org/experiments/ENCSR285MPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR285MPF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB032HEO

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: ENCBS576GRD at ENCODE; https://www.encodeproject.org/ENCBS576GRD/


title: PUMCH tumor 143

description: genomic DNA from LUAD

label: Cy3 and Cy147

value: IV


title: PUMCH tumor 144

description: genomic DNA from LUAD

label: Cy3 and Cy148

value: lung adenocarcinoma


title: Control MPRA from HepG2 (ENCLB319DIZ)

description:
https://www.encodeproject.org/experiments/ENCSR468WFP/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR468WFP
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB319DIZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HepG2 (ENCLB574VZO)

description:
https://www.encodeproject.org/experiments/ENCSR463IRX/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR463IRX
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR849IXM
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB574VZO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS450NYV at ENCODE; https://www.encodeproject.org/ENCBS450NYV/


title: DNase-seq from cerebellum (ENCLB763TOV)

description:
https://www.encodeproject.org/experiments/ENCSR283EEG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR283EEG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB763TOV

value: cerebellum

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS600ITJ at ENCODE; https://www.encodeproject.org/ENCBS600ITJ/


title: PUMCH tumor 147

description: genomic DNA from LUAD

label: Cy3 and Cy151

value: lung adenocarcinoma

value: I

value: Female


title: PUMCH tumor 141

description: genomic DNA from LUAD

label: Cy3 and Cy145

value: IV

value: Male


title: MPRA from HepG2 (ENCLB953LMJ)

description:
https://www.encodeproject.org/experiments/ENCSR463IRX/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR463IRX
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR849IXM
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB953LMJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS280SLR at ENCODE; https://www.encodeproject.org/ENCBS280SLR/


title: PUMCH tumor 140

description: genomic DNA from LUAD

label: Cy3 and Cy144


title: PUMCH tumor 142

description: genomic DNA from LUAD

label: Cy3 and Cy146


title: PUMCH tumor 138

description: genomic DNA from LUAD

label: Cy3 and Cy142

value: III


title: DNase-seq from hypothalamus (ENCLB876JMP)

description:
https://www.encodeproject.org/experiments/ENCSR272YHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272YHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB876JMP

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: male

value: adult

value: ENCBS956XKO at ENCODE; https://www.encodeproject.org/ENCBS956XKO/


title: PUMCH tumor 139

description: genomic DNA from LUAD

label: Cy3 and Cy143


title: MPRA from K562 (ENCLB857UJP)

description:
https://www.encodeproject.org/experiments/ENCSR460LZI/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR460LZI
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR327IIZ
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB857UJP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS069NOT at ENCODE; https://www.encodeproject.org/ENCBS069NOT/


title: MPRA from HepG2 (ENCLB541FJC)

description:
https://www.encodeproject.org/experiments/ENCSR463IRX/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR463IRX
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR849IXM
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB541FJC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS408HXQ at ENCODE; https://www.encodeproject.org/ENCBS408HXQ/


title: PUMCH tumor 137

description: genomic DNA from LUAD

label: Cy3 and Cy141

value: lung adenocarcinoma

value: I


title: DNase-seq from amygdala (ENCLB882HLO)

description:
https://www.encodeproject.org/experiments/ENCSR272JSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272JSI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB882HLO

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS010VWK at ENCODE; https://www.encodeproject.org/ENCBS010VWK/


title: DNase-seq from nucleus accumbens (ENCLB441RAV)

description:
https://www.encodeproject.org/experiments/ENCSR271UQD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR271UQD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB441RAV

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: ENCBS132NDE at ENCODE; https://www.encodeproject.org/ENCBS132NDE/


title: PUMCH tumor 136

description: genomic DNA from LUAD

label: Cy3 and Cy140

value: Female


title: PUMCH tumor 135

description: genomic DNA from LUAD

label: Cy3 and Cy139


title: DNase-seq from caudate nucleus (ENCLB388UZM)

description:
https://www.encodeproject.org/experiments/ENCSR269PMA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR269PMA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB388UZM

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: adult

value: ENCBS436BVN at ENCODE; https://www.encodeproject.org/ENCBS436BVN/


title: PUMCH tumor 133

description: genomic DNA from LUAD

label: Cy3 and Cy137

value: II

value: Male


title: MPRA from K562 (ENCLB269GBG)

description:
https://www.encodeproject.org/experiments/ENCSR460LZI/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR460LZI
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR327IIZ
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB269GBG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS518BIU at ENCODE; https://www.encodeproject.org/ENCBS518BIU/


title: DNase-seq from cerebellum (ENCLB081ITK)

description:
https://www.encodeproject.org/experiments/ENCSR283EEG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR283EEG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB081ITK

value: cerebellum

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS526WUW at ENCODE; https://www.encodeproject.org/ENCBS526WUW/


title: DNase-seq from caudate nucleus (ENCLB086MPJ)

description:
https://www.encodeproject.org/experiments/ENCSR267WZK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267WZK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB086MPJ

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: male

value: adult

value: ENCBS604RNN at ENCODE; https://www.encodeproject.org/ENCBS604RNN/


title: PUMCH tumor 132

description: genomic DNA from LUAD

label: Cy3 and Cy136

value: lung adenocarcinoma

value: I

value: Female


title: PUMCH tumor 130

description: genomic DNA from LUAD

label: Cy3 and Cy134

value: II

value: Male


title: PUMCH tumor 134

description: genomic DNA from LUAD

label: Cy3 and Cy138


title: PUMCH tumor 129

description: genomic DNA from LUAD

label: Cy3 and Cy133


title: MPRA from HEL (ENCLB381WTY)

description:
https://www.encodeproject.org/experiments/ENCSR436DRI/
***************
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 GP1BB promoter.
experiment encode accession: ENCSR436DRI
assay title: MPRA
possible controls: ENCSR901KLZ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB381WTY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: HEL

value: cell line

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

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS342AAX at ENCODE; https://www.encodeproject.org/ENCBS342AAX/


title: MPRA from K562 (ENCLB437DSZ)

description:
https://www.encodeproject.org/experiments/ENCSR460LZI/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR460LZI
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR327IIZ
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB437DSZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS919ZRZ at ENCODE; https://www.encodeproject.org/ENCBS919ZRZ/


title: PUMCH tumor 131

description: genomic DNA from LUAD

label: Cy3 and Cy135


title: MPRA from HEL (ENCLB411HDS)

description:
https://www.encodeproject.org/experiments/ENCSR436DRI/
***************
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 GP1BB promoter.
experiment encode accession: ENCSR436DRI
assay title: MPRA
possible controls: ENCSR901KLZ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB411HDS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: adult

value: ENCBS862KAM at ENCODE; https://www.encodeproject.org/ENCBS862KAM/


title: PUMCH tumor 127

description: genomic DNA from LUAD

label: Cy3 and Cy131

value: lung adenocarcinoma

value: I


title: MPRA from HEL (ENCLB415QQF)

description:
https://www.encodeproject.org/experiments/ENCSR436DRI/
***************
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 GP1BB promoter.
experiment encode accession: ENCSR436DRI
assay title: MPRA
possible controls: ENCSR901KLZ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB415QQF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS933KQU at ENCODE; https://www.encodeproject.org/ENCBS933KQU/


title: DNase-seq from cerebellum (ENCLB851OYL)

description:
https://www.encodeproject.org/experiments/ENCSR259SVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR259SVX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB851OYL

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS146VWU at ENCODE; https://www.encodeproject.org/ENCBS146VWU/


title: PUMCH tumor 128

description: genomic DNA from LUAD

label: Cy3 and Cy132

value: Female


title: PUMCH tumor 126

description: genomic DNA from LUAD

label: Cy3 and Cy130

value: III


title: PUMCH tumor 125

description: genomic DNA from LUAD

label: Cy3 and Cy129

value: II


title: DNase-seq from amygdala (ENCLB873INL)

description:
https://www.encodeproject.org/experiments/ENCSR257SMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR257SMO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB873INL

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: female

value: ENCBS719TJO at ENCODE; https://www.encodeproject.org/ENCBS719TJO/


title: DNase-seq from substantia nigra (ENCLB466SWU)

description:
https://www.encodeproject.org/experiments/ENCSR257KSS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR257KSS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB466SWU

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: male

value: adult

value: ENCBS731IAT at ENCODE; https://www.encodeproject.org/ENCBS731IAT/


title: PUMCH tumor 124

description: genomic DNA from LUAD

label: Cy3 and Cy128

value: lung adenocarcinoma

value: I


title: MPRA from HepG2 (ENCLB549BIP)

description:
https://www.encodeproject.org/experiments/ENCSR405QCT/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR405QCT
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR837DCD
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB549BIP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS351FUL at ENCODE; https://www.encodeproject.org/ENCBS351FUL/


title: MPRA from HepG2 (ENCLB363GSR)

description:
https://www.encodeproject.org/experiments/ENCSR405QCT/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR405QCT
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR837DCD
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB363GSR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS085ALE at ENCODE; https://www.encodeproject.org/ENCBS085ALE/


title: DNase-seq from Ammon's horn (ENCLB033IZA)

description:
https://www.encodeproject.org/experiments/ENCSR267RKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267RKG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB033IZA

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS810VRL at ENCODE; https://www.encodeproject.org/ENCBS810VRL/


title: PUMCH tumor 122

description: genomic DNA from LUAD

label: Cy3 and Cy126

value: Female


title: DNase-seq from substantia nigra (ENCLB592BQZ)

description:
https://www.encodeproject.org/experiments/ENCSR255IVN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR255IVN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB592BQZ

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: female

value: adult

value: ENCBS040MTJ at ENCODE; https://www.encodeproject.org/ENCBS040MTJ/


title: PUMCH tumor 120

description: genomic DNA from LUAD

label: Cy3 and Cy124

value: lung adenocarcinoma

value: I


title: DNase-seq from substantia nigra (ENCLB344IOW)

description:
https://www.encodeproject.org/experiments/ENCSR255IVN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR255IVN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB344IOW

value: ENCBS125JKG at ENCODE; https://www.encodeproject.org/ENCBS125JKG/


title: PUMCH tumor 119

description: genomic DNA from LUAD

label: Cy3 and Cy123


title: Control MPRA from HeLa (ENCLB841XUY)

description:
https://www.encodeproject.org/experiments/ENCSR393YZU/
***************
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 FOXE1 promoter.
experiment encode accession: ENCSR393YZU
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB841XUY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: HeLa

value: cell line

value: cervical adenocarcinoma

value: 31 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS191WEF at ENCODE; https://www.encodeproject.org/ENCBS191WEF/


title: DNase-seq from nucleus accumbens (ENCLB702CYF)

description:
https://www.encodeproject.org/experiments/ENCSR265MSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR265MSR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB702CYF

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS012EIY at ENCODE; https://www.encodeproject.org/ENCBS012EIY/


title: PUMCH tumor 118

description: genomic DNA from LUAD

label: Cy3 and Cy122

source_name: lung adenocarcinoma

value: Female


title: PUMCH tumor 117

description: genomic DNA from LUAD

label: Cy3 and Cy121

value: lung adenocarcinoma

value: IV

value: Male


title: Control MPRA from HeLa (ENCLB206FAS)

description:
https://www.encodeproject.org/experiments/ENCSR393YZU/
***************
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 FOXE1 promoter.
experiment encode accession: ENCSR393YZU
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB206FAS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HeLa

value: female

value: adult

value: ENCBS656BND at ENCODE; https://www.encodeproject.org/ENCBS656BND/


title: DNase-seq from substantia nigra (ENCLB265MDQ)

description:
https://www.encodeproject.org/experiments/ENCSR255IVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR255IVN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB265MDQ

value: substantia nigra

value: ENCBS724QGU at ENCODE; https://www.encodeproject.org/ENCBS724QGU/


title: Control MPRA from HeLa (ENCLB070IJP)

description:
https://www.encodeproject.org/experiments/ENCSR393YZU/
***************
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 FOXE1 promoter.
experiment encode accession: ENCSR393YZU
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB070IJP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: cervical adenocarcinoma

value: 31 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS973LDX at ENCODE; https://www.encodeproject.org/ENCBS973LDX/


title: DNase-seq from amygdala (ENCLB392SDU)

description:
https://www.encodeproject.org/experiments/ENCSR253RHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR253RHN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB392SDU

value: amygdala

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS260LCS at ENCODE; https://www.encodeproject.org/ENCBS260LCS/


title: PUMCH tumor 123

description: genomic DNA from LUAD

label: Cy3 and Cy127

value: lung adenocarcinoma

value: I

value: Female


title: PUMCH tumor 113

description: genomic DNA from LUAD

label: Cy3 and Cy117

value: Male


title: PUMCH tumor 114

description: genomic DNA from LUAD

label: Cy3 and Cy118


title: PUMCH tumor 115

description: genomic DNA from LUAD

label: Cy3 and Cy119

value: II


title: MPRA from HepG2 (ENCLB568QUF)

description:
https://www.encodeproject.org/experiments/ENCSR405QCT/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR405QCT
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR837DCD
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB568QUF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS757EJG at ENCODE; https://www.encodeproject.org/ENCBS757EJG/


title: PUMCH tumor 111

description: genomic DNA from LUAD

label: Cy3 and Cy115


title: Control MPRA from HepG2 (ENCLB736UTL)

description:
https://www.encodeproject.org/experiments/ENCSR383FIW/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.
experiment encode accession: ENCSR383FIW
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB736UTL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from anterior cingulate cortex (ENCLB308YFS)

description:
https://www.encodeproject.org/experiments/ENCSR251WRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR251WRE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB308YFS

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS747LRJ at ENCODE; https://www.encodeproject.org/ENCBS747LRJ/


title: Control MPRA from HepG2 (ENCLB740COH)

description:
https://www.encodeproject.org/experiments/ENCSR383FIW/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.
experiment encode accession: ENCSR383FIW
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB740COH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: PUMCH tumor 116

description: genomic DNA from LUAD

label: Cy3 and Cy120

value: lung adenocarcinoma

value: I

value: Female


title: DNase-seq from putamen (ENCLB408BHM)

description:
https://www.encodeproject.org/experiments/ENCSR249PKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR249PKR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB408BHM

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: female

value: Kristin Ardlie

value: ENCBS971XSD at ENCODE; https://www.encodeproject.org/ENCBS971XSD/


title: DNase-seq from putamen (ENCLB872WEF)

description:
https://www.encodeproject.org/experiments/ENCSR249FCV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR249FCV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB872WEF

value: ENCBS549HSL at ENCODE; https://www.encodeproject.org/ENCBS549HSL/


title: DNase-seq from substantia nigra (ENCLB217GGM)

description:
https://www.encodeproject.org/experiments/ENCSR241TSG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR241TSG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB217GGM

value: substantia nigra

value: male

value: ENCBS746SRT at ENCODE; https://www.encodeproject.org/ENCBS746SRT/


title: PUMCH tumor 109

description: genomic DNA from LUAD

label: Cy3 and Cy113

value: Male


title: PUMCH tumor 110

description: genomic DNA from LUAD

label: Cy3 and Cy114


title: PUMCH tumor 108

description: genomic DNA from LUAD

label: Cy3 and Cy112


title: MPRA from K562 (ENCLB299ACL)

description:
https://www.encodeproject.org/experiments/ENCSR382BVV/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR382BVV
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR186NQR
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB299ACL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS530JDU at ENCODE; https://www.encodeproject.org/ENCBS530JDU/


title: PUMCH tumor 107

description: genomic DNA from LUAD

label: Cy3 and Cy111

value: lung adenocarcinoma

value: I


title: DNase-seq from caudate nucleus (ENCLB633BNF)

description:
https://www.encodeproject.org/experiments/ENCSR240BUK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR240BUK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB633BNF

value: caudate nucleus

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS316LQM at ENCODE; https://www.encodeproject.org/ENCBS316LQM/


title: PUMCH tumor 112

description: genomic DNA from LUAD

label: Cy3 and Cy116

value: Female


title: PUMCH tumor 106

description: genomic DNA from LUAD

label: Cy3 and Cy110


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB141FLW)

description:
https://www.encodeproject.org/experiments/ENCSR238LSQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR238LSQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141FLW

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

value: C1 segment of cervical spinal cord

value: female

value: Kristin Ardlie

value: ENCBS954MAZ at ENCODE; https://www.encodeproject.org/ENCBS954MAZ/


title: PUMCH tumor 105

description: genomic DNA from LUAD

label: Cy3 and Cy109


title: MPRA from K562 (ENCLB791IUK)

description:
https://www.encodeproject.org/experiments/ENCSR382BVV/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR382BVV
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR186NQR
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB791IUK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS763HFF at ENCODE; https://www.encodeproject.org/ENCBS763HFF/


title: Control MPRA from HepG2 (ENCLB053MLF)

description:
https://www.encodeproject.org/experiments/ENCSR383FIW/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in an independent, second batch as HSS, and serves as an internal control to HSS_full.
experiment encode accession: ENCSR383FIW
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB053MLF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from K562 (ENCLB145ZTQ)

description:
https://www.encodeproject.org/experiments/ENCSR382BVV/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR382BVV
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR186NQR
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB145ZTQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: 53 year

value: ENCBS220LJR at ENCODE; https://www.encodeproject.org/ENCBS220LJR/


title: PUMCH tumor 100

description: genomic DNA from LUAD

label: Cy3 and Cy104

value: lung adenocarcinoma

value: II

value: Female


title: PUMCH tumor 103

description: genomic DNA from LUAD

label: Cy3 and Cy107

value: I


title: PUMCH tumor 102

description: genomic DNA from LUAD

label: Cy3 and Cy106


title: DNase-seq from Ammon's horn (ENCLB861BQE)

description:
https://www.encodeproject.org/experiments/ENCSR237HPK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237HPK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB861BQE

value: Ammon's horn

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS486QCC at ENCODE; https://www.encodeproject.org/ENCBS486QCC/


title: PUMCH tumor 104

description: genomic DNA from LUAD

label: Cy3 and Cy108


title: PUMCH tumor 99

description: genomic DNA from LUAD

label: Cy3 and Cy103


title: PUMCH tumor 101

description: genomic DNA from LUAD

label: Cy3 and Cy105

value: III


title: MPRA from HeLa (ENCLB830YVK)

description:
https://www.encodeproject.org/experiments/ENCSR373WOB/
***************
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 FOXE1 promoter.
experiment encode accession: ENCSR373WOB
assay title: MPRA
possible controls: ENCSR393YZU
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB830YVK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HeLa

value: cell line

value: cervical adenocarcinoma

value: adult

value: 31 year

value: Nadav Ahituv, UCSF

value: ENCBS191WEF at ENCODE; https://www.encodeproject.org/ENCBS191WEF/


title: MPRA from HeLa (ENCLB392PDY)

description:
https://www.encodeproject.org/experiments/ENCSR373WOB/
***************
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 FOXE1 promoter.
experiment encode accession: ENCSR373WOB
assay title: MPRA
possible controls: ENCSR393YZU
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB392PDY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ATCC

value: ENCBS973LDX at ENCODE; https://www.encodeproject.org/ENCBS973LDX/


title: DNase-seq from amygdala (ENCLB440NPO)

description:
https://www.encodeproject.org/experiments/ENCSR235WIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR235WIJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB440NPO

value: amygdala

value: ENCBS177XQD at ENCODE; https://www.encodeproject.org/ENCBS177XQD/


title: DNase-seq from substantia nigra (ENCLB682MFV)

description:
https://www.encodeproject.org/experiments/ENCSR237AHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR237AHR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB682MFV

value: substantia nigra

value: tissue

value: female

value: ENCBS653AYU at ENCODE; https://www.encodeproject.org/ENCBS653AYU/


title: PUMCH tumor 97

description: genomic DNA from LUAD

label: Cy3 and Cy101

value: lung adenocarcinoma

value: I

value: Female


title: Control MPRA from HepG2 (ENCLB343YQT)

description:
https://www.encodeproject.org/experiments/ENCSR366UIC/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR366UIC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB343YQT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: MPRA from HeLa (ENCLB672TSW)

description:
https://www.encodeproject.org/experiments/ENCSR373WOB/
***************
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 FOXE1 promoter.
experiment encode accession: ENCSR373WOB
assay title: MPRA
possible controls: ENCSR393YZU
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB672TSW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HeLa

value: cervical adenocarcinoma

value: adult

value: 31 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS656BND at ENCODE; https://www.encodeproject.org/ENCBS656BND/


title: DNase-seq from Ammon's horn (ENCLB501ISU)

description:
https://www.encodeproject.org/experiments/ENCSR234YGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR234YGD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB501ISU

value: Ammon's horn

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS212GAV at ENCODE; https://www.encodeproject.org/ENCBS212GAV/


title: PUMCH tumor 96

description: genomic DNA from LUAD

label: Cy3 and Cy100

value: lung adenocarcinoma

value: II

value: Female


title: Control MPRA from HepG2 (ENCLB416VLV)

description:
https://www.encodeproject.org/experiments/ENCSR366UIC/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR366UIC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB416VLV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: DNase-seq from nucleus accumbens (ENCLB112KWP)

description:
https://www.encodeproject.org/experiments/ENCSR229JFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR229JFT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB112KWP

value: nucleus accumbens

value: adult

value: ENCBS940FJA at ENCODE; https://www.encodeproject.org/ENCBS940FJA/


title: PUMCH tumor 94

description: genomic DNA from LUAD

label: Cy3 and Cy98

value: III

value: Male


title: PUMCH tumor 98

description: genomic DNA from LUAD

label: Cy3 and Cy102

value: I


title: PUMCH tumor 95

description: genomic DNA from LUAD

label: Cy3 and Cy99


title: PUMCH tumor 121

description: genomic DNA from LUAD

label: Cy3 and Cy125


title: PUMCH tumor 92

description: genomic DNA from LUAD

label: Cy3 and Cy96


title: PUMCH tumor 93

description: genomic DNA from LUAD

label: Cy3 and Cy97

value: IV


title: DNase-seq from substantia nigra (ENCLB784OQG)

description:
https://www.encodeproject.org/experiments/ENCSR222XKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR222XKC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB784OQG

value: substantia nigra

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS558SLR at ENCODE; https://www.encodeproject.org/ENCBS558SLR/


title: Control MPRA from HepG2 (ENCLB760FYJ)

description:
https://www.encodeproject.org/experiments/ENCSR366UIC/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR366UIC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB760FYJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PUMCH tumor 89

description: genomic DNA from LUAD

label: Cy3 and Cy93

value: lung adenocarcinoma

value: Female


title: DNase-seq from substantia nigra (ENCLB398GYK)

description:
https://www.encodeproject.org/experiments/ENCSR222XKC/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR222XKC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB398GYK

value: adult

value: ENCBS226CBJ at ENCODE; https://www.encodeproject.org/ENCBS226CBJ/


title: PUMCH tumor 88

description: genomic DNA from LUAD

label: Cy3 and Cy92

value: I


title: PUMCH tumor 85

description: genomic DNA from LUAD

label: Cy3 and Cy89


title: PUMCH tumor 87

description: genomic DNA from LUAD

label: Cy3 and Cy91


title: DNase-seq from substantia nigra (ENCLB713NMC)

description:
https://www.encodeproject.org/experiments/ENCSR222XKC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR222XKC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB713NMC

value: substantia nigra

value: ENCBS489WNC at ENCODE; https://www.encodeproject.org/ENCBS489WNC/


title: Control MPRA from HepG2 (ENCLB505XOH)

description:
https://www.encodeproject.org/experiments/ENCSR360LZF/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR360LZF
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB505XOH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: child

value: 15 year

value: ENCBS497PYP at ENCODE; https://www.encodeproject.org/ENCBS497PYP/


title: Control MPRA from HepG2 (ENCLB053EFM)

description:
https://www.encodeproject.org/experiments/ENCSR360LZF/
***************
biological replicate number: 4
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR360LZF
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB053EFM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS597FXX at ENCODE; https://www.encodeproject.org/ENCBS597FXX/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB343ERO)

description:
https://www.encodeproject.org/experiments/ENCSR222LOP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR222LOP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB343ERO

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS889DGU at ENCODE; https://www.encodeproject.org/ENCBS889DGU/


title: PUMCH tumor 83

description: genomic DNA from LUAD

label: Cy3 and Cy87

value: lung adenocarcinoma

value: Male


title: PUMCH tumor 91

description: genomic DNA from LUAD

label: Cy3 and Cy95

value: III

value: Female


title: PUMCH tumor 90

description: genomic DNA from LUAD

label: Cy3 and Cy94

value: IV


title: PUMCH tumor 84

description: genomic DNA from LUAD

label: Cy3 and Cy88


title: DNase-seq from putamen (ENCLB835FIB)

description:
https://www.encodeproject.org/experiments/ENCSR221TJZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR221TJZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB835FIB

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: male

value: adult

value: ENCBS124QYY at ENCODE; https://www.encodeproject.org/ENCBS124QYY/


title: Control MPRA from HepG2 (ENCLB773CLN)

description:
https://www.encodeproject.org/experiments/ENCSR356YBY/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR356YBY
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB773CLN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS981GEN at ENCODE; https://www.encodeproject.org/ENCBS981GEN/


title: PUMCH tumor 81

description: genomic DNA from LUAD

label: Cy3 and Cy85

value: I


title: Control MPRA from HepG2 (ENCLB376TET)

description:
https://www.encodeproject.org/experiments/ENCSR360LZF/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR360LZF
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB376TET
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS352PXL at ENCODE; https://www.encodeproject.org/ENCBS352PXL/


title: Control MPRA from HepG2 (ENCLB206HFS)

description:
https://www.encodeproject.org/experiments/ENCSR360LZF/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR360LZF
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB206HFS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS573RKN at ENCODE; https://www.encodeproject.org/ENCBS573RKN/


title: Control MPRA from HepG2 (ENCLB492ICC)

description:
https://www.encodeproject.org/experiments/ENCSR356YBY/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR356YBY
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB492ICC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS515CLC at ENCODE; https://www.encodeproject.org/ENCBS515CLC/


title: PUMCH tumor 78

description: genomic DNA from LUAD

label: Cy3 and Cy82

value: lung adenocarcinoma

value: Female


title: DNase-seq from Ammon's horn (ENCLB919OGT)

description:
https://www.encodeproject.org/experiments/ENCSR222VDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR222VDZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB919OGT

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS399ANH at ENCODE; https://www.encodeproject.org/ENCBS399ANH/


title: PUMCH tumor 79

description: genomic DNA from LUAD

label: Cy3 and Cy83


title: Control MPRA from HepG2 (ENCLB718CFR)

description:
https://www.encodeproject.org/experiments/ENCSR356YBY/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR356YBY
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB718CFR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS161DJX at ENCODE; https://www.encodeproject.org/ENCBS161DJX/


title: DNase-seq from putamen (ENCLB963EBA)

description:
https://www.encodeproject.org/experiments/ENCSR221TJZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR221TJZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB963EBA

value: putamen

value: adult

value: ENCBS022EIH at ENCODE; https://www.encodeproject.org/ENCBS022EIH/


title: PUMCH tumor 76

description: genomic DNA from LUAD

label: Cy3 and Cy80

value: I

value: Male


title: PUMCH tumor 86

description: genomic DNA from LUAD

label: Cy3 and Cy90

value: lung adenocarcinoma


title: DNase-seq from anterior cingulate cortex (ENCLB828PQB)

description:
https://www.encodeproject.org/experiments/ENCSR220ETD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR220ETD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB828PQB

source_name: Homo sapiens female adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: female

value: ENCBS381MMD at ENCODE; https://www.encodeproject.org/ENCBS381MMD/


title: DNase-seq from Ammon's horn (ENCLB346ATY)

description:
https://www.encodeproject.org/experiments/ENCSR214BAJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR214BAJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB346ATY

value: Ammon's horn

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS280EEO at ENCODE; https://www.encodeproject.org/ENCBS280EEO/


title: PUMCH tumor 75

description: genomic DNA from LUAD

label: Cy3 and Cy79

value: Female


title: DNase-seq from Ammon's horn (ENCLB411QRS)

description:
https://www.encodeproject.org/experiments/ENCSR214BAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR214BAJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB411QRS

value: male

value: Kristin Ardlie

value: ENCBS866MSM at ENCODE; https://www.encodeproject.org/ENCBS866MSM/


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB436QDL)

description:
https://www.encodeproject.org/experiments/ENCSR210NNR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR210NNR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB436QDL

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

value: C1 segment of cervical spinal cord

value: adult

value: ENCBS444CAF at ENCODE; https://www.encodeproject.org/ENCBS444CAF/


title: PUMCH tumor 80

description: genomic DNA from LUAD

label: Cy3 and Cy84

value: I


title: PUMCH tumor 72

description: genomic DNA from LUAD

label: Cy3 and Cy76

value: lung adenocarcinoma

value: III


title: PUMCH tumor 71

description: genomic DNA from LUAD

label: Cy3 and Cy75


title: PUMCH tumor 74

description: genomic DNA from LUAD

label: Cy3 and Cy78

value: Male


title: MPRA from HepG2 (ENCLB726GOT)

description:
https://www.encodeproject.org/experiments/ENCSR352YKN/
***************
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 F9 promoter.
experiment encode accession: ENCSR352YKN
assay title: MPRA
possible controls: ENCSR293DMS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB726GOT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS116QYC at ENCODE; https://www.encodeproject.org/ENCBS116QYC/


title: PUMCH tumor 82

description: genomic DNA from LUAD

label: Cy3 and Cy86

value: Female


title: DNase-seq from amygdala (ENCLB880YXE)

description:
https://www.encodeproject.org/experiments/ENCSR207NON/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR207NON
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB880YXE

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS921IWM at ENCODE; https://www.encodeproject.org/ENCBS921IWM/


title: PUMCH tumor 69

description: genomic DNA from LUAD

label: Cy3 and Cy73

value: lung adenocarcinoma

value: II


title: PUMCH tumor 68

description: genomic DNA from LUAD

label: Cy3 and Cy72

value: III


title: PUMCH tumor 77

description: genomic DNA from LUAD

label: Cy3 and Cy81

value: I


title: Control MPRA from WTC11 (ENCLB601CNC)

description:
https://www.encodeproject.org/experiments/ENCSR356TMB/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.
experiment encode accession: ENCSR356TMB
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB601CNC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using transduction

value: cell line

value: male

value: adult

value: 30 year

value: ENCBS640CUX at ENCODE; https://www.encodeproject.org/ENCBS640CUX/


title: PUMCH tumor 66

description: genomic DNA from LUAD

label: Cy3 and Cy70

value: Female


title: PUMCH tumor 73

description: genomic DNA from LUAD

label: Cy3 and Cy77

value: Male


title: MPRA from HepG2 (ENCLB642BLN)

description:
https://www.encodeproject.org/experiments/ENCSR352YKN/
***************
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 F9 promoter.
experiment encode accession: ENCSR352YKN
assay title: MPRA
possible controls: ENCSR293DMS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB642BLN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS339CKC at ENCODE; https://www.encodeproject.org/ENCBS339CKC/


title: DNase-seq from putamen (ENCLB943ICD)

description:
https://www.encodeproject.org/experiments/ENCSR207KAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR207KAZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB943ICD

value: putamen

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS634OOT at ENCODE; https://www.encodeproject.org/ENCBS634OOT/


title: Control MPRA from WTC11 (ENCLB203KIN)

description:
https://www.encodeproject.org/experiments/ENCSR356TMB/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.
experiment encode accession: ENCSR356TMB
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB203KIN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: adult

value: 30 year

value: ENCBS145GBM at ENCODE; https://www.encodeproject.org/ENCBS145GBM/


title: DNase-seq from caudate nucleus (ENCLB808YCR)

description:
https://www.encodeproject.org/experiments/ENCSR205ZJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR205ZJO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB808YCR

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS569PXW at ENCODE; https://www.encodeproject.org/ENCBS569PXW/


title: PUMCH tumor 67

description: genomic DNA from LUAD

label: Cy3 and Cy71

value: lung adenocarcinoma

value: I

value: Male


title: PUMCH tumor 70

description: genomic DNA from LUAD

label: Cy3 and Cy74


title: PUMCH tumor 65

description: genomic DNA from LUAD

label: Cy3 and Cy69

value: II


title: PUMCH tumor 64

description: genomic DNA from LUAD

label: Cy3 and Cy68


title: DNase-seq from substantia nigra (ENCLB141UYD)

description:
https://www.encodeproject.org/experiments/ENCSR200VJW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR200VJW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB141UYD

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: tissue

value: ENCBS403EGD at ENCODE; https://www.encodeproject.org/ENCBS403EGD/


title: PUMCH tumor 63

description: genomic DNA from LUAD

label: Cy3 and Cy67


title: PUMCH tumor 62

description: genomic DNA from LUAD

label: Cy3 and Cy66


title: MPRA from WTC11 (ENCLB767MAW)

description:
https://www.encodeproject.org/experiments/ENCSR336MKI/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR336MKI
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR356TMB
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB767MAW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS640CUX at ENCODE; https://www.encodeproject.org/ENCBS640CUX/


title: MPRA from WTC11 (ENCLB699KRT)

description:
https://www.encodeproject.org/experiments/ENCSR336MKI/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR336MKI
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR356TMB
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB699KRT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line


title: DNase-seq from anterior cingulate cortex (ENCLB585TOX)

description:
https://www.encodeproject.org/experiments/ENCSR199DJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR199DJG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB585TOX

value: anterior cingulate cortex

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS441YTG at ENCODE; https://www.encodeproject.org/ENCBS441YTG/


title: MPRA from HepG2 (ENCLB689LHG)

description:
https://www.encodeproject.org/experiments/ENCSR352YKN/
***************
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 F9 promoter.
experiment encode accession: ENCSR352YKN
assay title: MPRA
possible controls: ENCSR293DMS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB689LHG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS325AIX at ENCODE; https://www.encodeproject.org/ENCBS325AIX/


title: PUMCH tumor 61

description: genomic DNA from LUAD

label: Cy3 and Cy65

value: lung adenocarcinoma

value: III

value: Male


title: PUMCH tumor 59

description: genomic DNA from LUAD

label: Cy3 and Cy63

value: IV


title: Control MPRA from WTC11 (ENCLB760LPD)

description:
https://www.encodeproject.org/experiments/ENCSR356TMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.
experiment encode accession: ENCSR356TMB
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB760LPD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS541UHI at ENCODE; https://www.encodeproject.org/ENCBS541UHI/


title: MPRA from WTC11 (ENCLB991QNZ)

description:
https://www.encodeproject.org/experiments/ENCSR336MKI/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR336MKI
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR356TMB
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB991QNZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line


title: DNase-seq from putamen (ENCLB558VOV)

description:
https://www.encodeproject.org/experiments/ENCSR197HFX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197HFX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB558VOV

value: putamen

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS886ZZT at ENCODE; https://www.encodeproject.org/ENCBS886ZZT/


title: DNase-seq from caudate nucleus (ENCLB190KBK)

description:
https://www.encodeproject.org/experiments/ENCSR197HHU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR197HHU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB190KBK

value: caudate nucleus

value: male

value: ENCBS202NGJ at ENCODE; https://www.encodeproject.org/ENCBS202NGJ/


title: PUMCH tumor 58

description: genomic DNA from LUAD

label: Cy3 and Cy62

value: lung adenocarcinoma

value: III

value: Male


title: PUMCH tumor 57

description: genomic DNA from LUAD

label: Cy3 and Cy61

value: I


title: DNase-seq from caudate nucleus (ENCLB558CBW)

description:
https://www.encodeproject.org/experiments/ENCSR194HVD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR194HVD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB558CBW

value: adult

value: ENCBS761UBP at ENCODE; https://www.encodeproject.org/ENCBS761UBP/


title: Control MPRA from HepG2 (ENCLB442OVG)

description:
https://www.encodeproject.org/experiments/ENCSR335DOI/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR335DOI
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB442OVG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS420FND at ENCODE; https://www.encodeproject.org/ENCBS420FND/


title: PUMCH tumor 56

description: genomic DNA from LUAD

label: Cy3 and Cy60


title: PUMCH tumor 55

description: genomic DNA from LUAD

label: Cy3 and Cy59


title: Control MPRA from HepG2 (ENCLB261LIA)

description:
https://www.encodeproject.org/experiments/ENCSR335DOI/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR335DOI
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB261LIA
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS939AOV at ENCODE; https://www.encodeproject.org/ENCBS939AOV/


title: PUMCH tumor 54

description: genomic DNA from LUAD

label: Cy3 and Cy58


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB312OXC)

description:
https://www.encodeproject.org/experiments/ENCSR193LCA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR193LCA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB312OXC

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS948BMR at ENCODE; https://www.encodeproject.org/ENCBS948BMR/


title: Control MPRA from HepG2 (ENCLB479CRU)

description:
https://www.encodeproject.org/experiments/ENCSR335DOI/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR335DOI
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB479CRU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: ENCBS236XVS at ENCODE; https://www.encodeproject.org/ENCBS236XVS/


title: PUMCH tumor 53

description: genomic DNA from LUAD

label: Cy3 and Cy57

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: III

value: Male


title: PUMCH tumor 51

description: genomic DNA from LUAD

label: Cy3 and Cy55

value: Female


title: DNase-seq from amygdala (ENCLB261BVR)

description:
https://www.encodeproject.org/experiments/ENCSR185IID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR185IID
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB261BVR

value: amygdala

value: adult

value: ENCBS352ZEA at ENCODE; https://www.encodeproject.org/ENCBS352ZEA/


title: PUMCH tumor 60

description: genomic DNA from LUAD

label: Cy3 and Cy64

value: II


title: PUMCH tumor 49

description: genomic DNA from LUAD

label: Cy3 and Cy53


title: DNase-seq from hypothalamus (ENCLB528PLH)

description:
https://www.encodeproject.org/experiments/ENCSR182MRI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR182MRI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB528PLH

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: ENCBS728TBK at ENCODE; https://www.encodeproject.org/ENCBS728TBK/


title: PUMCH tumor 48

description: genomic DNA from LUAD

label: Cy3 and Cy52

value: I


title: Control MPRA from HepG2 (ENCLB623VAH)

description:
https://www.encodeproject.org/experiments/ENCSR331WRX/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR331WRX
assay title: Control MPRA
encode release date: 2022-08-17
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB623VAH
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: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS972OVN at ENCODE; https://www.encodeproject.org/ENCBS972OVN/


title: PUMCH tumor 47

description: genomic DNA from LUAD

label: Cy3 and Cy51

value: lung adenocarcinoma


title: DNase-seq from hypothalamus (ENCLB576ABX)

description:
https://www.encodeproject.org/experiments/ENCSR182MRI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR182MRI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB576ABX

value: tissue

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS850WNY at ENCODE; https://www.encodeproject.org/ENCBS850WNY/


title: PUMCH tumor 46

description: genomic DNA from LUAD

label: Cy3 and Cy50

value: IV

value: Female


title: Control MPRA from HepG2 (ENCLB898UME)

description:
https://www.encodeproject.org/experiments/ENCSR331WRX/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR331WRX
assay title: Control MPRA
encode release date: 2022-08-17
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB898UME
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS117QYD at ENCODE; https://www.encodeproject.org/ENCBS117QYD/


title: PUMCH tumor 52

description: genomic DNA from LUAD

label: Cy3 and Cy56

value: II

value: Male


title: PUMCH tumor 45

description: genomic DNA from LUAD

label: Cy3 and Cy49

value: III


title: DNase-seq from nucleus accumbens (ENCLB603FBM)

description:
https://www.encodeproject.org/experiments/ENCSR181MYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181MYF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB603FBM

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: adult

value: ENCBS221HVI at ENCODE; https://www.encodeproject.org/ENCBS221HVI/


title: PUMCH tumor 44

description: genomic DNA from LUAD

label: Cy3 and Cy48


title: MPRA from HEL (ENCLB935CGT)

description:
https://www.encodeproject.org/experiments/ENCSR330ZFH/
***************
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 BCL11A enhancer.
experiment encode accession: ENCSR330ZFH
assay title: MPRA
possible controls: ENCSR549UBJ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB935CGT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: HEL

value: cell line

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

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS934XEQ at ENCODE; https://www.encodeproject.org/ENCBS934XEQ/


title: DNase-seq from Ammon's horn (ENCLB229VWW)

description:
https://www.encodeproject.org/experiments/ENCSR181BYP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR181BYP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB229VWW

value: Ammon's horn

value: tissue

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS174PBG at ENCODE; https://www.encodeproject.org/ENCBS174PBG/


title: PUMCH tumor 50

description: genomic DNA from LUAD

label: Cy3 and Cy54

value: lung adenocarcinoma

value: II

value: Female


title: PUMCH tumor 43

description: genomic DNA from LUAD

label: Cy3 and Cy47

value: IV


title: PUMCH tumor 42

description: genomic DNA from LUAD

label: Cy3 and Cy46

value: III

value: Male


title: Control MPRA from HepG2 (ENCLB825LNI)

description:
https://www.encodeproject.org/experiments/ENCSR331WRX/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test HepG2 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR331WRX
assay title: Control MPRA
encode release date: 2022-08-17
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB825LNI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS952IEQ at ENCODE; https://www.encodeproject.org/ENCBS952IEQ/


title: PUMCH tumor 40

description: genomic DNA from LUAD

label: Cy3 and Cy44


title: MPRA from HEL (ENCLB546NDT)

description:
https://www.encodeproject.org/experiments/ENCSR330ZFH/
***************
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 BCL11A enhancer.
experiment encode accession: ENCSR330ZFH
assay title: MPRA
possible controls: ENCSR549UBJ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB546NDT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HEL

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

value: adult

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS805FHJ at ENCODE; https://www.encodeproject.org/ENCBS805FHJ/


title: DNase-seq from nucleus accumbens (ENCLB242RCD)

description:
https://www.encodeproject.org/experiments/ENCSR178IUD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR178IUD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB242RCD

value: nucleus accumbens

value: tissue

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS975SKZ at ENCODE; https://www.encodeproject.org/ENCBS975SKZ/


title: PUMCH tumor 38

description: genomic DNA from LUAD

label: Cy3 and Cy42

value: lung adenocarcinoma

value: III

value: Male


title: DNase-seq from substantia nigra (ENCLB888CFJ)

description:
https://www.encodeproject.org/experiments/ENCSR175QDE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR175QDE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB888CFJ

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: female

value: ENCBS159KZO at ENCODE; https://www.encodeproject.org/ENCBS159KZO/


title: PUMCH tumor 37

description: genomic DNA from LUAD

label: Cy3 and Cy41

value: Female


title: DNase-seq from hypothalamus (ENCLB380WDF)

description:
https://www.encodeproject.org/experiments/ENCSR171JAP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR171JAP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB380WDF

source_name: Homo sapiens female adult hypothalamus tissue

value: hypothalamus

value: adult

value: ENCBS565BGM at ENCODE; https://www.encodeproject.org/ENCBS565BGM/


title: Control MPRA from K562 (ENCLB535GJV)

description:
https://www.encodeproject.org/experiments/ENCSR327IIZ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR327IIZ
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB535GJV
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: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS069NOT at ENCODE; https://www.encodeproject.org/ENCBS069NOT/


title: PUMCH tumor 35

description: genomic DNA from LUAD

label: Cy3 and Cy39


title: Control MPRA from K562 (ENCLB621RDC)

description:
https://www.encodeproject.org/experiments/ENCSR327IIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR327IIZ
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB621RDC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS919ZRZ at ENCODE; https://www.encodeproject.org/ENCBS919ZRZ/


title: PUMCH tumor 34

description: genomic DNA from LUAD

label: Cy3 and Cy38

value: lung adenocarcinoma

value: I


title: DNase-seq from hypothalamus (ENCLB693RON)

description:
https://www.encodeproject.org/experiments/ENCSR171JAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR171JAP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB693RON

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS563VYH at ENCODE; https://www.encodeproject.org/ENCBS563VYH/


title: PUMCH tumor 36

description: genomic DNA from LUAD

label: Cy3 and Cy40

value: Male


title: PUMCH tumor 41

description: genomic DNA from LUAD

label: Cy3 and Cy45


title: MPRA from HEL (ENCLB526DUL)

description:
https://www.encodeproject.org/experiments/ENCSR330ZFH/
***************
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 BCL11A enhancer.
experiment encode accession: ENCSR330ZFH
assay title: MPRA
possible controls: ENCSR549UBJ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB526DUL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HEL

value: male

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

value: adult

value: 30 year

value: ENCBS840DTD at ENCODE; https://www.encodeproject.org/ENCBS840DTD/


title: PUMCH tumor 31

description: genomic DNA from LUAD

label: Cy3 and Cy35

value: Female


title: PUMCH tumor 32

description: genomic DNA from LUAD

label: Cy3 and Cy36

value: III


title: Control MPRA from K562 (ENCLB414IOF)

description:
https://www.encodeproject.org/experiments/ENCSR327IIZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR327IIZ
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB414IOF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS518BIU at ENCODE; https://www.encodeproject.org/ENCBS518BIU/


title: DNase-seq from amygdala (ENCLB025DTU)

description:
https://www.encodeproject.org/experiments/ENCSR169VIC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR169VIC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB025DTU

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS584ZXO at ENCODE; https://www.encodeproject.org/ENCBS584ZXO/


title: Control MPRA from HepG2 (ENCLB542VBB)

description:
https://www.encodeproject.org/experiments/ENCSR293DMS/
***************
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 F9 promoter.
experiment encode accession: ENCSR293DMS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB542VBB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS325AIX at ENCODE; https://www.encodeproject.org/ENCBS325AIX/


title: PUMCH tumor 30

description: genomic DNA from LUAD

label: Cy3 and Cy34

value: lung adenocarcinoma

value: II

value: Male


title: DNase-seq from cerebellum (ENCLB845AUO)

description:
https://www.encodeproject.org/experiments/ENCSR167NWY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR167NWY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB845AUO

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: adult

value: ENCBS438EBF at ENCODE; https://www.encodeproject.org/ENCBS438EBF/


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB086ZFZ)

description:
https://www.encodeproject.org/experiments/ENCSR178XHL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR178XHL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB086ZFZ

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

value: C1 segment of cervical spinal cord

value: female

value: ENCBS616CNX at ENCODE; https://www.encodeproject.org/ENCBS616CNX/


title: DNase-seq from amygdala (ENCLB300AAM)

description:
https://www.encodeproject.org/experiments/ENCSR165TAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR165TAZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB300AAM

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS034GFK at ENCODE; https://www.encodeproject.org/ENCBS034GFK/


title: PUMCH tumor 39

description: genomic DNA from LUAD

label: Cy3 and Cy43

value: Female


title: PUMCH tumor 27

description: genomic DNA from LUAD

label: Cy3 and Cy31

value: I


title: PUMCH tumor 28

description: genomic DNA from LUAD

label: Cy3 and Cy32


title: MPRA from HepG2 (ENCLB849DEH)

description:
https://www.encodeproject.org/experiments/ENCSR281FRP/
***************
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 SORT enhancer, using 3' to 5' direction.
experiment encode accession: ENCSR281FRP
assay title: MPRA
possible controls: ENCSR730SAC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB849DEH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS608OBT at ENCODE; https://www.encodeproject.org/ENCBS608OBT/


title: PUMCH tumor 33

description: genomic DNA from LUAD

label: Cy3 and Cy37

value: lung adenocarcinoma

value: II

value: Male


title: PUMCH tumor 26

description: genomic DNA from LUAD

label: Cy3 and Cy30


title: Control MPRA from HepG2 (ENCLB770OUG)

description:
https://www.encodeproject.org/experiments/ENCSR293DMS/
***************
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 F9 promoter.
experiment encode accession: ENCSR293DMS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB770OUG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS339CKC at ENCODE; https://www.encodeproject.org/ENCBS339CKC/