title: DNase-seq from cerebellum (ENCLB262RHQ)

description:
https://www.encodeproject.org/experiments/ENCSR358VXC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358VXC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB262RHQ

value: ENCBS901JRD at ENCODE; https://www.encodeproject.org/ENCBS901JRD/


title: NDTH tumor 72

status: Public on Mar 06 2026

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 Cy280

molecule: genomic DNA

organism: Homo sapiens

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: I

tag: age at diagnosis

tag: Sex

value: Female


title: NDTH tumor 73

description: genomic DNA from LUAD

label: Cy3 and Cy281

value: Male


title: MPRA from HepG2 (ENCLB173UIT)

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/ENCSR739VGY/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR739VGY
assay title: MPRA
possible controls: ENCSR278KFS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB173UIT
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

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

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

value: male

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Nadav Ahituv, UCSF

tag: source

value: ATCC

tag: link

value: ENCBS465IUB at ENCODE; https://www.encodeproject.org/ENCBS465IUB/


title: NDTH tumor 70

description: genomic DNA from LUAD

label: Cy3 and Cy278


title: Control MPRA from HepG2 (ENCLB421TNB)

description:
https://www.encodeproject.org/experiments/ENCSR730SAC/
***************
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 SORT enhancer, using 3' to 5' direction.
experiment encode accession: ENCSR730SAC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB421TNB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: genomic

value: ENCBS314WVI at ENCODE; https://www.encodeproject.org/ENCBS314WVI/


title: NDTH tumor 69

description: genomic DNA from LUAD

label: Cy3 and Cy277


title: DNase-seq from cerebellum (ENCLB589RCG)

description:
https://www.encodeproject.org/experiments/ENCSR353FCV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR353FCV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB589RCG

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS355ZUZ at ENCODE; https://www.encodeproject.org/ENCBS355ZUZ/


title: DNase-seq from nucleus accumbens (ENCLB686SAN)

description:
https://www.encodeproject.org/experiments/ENCSR351TVZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR351TVZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB686SAN

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: female

value: ENCBS711JAJ at ENCODE; https://www.encodeproject.org/ENCBS711JAJ/


title: NDTH tumor 66

description: genomic DNA from LUAD

label: Cy3 and Cy274

value: lung adenocarcinoma

value: I

value: Male


title: Control MPRA from HepG2 (ENCLB130GDL)

description:
https://www.encodeproject.org/experiments/ENCSR730SAC/
***************
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: ENCSR730SAC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB130GDL
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: ENCBS608OBT at ENCODE; https://www.encodeproject.org/ENCBS608OBT/


title: DNase-seq from cerebellum (ENCLB367UAB)

description:
https://www.encodeproject.org/experiments/ENCSR350KKE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR350KKE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB367UAB

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: adult

value: unknown

value: ENCBS998TDF at ENCODE; https://www.encodeproject.org/ENCBS998TDF/


title: NDTH tumor 67

description: genomic DNA from LUAD

label: Cy3 and Cy275


title: DNase-seq from amygdala (ENCLB335LOJ)

description:
https://www.encodeproject.org/experiments/ENCSR348BRS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR348BRS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB335LOJ

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS565AYG at ENCODE; https://www.encodeproject.org/ENCBS565AYG/


title: Control MPRA from HepG2 (ENCLB261YFX)

description:
https://www.encodeproject.org/experiments/ENCSR721BJI/
***************
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: ENCSR721BJI
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB261YFX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: ATCC

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


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB242CCF)

description:
https://www.encodeproject.org/experiments/ENCSR344AUJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR344AUJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB242CCF

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: female

value: ENCBS679HQM at ENCODE; https://www.encodeproject.org/ENCBS679HQM/


title: NDTH tumor 65

description: genomic DNA from LUAD

label: Cy3 and Cy273

value: lung adenocarcinoma

value: I

value: Female


title: DNase-seq from substantia nigra (ENCLB692ODT)

description:
https://www.encodeproject.org/experiments/ENCSR341XLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341XLE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB692ODT

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: male

value: ENCBS691RMK at ENCODE; https://www.encodeproject.org/ENCBS691RMK/


title: NDTH tumor 64

description: genomic DNA from LUAD

label: Cy3 and Cy272

value: Male


title: NDTH tumor 63

description: genomic DNA from LUAD

label: Cy3 and Cy271

value: III


title: NDTH tumor 68

description: genomic DNA from LUAD

label: Cy3 and Cy276


title: NDTH tumor 62

description: genomic DNA from LUAD

label: Cy3 and Cy270


title: NDTH tumor 61

description: genomic DNA from LUAD

label: Cy3 and Cy269


title: NDTH tumor 59

description: genomic DNA from LUAD

label: Cy3 and Cy267


title: Control MPRA from HepG2 (ENCLB195XPE)

description:
https://www.encodeproject.org/experiments/ENCSR721BJI/
***************
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: ENCSR721BJI
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB195XPE
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: ENCBS415QKE at ENCODE; https://www.encodeproject.org/ENCBS415QKE/


title: NDTH tumor 58

description: genomic DNA from LUAD

label: Cy3 and Cy266


title: NDTH tumor 71

description: genomic DNA from LUAD

label: Cy3 and Cy279


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB115XWO)

description:
https://www.encodeproject.org/experiments/ENCSR341WDJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341WDJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB115XWO

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS842QET at ENCODE; https://www.encodeproject.org/ENCBS842QET/


title: MPRA from HEK293T (ENCLB874DMI)

description:
https://www.encodeproject.org/experiments/ENCSR701WDZ/
***************
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 HNF4A promoter.
experiment encode accession: ENCSR701WDZ
assay title: MPRA
possible controls: ENCSR629KNC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB874DMI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: female

value: embryonic

value: ATCC

value: ENCBS020JOK at ENCODE; https://www.encodeproject.org/ENCBS020JOK/


title: DNase-seq from putamen (ENCLB770IDZ)

description:
https://www.encodeproject.org/experiments/ENCSR341AEE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR341AEE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB770IDZ

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: ENCBS333GLB at ENCODE; https://www.encodeproject.org/ENCBS333GLB/


title: NDTH tumor 56

description: genomic DNA from LUAD

label: Cy3 and Cy264

value: lung adenocarcinoma

value: I

value: Male


title: MPRA from HEK293T (ENCLB405KMZ)

description:
https://www.encodeproject.org/experiments/ENCSR701WDZ/
***************
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 HNF4A promoter.
experiment encode accession: ENCSR701WDZ
assay title: MPRA
possible controls: ENCSR629KNC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB405KMZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ENCBS732XWJ at ENCODE; https://www.encodeproject.org/ENCBS732XWJ/


title: NDTH tumor 60

description: genomic DNA from LUAD

label: Cy3 and Cy268

value: II


title: NDTH tumor 57

description: genomic DNA from LUAD

label: Cy3 and Cy265

value: Female


title: NDTH tumor 55

description: genomic DNA from LUAD

label: Cy3 and Cy263


title: DNase-seq from Ammon's horn (ENCLB473ZCZ)

description:
https://www.encodeproject.org/experiments/ENCSR338TTD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338TTD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB473ZCZ

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: male

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS610SHZ at ENCODE; https://www.encodeproject.org/ENCBS610SHZ/


title: Control MPRA from HepG2 (ENCLB993UVP)

description:
https://www.encodeproject.org/experiments/ENCSR721BJI/
***************
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: ENCSR721BJI
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB993UVP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

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


title: MPRA from HEL (ENCLB386RCJ)

description:
https://www.encodeproject.org/experiments/ENCSR686LKF/
***************
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 HBG1 promoter.
experiment encode accession: ENCSR686LKF
assay title: MPRA
possible controls: ENCSR651OGV
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB386RCJ
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: ENCBS152ARO at ENCODE; https://www.encodeproject.org/ENCBS152ARO/


title: DNase-seq from amygdala (ENCLB566WJO)

description:
https://www.encodeproject.org/experiments/ENCSR338TYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338TYX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB566WJO

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: female

value: Kristin Ardlie

value: ENCBS738QYT at ENCODE; https://www.encodeproject.org/ENCBS738QYT/


title: NDTH tumor 54

description: genomic DNA from LUAD

label: Cy3 and Cy262

value: lung adenocarcinoma

value: I

value: Male


title: NDTH tumor 53

description: genomic DNA from LUAD

label: Cy3 and Cy261

value: Female


title: DNase-seq from Ammon's horn (ENCLB205FUQ)

description:
https://www.encodeproject.org/experiments/ENCSR332ZVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR332ZVT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB205FUQ

value: Ammon's horn

value: tissue

value: male

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS835JLA at ENCODE; https://www.encodeproject.org/ENCBS835JLA/


title: NDTH tumor 51

description: genomic DNA from LUAD

label: Cy3 and Cy259

value: II


title: MPRA from HEL (ENCLB161OHF)

description:
https://www.encodeproject.org/experiments/ENCSR686LKF/
***************
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 HBG1 promoter.
experiment encode accession: ENCSR686LKF
assay title: MPRA
possible controls: ENCSR651OGV
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB161OHF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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: ENCBS313IZT at ENCODE; https://www.encodeproject.org/ENCBS313IZT/


title: NDTH tumor 47

description: genomic DNA from LUAD

label: Cy3 and Cy255

value: lung adenocarcinoma

value: I


title: MPRA from HEK293T (ENCLB806PAY)

description:
https://www.encodeproject.org/experiments/ENCSR701WDZ/
***************
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 HNF4A promoter.
experiment encode accession: ENCSR701WDZ
assay title: MPRA
possible controls: ENCSR629KNC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB806PAY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: embryonic

value: ENCBS108PTI at ENCODE; https://www.encodeproject.org/ENCBS108PTI/


title: NDTH tumor 50

description: genomic DNA from LUAD

label: Cy3 and Cy258

value: Female


title: Control MPRA from HEK293T (ENCLB498IKD)

description:
https://www.encodeproject.org/experiments/ENCSR672AWI/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs6983267.
experiment encode accession: ENCSR672AWI
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB498IKD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: unknown

value: ENCBS376KBR at ENCODE; https://www.encodeproject.org/ENCBS376KBR/


title: MPRA from HEL (ENCLB701JWW)

description:
https://www.encodeproject.org/experiments/ENCSR686LKF/
***************
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 HBG1 promoter.
experiment encode accession: ENCSR686LKF
assay title: MPRA
possible controls: ENCSR651OGV
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB701JWW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: adult

value: ENCBS062OMP at ENCODE; https://www.encodeproject.org/ENCBS062OMP/


title: DNase-seq from cerebellum (ENCLB768NVK)

description:
https://www.encodeproject.org/experiments/ENCSR332JNP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR332JNP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB768NVK

value: cerebellum

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS644NZS at ENCODE; https://www.encodeproject.org/ENCBS644NZS/


title: DNase-seq from cerebellum (ENCLB996KDP)

description:
https://www.encodeproject.org/experiments/ENCSR332JNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR332JNP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB996KDP

value: ENCBS239AWV at ENCODE; https://www.encodeproject.org/ENCBS239AWV/


title: NDTH tumor 48

description: genomic DNA from LUAD

label: Cy3 and Cy256

value: lung adenocarcinoma

value: Male


title: NDTH tumor 52

description: genomic DNA from LUAD

label: Cy3 and Cy260

value: I


title: NDTH tumor 44

description: genomic DNA from LUAD

label: Cy3 and Cy252


title: Control MPRA from HEK293T (ENCLB314NKR)

description:
https://www.encodeproject.org/experiments/ENCSR672AWI/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs6983267.
experiment encode accession: ENCSR672AWI
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB314NKR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: female

value: embryonic

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS900FQA at ENCODE; https://www.encodeproject.org/ENCBS900FQA/


title: NDTH tumor 41

description: genomic DNA from LUAD

label: Cy3 and Cy249


title: DNase-seq from nucleus accumbens (ENCLB208OED)

description:
https://www.encodeproject.org/experiments/ENCSR331JWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR331JWC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB208OED

value: nucleus accumbens

value: adult

value: unknown

value: ENCBS115JVO at ENCODE; https://www.encodeproject.org/ENCBS115JVO/


title: DNase-seq from cerebellum (ENCLB128WWP)

description:
https://www.encodeproject.org/experiments/ENCSR330JXZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR330JXZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB128WWP

value: cerebellum

value: tissue

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS895DWH at ENCODE; https://www.encodeproject.org/ENCBS895DWH/


title: NDTH tumor 45

description: genomic DNA from LUAD

label: Cy3 and Cy253

value: lung adenocarcinoma

value: Female


title: DNase-seq from cerebellum (ENCLB682TQW)

description:
https://www.encodeproject.org/experiments/ENCSR330JXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330JXZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB682TQW

value: Kristin Ardlie

value: ENCBS995SJM at ENCODE; https://www.encodeproject.org/ENCBS995SJM/


title: MPRA from HepG2 (ENCLB280PMX)

description:
https://www.encodeproject.org/experiments/ENCSR661ZUO/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR661ZUO
assay title: MPRA
assembly: hg19
possible controls: ENCSR974CHK
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB280PMX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS625PMB at ENCODE; https://www.encodeproject.org/ENCBS625PMB/


title: NDTH tumor 42

description: genomic DNA from LUAD

label: Cy3 and Cy250

value: I

value: Male


title: DNase-seq from cerebellum (ENCLB868HEC)

description:
https://www.encodeproject.org/experiments/ENCSR332JNP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR332JNP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB868HEC

value: adult

value: unknown

value: ENCBS594COI at ENCODE; https://www.encodeproject.org/ENCBS594COI/


title: NDTH tumor 39

description: genomic DNA from LUAD

label: Cy3 and Cy247


title: NDTH tumor 46

description: genomic DNA from LUAD

label: Cy3 and Cy254


title: NDTH tumor 49

description: genomic DNA from LUAD

label: Cy3 and Cy257


title: NDTH tumor 40

description: genomic DNA from LUAD

label: Cy3 and Cy248


title: Control MPRA from WTC11 (ENCLB140EVD)

description:
https://www.encodeproject.org/experiments/ENCSR653CPO/
***************
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 WTC11 enhancers and promoters of protein-coding genes.
experiment encode accession: ENCSR653CPO
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB140EVD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: male

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS266MUL at ENCODE; https://www.encodeproject.org/ENCBS266MUL/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB613ISX)

description:
https://www.encodeproject.org/experiments/ENCSR328YIC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR328YIC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB613ISX

value: dorsolateral prefrontal cortex

value: tissue

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS899VGM at ENCODE; https://www.encodeproject.org/ENCBS899VGM/


title: NDTH tumor 37

description: genomic DNA from LUAD

label: Cy3 and Cy245

value: lung adenocarcinoma


title: NDTH tumor 43

description: genomic DNA from LUAD

label: Cy3 and Cy251

value: I


title: MPRA from HepG2 (ENCLB834KUW)

description:
https://www.encodeproject.org/experiments/ENCSR661ZUO/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR661ZUO
assay title: MPRA
assembly: hg19
possible controls: ENCSR974CHK
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB834KUW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: Control MPRA from HEK293T (ENCLB314KBV)

description:
https://www.encodeproject.org/experiments/ENCSR672AWI/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs6983267.
experiment encode accession: ENCSR672AWI
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB314KBV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: unknown

value: embryonic

value: ENCBS767OBO at ENCODE; https://www.encodeproject.org/ENCBS767OBO/


title: NDTH tumor 36

description: genomic DNA from LUAD

label: Cy3 and Cy244

value: Female


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB534YLW)

description:
https://www.encodeproject.org/experiments/ENCSR320ELE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR320ELE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB534YLW

value: dorsolateral prefrontal cortex

value: adult

value: ENCBS406JBR at ENCODE; https://www.encodeproject.org/ENCBS406JBR/


title: NDTH tumor 34

description: genomic DNA from LUAD

label: Cy3 and Cy242

value: III


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB955EFJ)

description:
https://www.encodeproject.org/experiments/ENCSR320ELE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR320ELE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB955EFJ

value: tissue

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS577QFY at ENCODE; https://www.encodeproject.org/ENCBS577QFY/


title: NDTH tumor 38

description: genomic DNA from LUAD

label: Cy3 and Cy246

value: lung adenocarcinoma

value: I

value: Male


title: NDTH tumor 31

description: genomic DNA from LUAD

label: Cy3 and Cy239

value: II


title: Control MPRA from WTC11 (ENCLB001STM)

description:
https://www.encodeproject.org/experiments/ENCSR653CPO/
***************
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 WTC11 enhancers and promoters of protein-coding genes.
experiment encode accession: ENCSR653CPO
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB001STM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS394RXW at ENCODE; https://www.encodeproject.org/ENCBS394RXW/


title: NDTH tumor 30

description: genomic DNA from LUAD

label: Cy3 and Cy238


title: NDTH tumor 35

description: genomic DNA from LUAD

label: Cy3 and Cy243

value: Female


title: NDTH tumor 29

description: genomic DNA from LUAD

label: Cy3 and Cy237


title: NDTH tumor 32

description: genomic DNA from LUAD

label: Cy3 and Cy240


title: DNase-seq from amygdala (ENCLB911CFA)

description:
https://www.encodeproject.org/experiments/ENCSR318ULV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR318ULV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB911CFA

value: amygdala

value: adult

value: unknown

value: ENCBS078BJR at ENCODE; https://www.encodeproject.org/ENCBS078BJR/


title: Control MPRA from HEL (ENCLB701ZYK)

description:
https://www.encodeproject.org/experiments/ENCSR651OGV/
***************
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 HBG1 promoter.
experiment encode accession: ENCSR651OGV
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB701ZYK
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: ENCBS152ARO at ENCODE; https://www.encodeproject.org/ENCBS152ARO/


title: DNase-seq from anterior cingulate cortex (ENCLB690ORR)

description:
https://www.encodeproject.org/experiments/ENCSR316TRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR316TRV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB690ORR

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS715CCL at ENCODE; https://www.encodeproject.org/ENCBS715CCL/


title: NDTH tumor 25

description: genomic DNA from LUAD

label: Cy3 and Cy233

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: I

value: Male


title: Control MPRA from HEL (ENCLB682EVN)

description:
https://www.encodeproject.org/experiments/ENCSR651OGV/
***************
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 HBG1 promoter.
experiment encode accession: ENCSR651OGV
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB682EVN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS313IZT at ENCODE; https://www.encodeproject.org/ENCBS313IZT/


title: MPRA from HepG2 (ENCLB822SEH)

description:
https://www.encodeproject.org/experiments/ENCSR661ZUO/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR661ZUO
assay title: MPRA
assembly: hg19
possible controls: ENCSR974CHK
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB822SEH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: NDTH tumor 27

description: genomic DNA from LUAD

label: Cy3 and Cy235


title: NDTH tumor 28

description: genomic DNA from LUAD

label: Cy3 and Cy236

value: III


title: Control MPRA from WTC11 (ENCLB846UJF)

description:
https://www.encodeproject.org/experiments/ENCSR653CPO/
***************
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 WTC11 enhancers and promoters of protein-coding genes.
experiment encode accession: ENCSR653CPO
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB846UJF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: ENCBS483YIE at ENCODE; https://www.encodeproject.org/ENCBS483YIE/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB380TXE)

description:
https://www.encodeproject.org/experiments/ENCSR328YIC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328YIC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB380TXE

value: dorsolateral prefrontal cortex

value: tissue

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS969QTB at ENCODE; https://www.encodeproject.org/ENCBS969QTB/


title: DNase-seq from anterior cingulate cortex (ENCLB701JCM)

description:
https://www.encodeproject.org/experiments/ENCSR316TRV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR316TRV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB701JCM

value: anterior cingulate cortex

value: male

value: ENCBS553ZZR at ENCODE; https://www.encodeproject.org/ENCBS553ZZR/


title: NDTH tumor 21

description: genomic DNA from LUAD

label: Cy3 and Cy229

value: lung adenocarcinoma

value: I

value: Female


title: NDTH tumor 26

description: genomic DNA from LUAD

label: Cy3 and Cy234

value: II

value: Male


title: NDTH tumor 24

description: genomic DNA from LUAD

label: Cy3 and Cy232


title: Control MPRA from HepG2 (ENCLB191CCD)

description:
https://www.encodeproject.org/experiments/ENCSR642ECM/
***************
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 an independent, second batch as ORI, and serves as an internal control to ORI_full.
experiment encode accession: ENCSR642ECM
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB191CCD
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: ENCBS646KCG at ENCODE; https://www.encodeproject.org/ENCBS646KCG/


title: NDTH tumor 23

description: genomic DNA from LUAD

label: Cy3 and Cy231


title: NDTH tumor 20

description: genomic DNA from LUAD

label: Cy3 and Cy228


title: Control MPRA from HepG2 (ENCLB668KAW)

description:
https://www.encodeproject.org/experiments/ENCSR642ECM/
***************
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 an independent, second batch as ORI, and serves as an internal control to ORI_full.
experiment encode accession: ENCSR642ECM
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB668KAW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS824DAY at ENCODE; https://www.encodeproject.org/ENCBS824DAY/


title: DNase-seq from amygdala (ENCLB034KIT)

description:
https://www.encodeproject.org/experiments/ENCSR315RKJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR315RKJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034KIT

value: amygdala

value: tissue

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS219MXO at ENCODE; https://www.encodeproject.org/ENCBS219MXO/


title: NDTH tumor 22

description: genomic DNA from LUAD

label: Cy3 and Cy230

value: lung adenocarcinoma

value: I

value: Male


title: DNase-seq from amygdala (ENCLB821ZJL)

description:
https://www.encodeproject.org/experiments/ENCSR315RKJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR315RKJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB821ZJL

value: ENCBS008QWU at ENCODE; https://www.encodeproject.org/ENCBS008QWU/


title: DNase-seq from amygdala (ENCLB622JLS)

description:
https://www.encodeproject.org/experiments/ENCSR315RKJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR315RKJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB622JLS

value: ENCBS037DOX at ENCODE; https://www.encodeproject.org/ENCBS037DOX/


title: NDTH tumor 33

description: genomic DNA from LUAD

label: Cy3 and Cy241


title: Control MPRA from HepG2 (ENCLB318RQD)

description:
https://www.encodeproject.org/experiments/ENCSR642ECM/
***************
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 an independent, second batch as ORI, and serves as an internal control to ORI_full.
experiment encode accession: ENCSR642ECM
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB318RQD
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: ENCBS265FPZ at ENCODE; https://www.encodeproject.org/ENCBS265FPZ/


title: NDTH tumor 15

description: genomic DNA from LUAD

label: Cy3 and Cy223

value: Female


title: NDTH tumor 17

description: genomic DNA from LUAD

label: Cy3 and Cy225


title: Control MPRA from HEL (ENCLB673VYC)

description:
https://www.encodeproject.org/experiments/ENCSR651OGV/
***************
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 HBG1 promoter.
experiment encode accession: ENCSR651OGV
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB673VYC
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: ATCC

value: ENCBS062OMP at ENCODE; https://www.encodeproject.org/ENCBS062OMP/


title: DNase-seq from caudate nucleus (ENCLB348FOY)

description:
https://www.encodeproject.org/experiments/ENCSR314CFL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314CFL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB348FOY

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS248MWJ at ENCODE; https://www.encodeproject.org/ENCBS248MWJ/


title: MPRA from HepG2 (ENCLB825SVI)

description:
https://www.encodeproject.org/experiments/ENCSR632EPR/
***************
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: ENCSR632EPR
assay title: MPRA
possible controls: ENCSR331WRX
encode release date: 2022-08-17
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB825SVI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

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


title: MPRA from HepG2 (ENCLB750XBA)

description:
https://www.encodeproject.org/experiments/ENCSR632EPR/
***************
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: ENCSR632EPR
assay title: MPRA
possible controls: ENCSR331WRX
encode release date: 2022-08-17
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB750XBA
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: 15 year

value: Nadav Ahituv, UCSF

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


title: DNase-seq from substantia nigra (ENCLB131QPF)

description:
https://www.encodeproject.org/experiments/ENCSR314ZUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314ZUG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB131QPF

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: female

value: adult

value: ENCBS699FMV at ENCODE; https://www.encodeproject.org/ENCBS699FMV/


title: DNase-seq from hypothalamus (ENCLB823XVT)

description:
https://www.encodeproject.org/experiments/ENCSR314QWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314QWD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB823XVT

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: tissue

value: ENCBS701JHV at ENCODE; https://www.encodeproject.org/ENCBS701JHV/


title: NDTH tumor 18

description: genomic DNA from LUAD

label: Cy3 and Cy226

value: lung adenocarcinoma

value: I

value: Female


title: NDTH tumor 16

description: genomic DNA from LUAD

label: Cy3 and Cy224


title: NDTH tumor 19

description: genomic DNA from LUAD

label: Cy3 and Cy227


title: NDTH tumor 9

description: genomic DNA from LUAD

label: Cy3 and Cy217


title: NDTH tumor 12

description: genomic DNA from LUAD

label: Cy3 and Cy220

value: Male


title: Control MPRA from HEK293T (ENCLB685QSM)

description:
https://www.encodeproject.org/experiments/ENCSR629KNC/
***************
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 HNF4A promoter.
experiment encode accession: ENCSR629KNC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB685QSM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: unknown

value: embryonic

value: ATCC

value: ENCBS732XWJ at ENCODE; https://www.encodeproject.org/ENCBS732XWJ/


title: DNase-seq from substantia nigra (ENCLB181JFW)

description:
https://www.encodeproject.org/experiments/ENCSR312IVR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR312IVR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB181JFW

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS601DFU at ENCODE; https://www.encodeproject.org/ENCBS601DFU/


title: MPRA from HepG2 (ENCLB297KBH)

description:
https://www.encodeproject.org/experiments/ENCSR632EPR/
***************
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: ENCSR632EPR
assay title: MPRA
possible controls: ENCSR331WRX
encode release date: 2022-08-17
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB297KBH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

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


title: Control MPRA from HEK293T (ENCLB925RZX)

description:
https://www.encodeproject.org/experiments/ENCSR629KNC/
***************
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 HNF4A promoter.
experiment encode accession: ENCSR629KNC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB925RZX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: ENCBS020JOK at ENCODE; https://www.encodeproject.org/ENCBS020JOK/


title: NDTH tumor 7

description: genomic DNA from LUAD

label: Cy3 and Cy215

value: lung adenocarcinoma

value: II

value: Male


title: NDTH tumor 6

description: genomic DNA from LUAD

label: Cy3 and Cy214

value: I

value: Female


title: Control MPRA from HEK293T (ENCLB658XUY)

description:
https://www.encodeproject.org/experiments/ENCSR629KNC/
***************
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 HNF4A promoter.
experiment encode accession: ENCSR629KNC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB658XUY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: unknown

value: embryonic

value: ATCC

value: ENCBS108PTI at ENCODE; https://www.encodeproject.org/ENCBS108PTI/


title: DNase-seq from amygdala (ENCLB185UPX)

description:
https://www.encodeproject.org/experiments/ENCSR309ISJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR309ISJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB185UPX

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: tissue

value: male

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS013HAV at ENCODE; https://www.encodeproject.org/ENCBS013HAV/


title: NDTH tumor 5

description: genomic DNA from LUAD

label: Cy3 and Cy213

value: lung adenocarcinoma


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB258MDC)

description:
https://www.encodeproject.org/experiments/ENCSR310GCP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR310GCP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB258MDC

value: dorsolateral prefrontal cortex

value: ENCBS986UCK at ENCODE; https://www.encodeproject.org/ENCBS986UCK/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB620KGJ)

description:
https://www.encodeproject.org/experiments/ENCSR310GCP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR310GCP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB620KGJ

value: ENCBS613LWQ at ENCODE; https://www.encodeproject.org/ENCBS613LWQ/


title: Control MPRA from HepG2 (ENCLB208UER)

description:
https://www.encodeproject.org/experiments/ENCSR579XDB/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR579XDB
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB208UER
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

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


title: NDTH tumor 10

description: genomic DNA from LUAD

label: Cy3 and Cy218

value: III

value: Female


title: NDTH tumor 14

description: genomic DNA from LUAD

label: Cy3 and Cy222

value: I


title: NDTH tumor 11

description: genomic DNA from LUAD

label: Cy3 and Cy219


title: NDTH tumor 13

description: genomic DNA from LUAD

label: Cy3 and Cy221

value: Male


title: DNase-seq from amygdala (ENCLB130TGA)

description:
https://www.encodeproject.org/experiments/ENCSR309ISJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR309ISJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB130TGA

value: amygdala

value: tissue

value: male

value: adult

value: unknown

value: ENCBS966JNL at ENCODE; https://www.encodeproject.org/ENCBS966JNL/


title: NDTH tumor 2

description: genomic DNA from LUAD

label: Cy3 and Cy210

value: lung adenocarcinoma


title: NDTH tumor 8

description: genomic DNA from LUAD

label: Cy3 and Cy216


title: Control MPRA from HepG2 (ENCLB209DBX)

description:
https://www.encodeproject.org/experiments/ENCSR579XDB/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR579XDB
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB209DBX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: ATCC

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


title: DNase-seq from substantia nigra (ENCLB303QLK)

description:
https://www.encodeproject.org/experiments/ENCSR307ARR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR307ARR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB303QLK

value: substantia nigra

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS020FBB at ENCODE; https://www.encodeproject.org/ENCBS020FBB/


title: NDTH tumor 3

description: genomic DNA from LUAD

label: Cy3 and Cy211

value: Female


title: PUMCH tumor 203

description: genomic DNA from LUAD

label: Cy3 and Cy207

value: III


title: Control MPRA from HepG2 (ENCLB773HRS)

description:
https://www.encodeproject.org/experiments/ENCSR579XDB/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR579XDB
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB773HRS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

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


title: DNase-seq from hypothalamus (ENCLB686LFO)

description:
https://www.encodeproject.org/experiments/ENCSR308KZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR308KZF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB686LFO

source_name: Homo sapiens female adult hypothalamus tissue

value: hypothalamus

value: tissue

value: female

value: adult

value: unknown

value: ENCBS232IHI at ENCODE; https://www.encodeproject.org/ENCBS232IHI/


title: PUMCH tumor 202

description: genomic DNA from LUAD

label: Cy3 and Cy206

value: lung adenocarcinoma

value: I


title: PUMCH tumor 200

description: genomic DNA from LUAD

label: Cy3 and Cy204


title: PUMCH tumor 204

description: genomic DNA from LUAD

label: Cy3 and Cy208

value: Male


title: PUMCH tumor 198

description: genomic DNA from LUAD

label: Cy3 and Cy202


title: NDTH tumor 4

description: genomic DNA from LUAD

label: Cy3 and Cy212


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB981TVM)

description:
https://www.encodeproject.org/experiments/ENCSR306TVF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306TVF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB981TVM

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS690AZF at ENCODE; https://www.encodeproject.org/ENCBS690AZF/


title: Control MPRA from HEL (ENCLB295DFU)

description:
https://www.encodeproject.org/experiments/ENCSR549UBJ/
***************
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: ENCSR549UBJ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB295DFU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HEL

value: cell line

value: male

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

value: 30 year

value: ATCC

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


title: PUMCH tumor 201

description: genomic DNA from LUAD

label: Cy3 and Cy205

value: III


title: Control MPRA from HEL (ENCLB305AFZ)

description:
https://www.encodeproject.org/experiments/ENCSR549UBJ/
***************
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: ENCSR549UBJ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB305AFZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: Nadav Ahituv, UCSF

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


title: DNase-seq from amygdala (ENCLB292SOC)

description:
https://www.encodeproject.org/experiments/ENCSR306OZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306OZD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB292SOC

value: amygdala

value: tissue

value: unknown

value: ENCBS062JRS at ENCODE; https://www.encodeproject.org/ENCBS062JRS/


title: PUMCH tumor 196

description: genomic DNA from LUAD

label: Cy3 and Cy200

value: lung adenocarcinoma

value: I

value: Female


title: MPRA from WTC11 (ENCLB980AOB)

description:
https://www.encodeproject.org/experiments/ENCSR548AQS/
***************
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 neuronal enhancers and promoters.
experiment encode accession: ENCSR548AQS
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR517VUU
encode release date: 2024-01-09
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB980AOB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Coriell

value: ENCBS659PKW at ENCODE; https://www.encodeproject.org/ENCBS659PKW/


title: DNase-seq from nucleus accumbens (ENCLB365IYM)

description:
https://www.encodeproject.org/experiments/ENCSR306UAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306UAJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB365IYM

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS061QHA at ENCODE; https://www.encodeproject.org/ENCBS061QHA/


title: Control MPRA from HEL (ENCLB585BCC)

description:
https://www.encodeproject.org/experiments/ENCSR549UBJ/
***************
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: ENCSR549UBJ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB585BCC
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: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from hypothalamus (ENCLB228XKF)

description:
https://www.encodeproject.org/experiments/ENCSR304GAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR304GAB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB228XKF

value: hypothalamus

value: tissue

value: unknown

value: ENCBS646VUN at ENCODE; https://www.encodeproject.org/ENCBS646VUN/


title: PUMCH tumor 197

description: genomic DNA from LUAD

label: Cy3 and Cy201

value: lung adenocarcinoma

value: I

value: Female


title: PUMCH tumor 195

description: genomic DNA from LUAD

label: Cy3 and Cy199


title: PUMCH tumor 199

description: genomic DNA from LUAD

label: Cy3 and Cy203

value: III

value: Male


title: MPRA from WTC11 (ENCLB140CLT)

description:
https://www.encodeproject.org/experiments/ENCSR548AQS/
***************
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 neuronal enhancers and promoters.
experiment encode accession: ENCSR548AQS
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR517VUU
encode release date: 2024-01-09
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB140CLT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Coriell

value: ENCBS825OJD at ENCODE; https://www.encodeproject.org/ENCBS825OJD/


title: NDTH tumor 1

description: genomic DNA from LUAD

label: Cy3 and Cy209


title: PUMCH tumor 194

description: genomic DNA from LUAD

label: Cy3 and Cy198


title: PUMCH tumor 193

description: genomic DNA from LUAD

label: Cy3 and Cy197


title: PUMCH tumor 191

description: genomic DNA from LUAD

label: Cy3 and Cy195


title: PUMCH tumor 192

description: genomic DNA from LUAD

label: Cy3 and Cy196


title: PUMCH tumor 190

description: genomic DNA from LUAD

label: Cy3 and Cy194


title: DNase-seq from amygdala (ENCLB649NGF)

description:
https://www.encodeproject.org/experiments/ENCSR306EVC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306EVC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB649NGF

value: amygdala

value: male

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS886KDA at ENCODE; https://www.encodeproject.org/ENCBS886KDA/


title: Control MPRA from HepG2 (ENCLB361PTC)

description:
https://www.encodeproject.org/experiments/ENCSR547NTG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR547NTG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB361PTC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PUMCH tumor 189

description: genomic DNA from LUAD

label: Cy3 and Cy193

value: lung adenocarcinoma

value: I

value: Female


title: DNase-seq from anterior cingulate cortex (ENCLB006DYX)

description:
https://www.encodeproject.org/experiments/ENCSR304EJF/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR304EJF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB006DYX

value: anterior cingulate cortex

value: tissue

value: unknown

value: ENCBS053LWH at ENCODE; https://www.encodeproject.org/ENCBS053LWH/


title: PUMCH tumor 188

description: genomic DNA from LUAD

label: Cy3 and Cy192


title: Control MPRA from HepG2 (ENCLB844GXN)

description:
https://www.encodeproject.org/experiments/ENCSR547NTG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR547NTG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB844GXN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

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


title: Control MPRA from HepG2 (ENCLB040BXP)

description:
https://www.encodeproject.org/experiments/ENCSR547NTG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the HSS (STARR-seq) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as HSS_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR547NTG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB040BXP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: MPRA from WTC11 (ENCLB187PCV)

description:
https://www.encodeproject.org/experiments/ENCSR548AQS/
***************
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 neuronal enhancers and promoters.
experiment encode accession: ENCSR548AQS
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR517VUU
encode release date: 2024-01-09
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB187PCV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: 30 year

value: Coriell

value: ENCBS160ZPI at ENCODE; https://www.encodeproject.org/ENCBS160ZPI/


title: DNase-seq from anterior cingulate cortex (ENCLB532LIU)

description:
https://www.encodeproject.org/experiments/ENCSR304EJF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR304EJF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB532LIU

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS204IDT at ENCODE; https://www.encodeproject.org/ENCBS204IDT/


title: PUMCH tumor 186

description: genomic DNA from LUAD

label: Cy3 and Cy190

value: lung adenocarcinoma

value: I


title: PUMCH tumor 187

description: genomic DNA from LUAD

label: Cy3 and Cy191

value: Male


title: PUMCH tumor 185

description: genomic DNA from LUAD

label: Cy3 and Cy189

value: III


title: DNase-seq from substantia nigra (ENCLB799PGK)

description:
https://www.encodeproject.org/experiments/ENCSR301QGF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR301QGF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB799PGK

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: tissue

value: unknown

value: ENCBS095MTM at ENCODE; https://www.encodeproject.org/ENCBS095MTM/


title: PUMCH tumor 181

description: genomic DNA from LUAD

label: Cy3 and Cy185

value: Female


title: Control MPRA from HepG2 (ENCLB881NGC)

description:
https://www.encodeproject.org/experiments/ENCSR542KWX/
***************
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: ENCSR542KWX
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB881NGC
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: ENCBS316VVP at ENCODE; https://www.encodeproject.org/ENCBS316VVP/


title: PUMCH tumor 180

description: genomic DNA from LUAD

label: Cy3 and Cy184

value: lung adenocarcinoma


title: PUMCH tumor 184

description: genomic DNA from LUAD

label: Cy3 and Cy188

value: I


title: DNase-seq from substantia nigra (ENCLB224CSQ)

description:
https://www.encodeproject.org/experiments/ENCSR301QGF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR301QGF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB224CSQ

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS455PDO at ENCODE; https://www.encodeproject.org/ENCBS455PDO/


title: PUMCH tumor 179

description: genomic DNA from LUAD

label: Cy3 and Cy183


title: Control MPRA from HepG2 (ENCLB277EQV)

description:
https://www.encodeproject.org/experiments/ENCSR542KWX/
***************
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: ENCSR542KWX
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB277EQV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS409LQX at ENCODE; https://www.encodeproject.org/ENCBS409LQX/


title: Control MPRA from HepG2 (ENCLB077AUD)

description:
https://www.encodeproject.org/experiments/ENCSR542KWX/
***************
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: ENCSR542KWX
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB077AUD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS313OWA at ENCODE; https://www.encodeproject.org/ENCBS313OWA/


title: PUMCH tumor 183

description: genomic DNA from LUAD

label: Cy3 and Cy187

value: Male


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB104XHI)

description:
https://www.encodeproject.org/experiments/ENCSR300AQA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR300AQA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB104XHI

value: dorsolateral prefrontal cortex

value: tissue

value: female

value: unknown

value: ENCBS886LVQ at ENCODE; https://www.encodeproject.org/ENCBS886LVQ/


title: DNase-seq from anterior cingulate cortex (ENCLB068NNM)

description:
https://www.encodeproject.org/experiments/ENCSR304EJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR304EJF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB068NNM

value: anterior cingulate cortex

value: male

value: ENCBS411EJZ at ENCODE; https://www.encodeproject.org/ENCBS411EJZ/


title: Control MPRA from K562 (ENCLB393CVT)

description:
https://www.encodeproject.org/experiments/ENCSR540PAH/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.
experiment encode accession: ENCSR540PAH
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB393CVT
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: ENCBS449YMQ at ENCODE; https://www.encodeproject.org/ENCBS449YMQ/


title: DNase-seq from substantia nigra (ENCLB092TKR)

description:
https://www.encodeproject.org/experiments/ENCSR298WTS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298WTS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB092TKR

value: substantia nigra

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS371LMY at ENCODE; https://www.encodeproject.org/ENCBS371LMY/


title: PUMCH tumor 178

description: genomic DNA from LUAD

label: Cy3 and Cy182

value: lung adenocarcinoma

value: I

value: Male


title: Control MPRA from K562 (ENCLB538EPQ)

description:
https://www.encodeproject.org/experiments/ENCSR540PAH/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.
experiment encode accession: ENCSR540PAH
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB538EPQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

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


title: PUMCH tumor 177

description: genomic DNA from LUAD

label: Cy3 and Cy181

value: III


title: PUMCH tumor 182

description: genomic DNA from LUAD

label: Cy3 and Cy186

value: Female


title: DNase-seq from caudate nucleus (ENCLB897AIT)

description:
https://www.encodeproject.org/experiments/ENCSR298CUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298CUB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB897AIT

value: caudate nucleus

value: tissue

value: male

value: unknown

value: ENCBS800GXP at ENCODE; https://www.encodeproject.org/ENCBS800GXP/


title: DNase-seq from putamen (ENCLB837FAE)

description:
https://www.encodeproject.org/experiments/ENCSR298CAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298CAP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB837FAE

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: ENCBS436NLX at ENCODE; https://www.encodeproject.org/ENCBS436NLX/


title: PUMCH tumor 175

description: genomic DNA from LUAD

label: Cy3 and Cy179


title: Control MPRA from K562 (ENCLB674EKZ)

description:
https://www.encodeproject.org/experiments/ENCSR540PAH/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the PKLR promoter.
experiment encode accession: ENCSR540PAH
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB674EKZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PUMCH tumor 174

description: genomic DNA from LUAD

label: Cy3 and Cy178

value: lung adenocarcinoma

value: I


title: DNase-seq from putamen (ENCLB188ZWL)

description:
https://www.encodeproject.org/experiments/ENCSR297KYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR297KYW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB188ZWL

source_name: Homo sapiens female adult putamen tissue

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS528WLO at ENCODE; https://www.encodeproject.org/ENCBS528WLO/


title: PUMCH tumor 173

description: genomic DNA from LUAD

label: Cy3 and Cy177

value: Female


title: Control MPRA from WTC11 (ENCLB587EXP)

description:
https://www.encodeproject.org/experiments/ENCSR517VUU/
***************
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 neuronal enhancers and promoters.
experiment encode accession: ENCSR517VUU
assay title: Control MPRA
encode release date: 2024-01-09
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB587EXP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: 30 year

value: Coriell

value: ENCBS825OJD at ENCODE; https://www.encodeproject.org/ENCBS825OJD/


title: PUMCH tumor 171

description: genomic DNA from LUAD

label: Cy3 and Cy175

value: Male


title: Control MPRA from WTC11 (ENCLB151FWQ)

description:
https://www.encodeproject.org/experiments/ENCSR517VUU/
***************
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 neuronal enhancers and promoters.
experiment encode accession: ENCSR517VUU
assay title: Control MPRA
encode release date: 2024-01-09
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB151FWQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: adult

value: ENCBS160ZPI at ENCODE; https://www.encodeproject.org/ENCBS160ZPI/


title: PUMCH tumor 172

description: genomic DNA from LUAD

label: Cy3 and Cy176


title: PUMCH tumor 176

description: genomic DNA from LUAD

label: Cy3 and Cy180


title: DNase-seq from amygdala (ENCLB458CAR)

description:
https://www.encodeproject.org/experiments/ENCSR293IQG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR293IQG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB458CAR

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: tissue

value: unknown

value: ENCBS788KEL at ENCODE; https://www.encodeproject.org/ENCBS788KEL/


title: PUMCH tumor 170

description: genomic DNA from LUAD

label: Cy3 and Cy174

value: lung adenocarcinoma

value: I


title: DNase-seq from Ammon's horn (ENCLB903EDV)

description:
https://www.encodeproject.org/experiments/ENCSR292WDL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR292WDL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB903EDV

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS369NQK at ENCODE; https://www.encodeproject.org/ENCBS369NQK/


title: PUMCH tumor 168

description: genomic DNA from LUAD

label: Cy3 and Cy172

value: Female


title: DNase-seq from Ammon's horn (ENCLB556QUY)

description:
https://www.encodeproject.org/experiments/ENCSR291TYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291TYM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB556QUY

value: male

value: ENCBS980XKB at ENCODE; https://www.encodeproject.org/ENCBS980XKB/


title: Control MPRA from WTC11 (ENCLB297SCZ)

description:
https://www.encodeproject.org/experiments/ENCSR517VUU/
***************
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 neuronal enhancers and promoters.
experiment encode accession: ENCSR517VUU
assay title: Control MPRA
encode release date: 2024-01-09
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB297SCZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: 30 year

value: Nadav Ahituv, UCSF

value: Coriell

value: ENCBS659PKW at ENCODE; https://www.encodeproject.org/ENCBS659PKW/


title: PUMCH tumor 167

description: genomic DNA from LUAD

label: Cy3 and Cy171

source_name: lung adenocarcinoma


title: PUMCH tumor 163

description: genomic DNA from LUAD

label: Cy3 and Cy167


title: PUMCH tumor 161

description: genomic DNA from LUAD

label: Cy3 and Cy165

value: Male


title: PUMCH tumor 169

description: genomic DNA from LUAD

label: Cy3 and Cy173


title: MPRA from HepG2 (ENCLB290KQB)

description:
https://www.encodeproject.org/experiments/ENCSR509EUX/
***************
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: ENCSR509EUX
assay title: MPRA
assembly: hg19
possible controls: ENCSR356YBY
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB290KQB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: ATCC

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


title: PUMCH tumor 165

description: genomic DNA from LUAD

label: Cy3 and Cy169

value: lung adenocarcinoma

value: I


title: PUMCH tumor 164

description: genomic DNA from LUAD

label: Cy3 and Cy168

value: III


title: MPRA from HepG2 (ENCLB157AUS)

description:
https://www.encodeproject.org/experiments/ENCSR509EUX/
***************
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: ENCSR509EUX
assay title: MPRA
assembly: hg19
possible controls: ENCSR356YBY
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB157AUS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: PUMCH tumor 166

description: genomic DNA from LUAD

label: Cy3 and Cy170

value: Female


title: MPRA from HepG2 (ENCLB840UXO)

description:
https://www.encodeproject.org/experiments/ENCSR509EUX/
***************
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: ENCSR509EUX
assay title: MPRA
assembly: hg19
possible controls: ENCSR356YBY
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB840UXO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

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


title: DNase-seq from nucleus accumbens (ENCLB233QUD)

description:
https://www.encodeproject.org/experiments/ENCSR289IBE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR289IBE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB233QUD

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS550OCH at ENCODE; https://www.encodeproject.org/ENCBS550OCH/


title: DNase-seq from nucleus accumbens (ENCLB808GDJ)

description:
https://www.encodeproject.org/experiments/ENCSR290PWH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR290PWH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB808GDJ

value: ENCBS958MJK at ENCODE; https://www.encodeproject.org/ENCBS958MJK/


title: PUMCH tumor 159

description: genomic DNA from LUAD

label: Cy3 and Cy163

value: Male


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB997IEG)

description:
https://www.encodeproject.org/experiments/ENCSR293ISO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR293ISO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB997IEG

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: ENCBS086RIU at ENCODE; https://www.encodeproject.org/ENCBS086RIU/


title: DNase-seq from putamen (ENCLB411WJA)

description:
https://www.encodeproject.org/experiments/ENCSR287KKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287KKC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB411WJA

value: putamen

value: ENCBS942BLU at ENCODE; https://www.encodeproject.org/ENCBS942BLU/


title: Control MPRA from HEK293T (ENCLB247ZBJ)

description:
https://www.encodeproject.org/experiments/ENCSR484ECL/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
experiment encode accession: ENCSR484ECL
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB247ZBJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: female

value: embryonic

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PUMCH tumor 160

description: genomic DNA from LUAD

label: Cy3 and Cy164

value: lung adenocarcinoma

value: I


title: Control MPRA from HEK293T (ENCLB060YSC)

description:
https://www.encodeproject.org/experiments/ENCSR484ECL/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
experiment encode accession: ENCSR484ECL
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB060YSC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: unknown

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


title: PUMCH tumor 156

description: genomic DNA from LUAD

label: Cy3 and Cy160

value: II


title: DNase-seq from putamen (ENCLB545ZRA)

description:
https://www.encodeproject.org/experiments/ENCSR287KKC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR287KKC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB545ZRA

value: tissue

value: male

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS796PYM at ENCODE; https://www.encodeproject.org/ENCBS796PYM/


title: PUMCH tumor 162

description: genomic DNA from LUAD

label: Cy3 and Cy166

value: Female


title: MPRA from HepG2 (ENCLB972LDJ)

description:
https://www.encodeproject.org/experiments/ENCSR478ESZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a 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: ENCLB972LDJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS153VNE at ENCODE; https://www.encodeproject.org/ENCBS153VNE/


title: PUMCH tumor 158

description: genomic DNA from LUAD

label: Cy3 and Cy162

value: lung adenocarcinoma

value: Male


title: PUMCH tumor 154

description: genomic DNA from LUAD

label: Cy3 and Cy158

value: I


title: DNase-seq from substantia nigra (ENCLB530VLB)

description:
https://www.encodeproject.org/experiments/ENCSR286RDE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR286RDE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB530VLB

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: female

value: unknown

value: ENCBS223RDH at ENCODE; https://www.encodeproject.org/ENCBS223RDH/


title: PUMCH tumor 157

description: genomic DNA from LUAD

label: Cy3 and Cy161


title: PUMCH tumor 155

description: genomic DNA from LUAD

label: Cy3 and Cy159

value: III


title: PUMCH tumor 149

description: genomic DNA from LUAD

label: Cy3 and Cy153


title: PUMCH tumor 152

description: genomic DNA from LUAD

label: Cy3 and Cy156


title: PUMCH tumor 153

description: genomic DNA from LUAD

label: Cy3 and Cy157


title: MPRA from HepG2 (ENCLB917XWU)

description:
https://www.encodeproject.org/experiments/ENCSR478ESZ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a 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: ENCLB917XWU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: male

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS154QNZ at ENCODE; https://www.encodeproject.org/ENCBS154QNZ/


title: DNase-seq from substantia nigra (ENCLB054BKC)

description:
https://www.encodeproject.org/experiments/ENCSR285WND/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR285WND
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB054BKC

value: tissue

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS484EBC at ENCODE; https://www.encodeproject.org/ENCBS484EBC/


title: PUMCH tumor 148

description: genomic DNA from LUAD

label: Cy3 and Cy152

value: lung adenocarcinoma

value: Female


title: PUMCH tumor 151

description: genomic DNA from LUAD

label: Cy3 and Cy155

value: I


title: Control MPRA from HEK293T (ENCLB697MTK)

description:
https://www.encodeproject.org/experiments/ENCSR484ECL/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MSMB promoter.
experiment encode accession: ENCSR484ECL
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB697MTK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: embryonic

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


title: PUMCH tumor 150

description: genomic DNA from LUAD

label: Cy3 and Cy154


title: DNase-seq from caudate nucleus (ENCLB201HLY)

description:
https://www.encodeproject.org/experiments/ENCSR284PSE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR284PSE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB201HLY

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: female

value: unknown

value: ENCBS687DMD at ENCODE; https://www.encodeproject.org/ENCBS687DMD/