title: DNase-seq from dorsolateral prefrontal cortex (ENCLB103UGL)

description:
https://www.encodeproject.org/experiments/ENCSR465RJI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR465RJI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB103UGL

value: dorsolateral prefrontal cortex

value: ENCBS725QLE at ENCODE; https://www.encodeproject.org/ENCBS725QLE/


title: Control MPRA from K562 (ENCLB416ATA)

status: Public on Mar 06 2026

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR897BXT/
***************
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 all protein-coding genes.
experiment encode accession: ENCSR897BXT
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB416ATA
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: line

value: cell line

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Nadav Ahituv, UCSF

tag: source

value: ATCC

tag: link

value: ENCBS519AAC at ENCODE; https://www.encodeproject.org/ENCBS519AAC/


title: DNase-seq from anterior cingulate cortex (ENCLB145YCQ)

description:
https://www.encodeproject.org/experiments/ENCSR459HEA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR459HEA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB145YCQ

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: tissue

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS031LAW at ENCODE; https://www.encodeproject.org/ENCBS031LAW/


title: Control MPRA from HEL (ENCLB058EIZ)

description:
https://www.encodeproject.org/experiments/ENCSR901KLZ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the GP1BB promoter.
experiment encode accession: ENCSR901KLZ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB058EIZ
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: Erythroleukemia, negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: 30 year

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


title: Control MPRA from HEL (ENCLB428ZBL)

description:
https://www.encodeproject.org/experiments/ENCSR901KLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the GP1BB promoter.
experiment encode accession: ENCSR901KLZ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB428ZBL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

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


title: Control MPRA from K562 (ENCLB880ZAK)

description:
https://www.encodeproject.org/experiments/ENCSR897BXT/
***************
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 all protein-coding genes.
experiment encode accession: ENCSR897BXT
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB880ZAK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ENCBS958VMI at ENCODE; https://www.encodeproject.org/ENCBS958VMI/


title: DNase-seq from caudate nucleus (ENCLB238YFG)

description:
https://www.encodeproject.org/experiments/ENCSR454INE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR454INE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB238YFG

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: ENCBS356JQD at ENCODE; https://www.encodeproject.org/ENCBS356JQD/


title: DNase-seq from anterior cingulate cortex (ENCLB839QKR)

description:
https://www.encodeproject.org/experiments/ENCSR459HEA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR459HEA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB839QKR

value: anterior cingulate cortex

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS803DJC at ENCODE; https://www.encodeproject.org/ENCBS803DJC/


title: DNase-seq from putamen (ENCLB530OQH)

description:
https://www.encodeproject.org/experiments/ENCSR458KJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR458KJY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB530OQH

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: Kristin Ardlie

value: ENCBS475TAX at ENCODE; https://www.encodeproject.org/ENCBS475TAX/


title: Control MPRA from HEL (ENCLB588RSF)

description:
https://www.encodeproject.org/experiments/ENCSR901KLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the GP1BB promoter.
experiment encode accession: ENCSR901KLZ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB588RSF
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: ENCBS933KQU at ENCODE; https://www.encodeproject.org/ENCBS933KQU/


title: DNase-seq from nucleus accumbens (ENCLB213AVW)

description:
https://www.encodeproject.org/experiments/ENCSR453MLG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR453MLG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB213AVW

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: female

value: adult

value: ENCBS408XAE at ENCODE; https://www.encodeproject.org/ENCBS408XAE/


title: Control MPRA from K562 (ENCLB830TOX)

description:
https://www.encodeproject.org/experiments/ENCSR897BXT/
***************
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 all protein-coding genes.
experiment encode accession: ENCSR897BXT
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB830TOX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS821CGA at ENCODE; https://www.encodeproject.org/ENCBS821CGA/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB911BPL)

description:
https://www.encodeproject.org/experiments/ENCSR453BZU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR453BZU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB911BPL

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS716NDM at ENCODE; https://www.encodeproject.org/ENCBS716NDM/


title: Control MPRA from HepG2 (ENCLB542MAR)

description:
https://www.encodeproject.org/experiments/ENCSR902NRZ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR902NRZ
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB542MAR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ENCBS852YLY at ENCODE; https://www.encodeproject.org/ENCBS852YLY/


title: DNase-seq from cerebellum (ENCLB563VBY)

description:
https://www.encodeproject.org/experiments/ENCSR451ECU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR451ECU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB563VBY

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: female

value: adult

value: ENCBS305BJD at ENCODE; https://www.encodeproject.org/ENCBS305BJD/


title: DNase-seq from nucleus accumbens (ENCLB616BAT)

description:
https://www.encodeproject.org/experiments/ENCSR467ZWA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR467ZWA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB616BAT

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: ENCBS826QPB at ENCODE; https://www.encodeproject.org/ENCBS826QPB/


title: DNase-seq from substantia nigra (ENCLB543MEE)

description:
https://www.encodeproject.org/experiments/ENCSR451SQM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR451SQM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB543MEE

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: male

value: unknown

value: ENCBS117OMP at ENCODE; https://www.encodeproject.org/ENCBS117OMP/


title: DNase-seq from anterior cingulate cortex (ENCLB831JCY)

description:
https://www.encodeproject.org/experiments/ENCSR450EGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR450EGX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB831JCY

value: anterior cingulate cortex

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS848PGL at ENCODE; https://www.encodeproject.org/ENCBS848PGL/


title: MPRA from HEK293T (ENCLB722VGX)

description:
https://www.encodeproject.org/experiments/ENCSR883DOL/
***************
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: ENCSR883DOL
assay title: MPRA
possible controls: ENCSR672AWI
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB722VGX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: transcriptomic

molecule: total RNA

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

value: cell line

value: embryonic

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HEK293T (ENCLB897UFH)

description:
https://www.encodeproject.org/experiments/ENCSR883DOL/
***************
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: ENCSR883DOL
assay title: MPRA
possible controls: ENCSR672AWI
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB897UFH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

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


title: MPRA from HepG2 (ENCLB654GRT)

description:
https://www.encodeproject.org/experiments/ENCSR881ERG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR881ERG
assay title: MPRA
assembly: hg19
possible controls: ENCSR360LZF
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB654GRT
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: ENCBS352PXL at ENCODE; https://www.encodeproject.org/ENCBS352PXL/


title: MPRA from HEK293T (ENCLB588JKP)

description:
https://www.encodeproject.org/experiments/ENCSR883DOL/
***************
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: ENCSR883DOL
assay title: MPRA
possible controls: ENCSR672AWI
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB588JKP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: unknown

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


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB578IHT)

description:
https://www.encodeproject.org/experiments/ENCSR447ZCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR447ZCY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB578IHT

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: ENCBS977VNG at ENCODE; https://www.encodeproject.org/ENCBS977VNG/


title: MPRA from HepG2 (ENCLB721OFT)

description:
https://www.encodeproject.org/experiments/ENCSR881ERG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR881ERG
assay title: MPRA
assembly: hg19
possible controls: ENCSR360LZF
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB721OFT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

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


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB099UVZ)

description:
https://www.encodeproject.org/experiments/ENCSR441NLO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR441NLO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB099UVZ

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

value: C1 segment of cervical spinal cord

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS887SAL at ENCODE; https://www.encodeproject.org/ENCBS887SAL/


title: MPRA from HepG2 (ENCLB116RTI)

description:
https://www.encodeproject.org/experiments/ENCSR881ERG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR881ERG
assay title: MPRA
assembly: hg19
possible controls: ENCSR360LZF
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB116RTI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from Ammon's horn (ENCLB883DXG)

description:
https://www.encodeproject.org/experiments/ENCSR444OFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR444OFO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB883DXG

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: unknown

value: ENCBS721ARY at ENCODE; https://www.encodeproject.org/ENCBS721ARY/


title: Control MPRA from HepG2 (ENCLB597VXU)

description:
https://www.encodeproject.org/experiments/ENCSR849IXM/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR849IXM
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB597VXU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

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


title: MPRA from HepG2 (ENCLB014BBJ)

description:
https://www.encodeproject.org/experiments/ENCSR881ERG/
***************
biological replicate number: 4
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of the same set of elements in both the forward and reverse orientations in parallel.
experiment encode accession: ENCSR881ERG
assay title: MPRA
assembly: hg19
possible controls: ENCSR360LZF
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB014BBJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: child

value: 15 year

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


title: Control MPRA from HepG2 (ENCLB240ULA)

description:
https://www.encodeproject.org/experiments/ENCSR849IXM/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR849IXM
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB240ULA
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

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


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB127LEM)

description:
https://www.encodeproject.org/experiments/ENCSR441FBD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR441FBD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB127LEM

value: dorsolateral prefrontal cortex

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS913YMO at ENCODE; https://www.encodeproject.org/ENCBS913YMO/


title: Control MPRA from HepG2 (ENCLB958CWS)

description:
https://www.encodeproject.org/experiments/ENCSR849IXM/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562/Hepg2 enhancers as a pilot library to a larger-scale experiment.
experiment encode accession: ENCSR849IXM
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB958CWS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from nucleus accumbens (ENCLB101OPS)

description:
https://www.encodeproject.org/experiments/ENCSR440YHV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR440YHV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB101OPS

value: nucleus accumbens

value: female

value: unknown

value: ENCBS998QFX at ENCODE; https://www.encodeproject.org/ENCBS998QFX/


title: DNase-seq from Ammon's horn (ENCLB965MQH)

description:
https://www.encodeproject.org/experiments/ENCSR439NVW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR439NVW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB965MQH

value: Ammon's horn

value: male

value: ENCBS776RQR at ENCODE; https://www.encodeproject.org/ENCBS776RQR/


title: Control MPRA from HaCaT (ENCLB717MGH)

description:
https://www.encodeproject.org/experiments/ENCSR849FAC/
***************
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 IRF6 enhancer.
experiment encode accession: ENCSR849FAC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB717MGH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: HaCaT

value: cell line

value: Immortalized human keratinocyte, negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: adult

value: 65 year

value: ENCBS067HKL at ENCODE; https://www.encodeproject.org/ENCBS067HKL/


title: Control MPRA from HaCaT (ENCLB713PXV)

description:
https://www.encodeproject.org/experiments/ENCSR849FAC/
***************
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 IRF6 enhancer.
experiment encode accession: ENCSR849FAC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB713PXV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS137PXF at ENCODE; https://www.encodeproject.org/ENCBS137PXF/


title: DNase-seq from putamen (ENCLB039VYZ)

description:
https://www.encodeproject.org/experiments/ENCSR434CMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR434CMW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB039VYZ

value: putamen

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS172YCQ at ENCODE; https://www.encodeproject.org/ENCBS172YCQ/


title: MPRA from K562 (ENCLB212LBM)

description:
https://www.encodeproject.org/experiments/ENCSR845WND/
***************
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: ENCSR845WND
assay title: MPRA
possible controls: ENCSR166BQV
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB212LBM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS005XNP at ENCODE; https://www.encodeproject.org/ENCBS005XNP/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB176FJE)

description:
https://www.encodeproject.org/experiments/ENCSR437SJV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR437SJV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB176FJE

value: dorsolateral prefrontal cortex

value: male

value: unknown

value: ENCBS858IIV at ENCODE; https://www.encodeproject.org/ENCBS858IIV/


title: DNase-seq from caudate nucleus (ENCLB078BWW)

description:
https://www.encodeproject.org/experiments/ENCSR433MMU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR433MMU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB078BWW

value: caudate nucleus

value: adult

value: ENCBS226KAB at ENCODE; https://www.encodeproject.org/ENCBS226KAB/


title: Control MPRA from HaCaT (ENCLB542MOD)

description:
https://www.encodeproject.org/experiments/ENCSR849FAC/
***************
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 IRF6 enhancer.
experiment encode accession: ENCSR849FAC
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB542MOD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HaCaT

value: cell line

value: Immortalized human keratinocyte, negative for Bac/Fung/Myc, negative for HIV-1/HBV/HCV

value: 65 year

value: ENCBS878WMS at ENCODE; https://www.encodeproject.org/ENCBS878WMS/


title: DNase-seq from hypothalamus (ENCLB551HEN)

description:
https://www.encodeproject.org/experiments/ENCSR442UYJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR442UYJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB551HEN

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS992POJ at ENCODE; https://www.encodeproject.org/ENCBS992POJ/


title: MPRA from K562 (ENCLB589DIV)

description:
https://www.encodeproject.org/experiments/ENCSR845WND/
***************
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: ENCSR845WND
assay title: MPRA
possible controls: ENCSR166BQV
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB589DIV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS506NZL at ENCODE; https://www.encodeproject.org/ENCBS506NZL/


title: MPRA from HepG2 (ENCLB515AZP)

description:
https://www.encodeproject.org/experiments/ENCSR839LDC/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR839LDC
assay title: MPRA
assembly: hg19
possible controls: ENCSR902NRZ
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB515AZP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: DNase-seq from cerebellum (ENCLB002CMA)

description:
https://www.encodeproject.org/experiments/ENCSR429DNW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR429DNW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB002CMA

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: adult

value: unknown

value: ENCBS144JPC at ENCODE; https://www.encodeproject.org/ENCBS144JPC/


title: DNase-seq from substantia nigra (ENCLB544PBC)

description:
https://www.encodeproject.org/experiments/ENCSR429BZH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR429BZH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB544PBC

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS143HIP at ENCODE; https://www.encodeproject.org/ENCBS143HIP/


title: DNase-seq from cerebellum (ENCLB946BWD)

description:
https://www.encodeproject.org/experiments/ENCSR529ECX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR529ECX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB946BWD

value: female

value: ENCBS341HFQ at ENCODE; https://www.encodeproject.org/ENCBS341HFQ/


title: MPRA from HepG2 (ENCLB984HAX)

description:
https://www.encodeproject.org/experiments/ENCSR839LDC/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR839LDC
assay title: MPRA
assembly: hg19
possible controls: ENCSR902NRZ
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB984HAX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from nucleus accumbens (ENCLB631FNE)

description:
https://www.encodeproject.org/experiments/ENCSR426LAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR426LAJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB631FNE

value: nucleus accumbens

value: ENCBS245AMW at ENCODE; https://www.encodeproject.org/ENCBS245AMW/


title: Control MPRA from HepG2 (ENCLB198RAG)

description:
https://www.encodeproject.org/experiments/ENCSR837DCD/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.
experiment encode accession: ENCSR837DCD
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB198RAG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: DNase-seq from caudate nucleus (ENCLB403FMD)

description:
https://www.encodeproject.org/experiments/ENCSR433MMU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR433MMU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB403FMD

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: adult

value: unknown

value: ENCBS277RBA at ENCODE; https://www.encodeproject.org/ENCBS277RBA/


title: MPRA from HepG2 (ENCLB941SMU)

description:
https://www.encodeproject.org/experiments/ENCSR839LDC/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 5' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR839LDC
assay title: MPRA
assembly: hg19
possible controls: ENCSR902NRZ
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB941SMU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS852YLY at ENCODE; https://www.encodeproject.org/ENCBS852YLY/


title: neonatal sample large 11

city: Duarte

first: Sangeeta

last: Dhawan

address: 1500 E Duarte Rd

department: Translational Research and Cellular Therapeutics

institute: City of Hope

description: Library name: M3_M

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

organism: Mus musculus

source_name: Pancreatic islet

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

tag: tissue

value: Pancreatic islet

tag: batch

value: Batch 1


title: MPRA from K562 (ENCLB114AOK)

description:
https://www.encodeproject.org/experiments/ENCSR845WND/
***************
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: ENCSR845WND
assay title: MPRA
possible controls: ENCSR166BQV
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB114AOK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS327XNR at ENCODE; https://www.encodeproject.org/ENCBS327XNR/


title: Control MPRA from HepG2 (ENCLB390QPN)

description:
https://www.encodeproject.org/experiments/ENCSR837DCD/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.
experiment encode accession: ENCSR837DCD
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB390QPN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: Control MPRA from HepG2 (ENCLB990QQU)

description:
https://www.encodeproject.org/experiments/ENCSR837DCD/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential enhancers from HepG2, K562, and WTC11 cells, and promoters of protein-coding genes.
experiment encode accession: ENCSR837DCD
assay title: Control MPRA
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB990QQU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: DNase-seq from caudate nucleus (ENCLB600FAG)

description:
https://www.encodeproject.org/experiments/ENCSR433MMU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR433MMU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB600FAG

value: caudate nucleus

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS544GIS at ENCODE; https://www.encodeproject.org/ENCBS544GIS/


title: DNase-seq from Ammon's horn (ENCLB551NHT)

description:
https://www.encodeproject.org/experiments/ENCSR423RVG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR423RVG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB551NHT

value: Ammon's horn

value: ENCBS784GLQ at ENCODE; https://www.encodeproject.org/ENCBS784GLQ/


title: DNase-seq from putamen (ENCLB104FTS)

description:
https://www.encodeproject.org/experiments/ENCSR422TKP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR422TKP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB104FTS

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: female

value: ENCBS211TCJ at ENCODE; https://www.encodeproject.org/ENCBS211TCJ/


title: DNase-seq from Ammon's horn (ENCLB644GZL)

description:
https://www.encodeproject.org/experiments/ENCSR422LOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR422LOI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB644GZL

value: male

value: ENCBS990CWV at ENCODE; https://www.encodeproject.org/ENCBS990CWV/


title: MPRA from HEK293T (ENCLB164PVQ)

description:
https://www.encodeproject.org/experiments/ENCSR821FQH/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR821FQH
assay title: MPRA
possible controls: ENCSR916DHS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB164PVQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: embryonic

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HEK293T (ENCLB955CRW)

description:
https://www.encodeproject.org/experiments/ENCSR821FQH/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR821FQH
assay title: MPRA
possible controls: ENCSR916DHS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB955CRW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: MPRA from HEK293T (ENCLB526FNR)

description:
https://www.encodeproject.org/experiments/ENCSR821FQH/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR821FQH
assay title: MPRA
possible controls: ENCSR916DHS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB526FNR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: unknown

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


title: DNase-seq from hypothalamus (ENCLB395EUM)

description:
https://www.encodeproject.org/experiments/ENCSR419TLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR419TLP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB395EUM

value: hypothalamus

value: tissue

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS879HBH at ENCODE; https://www.encodeproject.org/ENCBS879HBH/


title: Control MPRA from SK-MEL-28 (ENCLB657FDY)

description:
https://www.encodeproject.org/experiments/ENCSR814CZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.
experiment encode accession: ENCSR814CZJ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB657FDY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

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

value: 51 year

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


title: DNase-seq from amygdala (ENCLB153EBZ)

description:
https://www.encodeproject.org/experiments/ENCSR421CNQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR421CNQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB153EBZ

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: male

value: ENCBS855ICU at ENCODE; https://www.encodeproject.org/ENCBS855ICU/


title: Control MPRA from SK-MEL-28 (ENCLB119QYV)

description:
https://www.encodeproject.org/experiments/ENCSR814CZJ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.
experiment encode accession: ENCSR814CZJ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB119QYV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from caudate nucleus (ENCLB204XRO)

description:
https://www.encodeproject.org/experiments/ENCSR417NHZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR417NHZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB204XRO

value: caudate nucleus

value: unknown

value: ENCBS956NVK at ENCODE; https://www.encodeproject.org/ENCBS956NVK/


title: DNase-seq from Ammon's horn (ENCLB662HYO)

description:
https://www.encodeproject.org/experiments/ENCSR414DVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR414DVM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB662HYO

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: female

value: adult

value: ENCBS726KJE at ENCODE; https://www.encodeproject.org/ENCBS726KJE/


title: Control MPRA from SK-MEL-28 (ENCLB655HGF)

description:
https://www.encodeproject.org/experiments/ENCSR814CZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the IRF4 enhancer.
experiment encode accession: ENCSR814CZJ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB655HGF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: 51 year

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


title: MPRA from LNCAP (ENCLB577SNN)

description:
https://www.encodeproject.org/experiments/ENCSR812ICI/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs11986220.
experiment encode accession: ENCSR812ICI
assay title: MPRA
possible controls: ENCSR905UEC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB577SNN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: LNCAP

value: male

value: prostate adenocarcinoma

value: 50 year

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


title: DNase-seq from putamen (ENCLB390AXW)

description:
https://www.encodeproject.org/experiments/ENCSR413XPN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR413XPN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB390AXW

value: putamen

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS385RWQ at ENCODE; https://www.encodeproject.org/ENCBS385RWQ/


title: MPRA from LNCAP (ENCLB936LJO)

description:
https://www.encodeproject.org/experiments/ENCSR812ICI/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs11986220.
experiment encode accession: ENCSR812ICI
assay title: MPRA
possible controls: ENCSR905UEC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB936LJO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from anterior cingulate cortex (ENCLB950EBX)

description:
https://www.encodeproject.org/experiments/ENCSR412XNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR412XNT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB950EBX

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: tissue

value: adult

value: unknown

value: ENCBS517ADU at ENCODE; https://www.encodeproject.org/ENCBS517ADU/


title: Control MPRA from glial cell (ENCLB343EGP)

description:
https://www.encodeproject.org/experiments/ENCSR799YAF/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR799YAF
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB343EGP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: glial cell

value: primary cell

value: male

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

value: ENCBS927UKN at ENCODE; https://www.encodeproject.org/ENCBS927UKN/


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB609TRQ)

description:
https://www.encodeproject.org/experiments/ENCSR421GCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR421GCN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB609TRQ

value: C1 segment of cervical spinal cord

value: female

value: John Stamatoyannopoulos, UW

value: ENCBS733JAI at ENCODE; https://www.encodeproject.org/ENCBS733JAI/


title: Control MPRA from glial cell (ENCLB962ZBQ)

description:
https://www.encodeproject.org/experiments/ENCSR799YAF/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR799YAF
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB962ZBQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ENCBS733SEF at ENCODE; https://www.encodeproject.org/ENCBS733SEF/


title: DNase-seq from Ammon's horn (ENCLB426PRX)

description:
https://www.encodeproject.org/experiments/ENCSR404CHS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR404CHS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB426PRX

value: Ammon's horn

value: Kristin Ardlie

value: ENCBS906ZCV at ENCODE; https://www.encodeproject.org/ENCBS906ZCV/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB355PJX)

description:
https://www.encodeproject.org/experiments/ENCSR405CSK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR405CSK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB355PJX

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: ENCBS563NIX at ENCODE; https://www.encodeproject.org/ENCBS563NIX/


title: DNase-seq from cerebellum (ENCLB191UCN)

description:
https://www.encodeproject.org/experiments/ENCSR401GHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR401GHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB191UCN

value: cerebellum

value: unknown

value: ENCBS069KUP at ENCODE; https://www.encodeproject.org/ENCBS069KUP/


title: Control MPRA from glial cell (ENCLB666BST)

description:
https://www.encodeproject.org/experiments/ENCSR799YAF/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR799YAF
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB666BST
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: primary cell

value: male

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

value: ATCC

value: ENCBS819RKG at ENCODE; https://www.encodeproject.org/ENCBS819RKG/


title: MPRA from HepG2 (ENCLB549HSP)

description:
https://www.encodeproject.org/experiments/ENCSR787MOJ/
***************
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: ENCSR787MOJ
assay title: MPRA
assembly: hg19
possible controls: ENCSR642ECM
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB549HSP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ENCBS265FPZ at ENCODE; https://www.encodeproject.org/ENCBS265FPZ/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB555VCU)

description:
https://www.encodeproject.org/experiments/ENCSR397DUU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR397DUU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB555VCU

value: dorsolateral prefrontal cortex

value: tissue

value: female

value: adult

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS096QYD at ENCODE; https://www.encodeproject.org/ENCBS096QYD/


title: DNase-seq from cerebellum (ENCLB890EHI)

description:
https://www.encodeproject.org/experiments/ENCSR401GHH/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR401GHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB890EHI

value: cerebellum

value: male

value: unknown

value: ENCBS845DPW at ENCODE; https://www.encodeproject.org/ENCBS845DPW/


title: DNase-seq from Ammon's horn (ENCLB609ACD)

description:
https://www.encodeproject.org/experiments/ENCSR404CEY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR404CEY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB609ACD

source_name: Homo sapiens male adult Ammon's horn tissue

value: Ammon's horn

value: ENCBS850NKB at ENCODE; https://www.encodeproject.org/ENCBS850NKB/


title: DNase-seq from cerebellum (ENCLB389IGI)

description:
https://www.encodeproject.org/experiments/ENCSR401GHH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR401GHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB389IGI

value: ENCBS441ZYK at ENCODE; https://www.encodeproject.org/ENCBS441ZYK/


title: DNase-seq from caudate nucleus (ENCLB851THE)

description:
https://www.encodeproject.org/experiments/ENCSR397CSB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR397CSB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB851THE

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS077NWW at ENCODE; https://www.encodeproject.org/ENCBS077NWW/


title: MPRA from HepG2 (ENCLB609PTF)

description:
https://www.encodeproject.org/experiments/ENCSR787MOJ/
***************
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: ENCSR787MOJ
assay title: MPRA
assembly: hg19
possible controls: ENCSR642ECM
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB609PTF
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: MPRA from HepG2 (ENCLB547UHH)

description:
https://www.encodeproject.org/experiments/ENCSR787MOJ/
***************
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: ENCSR787MOJ
assay title: MPRA
assembly: hg19
possible controls: ENCSR642ECM
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB547UHH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: MPRA from glial cell (ENCLB234GYI)

description:
https://www.encodeproject.org/experiments/ENCSR782GCT/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR782GCT
assay title: MPRA
possible controls: ENCSR958QFH
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB234GYI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: glial cell

value: primary cell

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

value: adult

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


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB390ZYX)

description:
https://www.encodeproject.org/experiments/ENCSR389ZCR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR389ZCR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB390ZYX

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: male

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS871WNF at ENCODE; https://www.encodeproject.org/ENCBS871WNF/


title: MPRA from glial cell (ENCLB982XHZ)

description:
https://www.encodeproject.org/experiments/ENCSR782GCT/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR782GCT
assay title: MPRA
possible controls: ENCSR958QFH
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB982XHZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: MPRA from glial cell (ENCLB211KIR)

description:
https://www.encodeproject.org/experiments/ENCSR782GCT/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR782GCT
assay title: MPRA
possible controls: ENCSR958QFH
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB211KIR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

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


title: DNase-seq from anterior cingulate cortex (ENCLB576PWR)

description:
https://www.encodeproject.org/experiments/ENCSR395CLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR395CLE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB576PWR

value: anterior cingulate cortex

value: ENCBS366WUN at ENCODE; https://www.encodeproject.org/ENCBS366WUN/


title: MPRA from LNCAP (ENCLB938IYL)

description:
https://www.encodeproject.org/experiments/ENCSR812ICI/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the MYC enhancer around SNP rs11986220.
experiment encode accession: ENCSR812ICI
assay title: MPRA
possible controls: ENCSR905UEC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB938IYL
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: LNCAP

value: cell line

value: prostate adenocarcinoma

value: 50 year

value: ATCC

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


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB126MBT)

description:
https://www.encodeproject.org/experiments/ENCSR389ZCR/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR389ZCR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB126MBT

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: ENCBS927JZA at ENCODE; https://www.encodeproject.org/ENCBS927JZA/


title: DNase-seq from cerebellum (ENCLB159GOZ)

description:
https://www.encodeproject.org/experiments/ENCSR393SRR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR393SRR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB159GOZ

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: female

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS155FEQ at ENCODE; https://www.encodeproject.org/ENCBS155FEQ/


title: Control MPRA from glial cell (ENCLB600FQT)

description:
https://www.encodeproject.org/experiments/ENCSR772XSY/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR772XSY
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB600FQT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: glial cell

value: primary cell

value: male

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

value: Nadav Ahituv, UCSF

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


title: Control MPRA from HEL (ENCLB792ZHA)

description:
https://www.encodeproject.org/experiments/ENCSR769LVZ/
***************
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 HBB promoter.
experiment encode accession: ENCSR769LVZ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB792ZHA
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: ATCC

value: ENCBS137CKZ at ENCODE; https://www.encodeproject.org/ENCBS137CKZ/


title: DNase-seq from anterior cingulate cortex (ENCLB060MCQ)

description:
https://www.encodeproject.org/experiments/ENCSR389MRF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR389MRF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB060MCQ

value: anterior cingulate cortex

value: tissue

value: adult

value: ENCBS391AML at ENCODE; https://www.encodeproject.org/ENCBS391AML/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB334QQN)

description:
https://www.encodeproject.org/experiments/ENCSR389ZCR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR389ZCR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB334QQN

value: dorsolateral prefrontal cortex

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS798PPX at ENCODE; https://www.encodeproject.org/ENCBS798PPX/


title: Control MPRA from glial cell (ENCLB920IYS)

description:
https://www.encodeproject.org/experiments/ENCSR772XSY/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR772XSY
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB920IYS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: primary cell

value: male

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

value: Nadav Ahituv, UCSF

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


title: Control MPRA from glial cell (ENCLB697OYI)

description:
https://www.encodeproject.org/experiments/ENCSR772XSY/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR772XSY
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB697OYI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ATCC

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


title: Control MPRA from HEL (ENCLB136OJD)

description:
https://www.encodeproject.org/experiments/ENCSR769LVZ/
***************
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 HBB promoter.
experiment encode accession: ENCSR769LVZ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB136OJD
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: ENCBS194CGU at ENCODE; https://www.encodeproject.org/ENCBS194CGU/


title: DNase-seq from putamen (ENCLB935OQQ)

description:
https://www.encodeproject.org/experiments/ENCSR386SSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR386SSR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB935OQQ

value: putamen

value: tissue

value: female

value: adult

value: unknown

value: ENCBS375AQF at ENCODE; https://www.encodeproject.org/ENCBS375AQF/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB709NDQ)

description:
https://www.encodeproject.org/experiments/ENCSR384VQA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR384VQA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB709NDQ

value: dorsolateral prefrontal cortex

value: male

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS554IQX at ENCODE; https://www.encodeproject.org/ENCBS554IQX/


title: DNase-seq from cerebellum (ENCLB261LOJ)

description:
https://www.encodeproject.org/experiments/ENCSR383VQO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR383VQO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB261LOJ

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: ENCBS780MKV at ENCODE; https://www.encodeproject.org/ENCBS780MKV/


title: DNase-seq from substantia nigra (ENCLB378FNW)

description:
https://www.encodeproject.org/experiments/ENCSR426CDK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR426CDK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB378FNW

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: ENCBS932ADC at ENCODE; https://www.encodeproject.org/ENCBS932ADC/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB741DUG)

description:
https://www.encodeproject.org/experiments/ENCSR383PEK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR383PEK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB741DUG

value: ENCBS410RGX at ENCODE; https://www.encodeproject.org/ENCBS410RGX/


title: MPRA from HepG2 (ENCLB405ZNR)

description:
https://www.encodeproject.org/experiments/ENCSR760GMX/
***************
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. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR760GMX
assay title: MPRA
assembly: hg19
possible controls: ENCSR118NBQ
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB405ZNR
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: ENCBS468GLN at ENCODE; https://www.encodeproject.org/ENCBS468GLN/


title: DNase-seq from caudate nucleus (ENCLB010QJO)

description:
https://www.encodeproject.org/experiments/ENCSR375VVY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR375VVY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB010QJO

source_name: Homo sapiens male adult caudate nucleus tissue

value: caudate nucleus

value: tissue

value: adult

value: unknown

value: ENCBS194VGA at ENCODE; https://www.encodeproject.org/ENCBS194VGA/


title: MPRA from HepG2 (ENCLB698NYB)

description:
https://www.encodeproject.org/experiments/ENCSR760GMX/
***************
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. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR760GMX
assay title: MPRA
assembly: hg19
possible controls: ENCSR118NBQ
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB698NYB
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: ENCBS551EAN at ENCODE; https://www.encodeproject.org/ENCBS551EAN/


title: DNase-seq from hypothalamus (ENCLB963BCQ)

description:
https://www.encodeproject.org/experiments/ENCSR375RLN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR375RLN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB963BCQ

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS709CZN at ENCODE; https://www.encodeproject.org/ENCBS709CZN/


title: MPRA from glial cell (ENCLB333RVP)

description:
https://www.encodeproject.org/experiments/ENCSR759LCV/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR759LCV
assay title: MPRA
possible controls: ENCSR799YAF
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB333RVP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: primary cell

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

value: ENCBS927UKN at ENCODE; https://www.encodeproject.org/ENCBS927UKN/


title: DNase-seq from caudate nucleus (ENCLB975JGR)

description:
https://www.encodeproject.org/experiments/ENCSR375VVY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR375VVY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB975JGR

value: ENCBS274OBY at ENCODE; https://www.encodeproject.org/ENCBS274OBY/


title: DNase-seq from hypothalamus (ENCLB193VYG)

description:
https://www.encodeproject.org/experiments/ENCSR366PXI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR366PXI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB193VYG

source_name: Homo sapiens female adult hypothalamus tissue

value: female

value: ENCBS820RLL at ENCODE; https://www.encodeproject.org/ENCBS820RLL/


title: Control MPRA from HepG2 (ENCLB486PPD)

description:
https://www.encodeproject.org/experiments/ENCSR752EIG/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of a mix of short, medium, and long elements in parallel.
experiment encode accession: ENCSR752EIG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB486PPD
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: ENCBS223TAZ at ENCODE; https://www.encodeproject.org/ENCBS223TAZ/


title: DNase-seq from substantia nigra (ENCLB101SQP)

description:
https://www.encodeproject.org/experiments/ENCSR369HYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR369HYM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB101SQP

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: tissue

value: male

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS764DAE at ENCODE; https://www.encodeproject.org/ENCBS764DAE/


title: DNase-seq from cerebellum (ENCLB475VJD)

description:
https://www.encodeproject.org/experiments/ENCSR370NOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR370NOI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB475VJD

value: cerebellum

value: Kristin Ardlie

value: ENCBS111WOQ at ENCODE; https://www.encodeproject.org/ENCBS111WOQ/


title: Control MPRA from HepG2 (ENCLB017XJP)

description:
https://www.encodeproject.org/experiments/ENCSR752EIG/
***************
biological replicate number: 4
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of a mix of short, medium, and long elements in parallel.
experiment encode accession: ENCSR752EIG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB017XJP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: ENCBS949OMH at ENCODE; https://www.encodeproject.org/ENCBS949OMH/


title: MPRA from glial cell (ENCLB603CCF)

description:
https://www.encodeproject.org/experiments/ENCSR759LCV/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR759LCV
assay title: MPRA
possible controls: ENCSR799YAF
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB603CCF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: glial cell

value: primary cell

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

value: ENCBS819RKG at ENCODE; https://www.encodeproject.org/ENCBS819RKG/


title: MPRA from glial cell (ENCLB924FKE)

description:
https://www.encodeproject.org/experiments/ENCSR759LCV/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the TERT promoter.
experiment encode accession: ENCSR759LCV
assay title: MPRA
possible controls: ENCSR799YAF
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB924FKE
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS733SEF at ENCODE; https://www.encodeproject.org/ENCBS733SEF/


title: Control MPRA from HEL (ENCLB627KCY)

description:
https://www.encodeproject.org/experiments/ENCSR769LVZ/
***************
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 HBB promoter.
experiment encode accession: ENCSR769LVZ
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB627KCY
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: 30 year

value: ENCBS558IPH at ENCODE; https://www.encodeproject.org/ENCBS558IPH/


title: NDTH tumor 88

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 Cy296

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.

value: lung adenocarcinoma

tag: tumor stage

value: II

tag: age at diagnosis

value: Male


title: NDTH tumor 87

description: genomic DNA from LUAD

label: Cy3 and Cy295

value: I


title: DNase-seq from nucleus accumbens (ENCLB564GXW)

description:
https://www.encodeproject.org/experiments/ENCSR359SKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR359SKY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB564GXW

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS463JTY at ENCODE; https://www.encodeproject.org/ENCBS463JTY/


title: Control MPRA from HepG2 (ENCLB623MFW)

description:
https://www.encodeproject.org/experiments/ENCSR752EIG/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of a mix of short, medium, and long elements in parallel.
experiment encode accession: ENCSR752EIG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB623MFW
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: ENCBS709WHM at ENCODE; https://www.encodeproject.org/ENCBS709WHM/


title: NDTH tumor 86

description: genomic DNA from LUAD

label: Cy3 and Cy294

value: lung adenocarcinoma

value: Male


title: NDTH tumor 84

description: genomic DNA from LUAD

label: Cy3 and Cy292

value: I


title: NDTH tumor 83

description: genomic DNA from LUAD

label: Cy3 and Cy291


title: Control MPRA from HepG2 (ENCLB275ESP)

description:
https://www.encodeproject.org/experiments/ENCSR752EIG/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4 vector upstream of a minimal promoter. Test of a mix of short, medium, and long elements in parallel.
experiment encode accession: ENCSR752EIG
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB275ESP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: ENCBS763SXB at ENCODE; https://www.encodeproject.org/ENCBS763SXB/


title: MPRA from HepG2 (ENCLB983ZFK)

description:
https://www.encodeproject.org/experiments/ENCSR760GMX/
***************
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. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR760GMX
assay title: MPRA
assembly: hg19
possible controls: ENCSR118NBQ
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB983ZFK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS678RFP at ENCODE; https://www.encodeproject.org/ENCBS678RFP/


title: Control MPRA from HepG2 (ENCLB846OJU)

description:
https://www.encodeproject.org/experiments/ENCSR742NIM/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a wild type integrase to allow genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR742NIM
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB846OJU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

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


title: NDTH tumor 85

description: genomic DNA from LUAD

label: Cy3 and Cy293

value: Female


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB500FXL)

description:
https://www.encodeproject.org/experiments/ENCSR362LXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR362LXQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB500FXL

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS673QAR at ENCODE; https://www.encodeproject.org/ENCBS673QAR/


title: Control MPRA from HepG2 (ENCLB464SLO)

description:
https://www.encodeproject.org/experiments/ENCSR742NIM/
***************
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: ENCSR742NIM
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB464SLO
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: ENCBS154QNZ at ENCODE; https://www.encodeproject.org/ENCBS154QNZ/


title: NDTH tumor 82

description: genomic DNA from LUAD

label: Cy3 and Cy290

value: lung adenocarcinoma

value: III

value: Male


title: Control MPRA from HepG2 (ENCLB161MBK)

description:
https://www.encodeproject.org/experiments/ENCSR742NIM/
***************
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: ENCSR742NIM
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB161MBK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

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


title: NDTH tumor 81

description: genomic DNA from LUAD

label: Cy3 and Cy289

value: I


title: NDTH tumor 79

description: genomic DNA from LUAD

label: Cy3 and Cy287


title: NDTH tumor 80

description: genomic DNA from LUAD

label: Cy3 and Cy288


title: DNase-seq from nucleus accumbens (ENCLB725DVI)

description:
https://www.encodeproject.org/experiments/ENCSR359SKY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR359SKY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB725DVI

value: nucleus accumbens

value: tissue

value: female

value: adult

value: unknown

value: ENCBS526DZB at ENCODE; https://www.encodeproject.org/ENCBS526DZB/


title: NDTH tumor 78

description: genomic DNA from LUAD

label: Cy3 and Cy286

value: II

value: Female


title: DNase-seq from hypothalamus (ENCLB550VVO)

description:
https://www.encodeproject.org/experiments/ENCSR366PXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR366PXI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB550VVO

value: hypothalamus

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS948OMT at ENCODE; https://www.encodeproject.org/ENCBS948OMT/


title: NDTH tumor 75

description: genomic DNA from LUAD

label: Cy3 and Cy283

value: lung adenocarcinoma


title: NDTH tumor 76

description: genomic DNA from LUAD

label: Cy3 and Cy284


title: DNase-seq from caudate nucleus (ENCLB152IVY)

description:
https://www.encodeproject.org/experiments/ENCSR356CVQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR356CVQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB152IVY

value: caudate nucleus

value: ENCBS742QJP at ENCODE; https://www.encodeproject.org/ENCBS742QJP/


title: NDTH tumor 77

description: genomic DNA from LUAD

label: Cy3 and Cy285

value: Male


title: MPRA from HepG2 (ENCLB707XYE)

description:
https://www.encodeproject.org/experiments/ENCSR739VGY/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR739VGY
assay title: MPRA
possible controls: ENCSR278KFS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB707XYE
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS693TYP at ENCODE; https://www.encodeproject.org/ENCBS693TYP/


title: NDTH tumor 74

description: genomic DNA from LUAD

label: Cy3 and Cy282

value: III


title: DNase-seq from cerebellum (ENCLB459VNA)

description:
https://www.encodeproject.org/experiments/ENCSR353FCV/
***************
biological replicate number: 2
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: ENCLB459VNA

value: cerebellum

value: tissue

value: adult

value: unknown

value: ENCBS960PNC at ENCODE; https://www.encodeproject.org/ENCBS960PNC/


title: MPRA from HepG2 (ENCLB749AZI)

description:
https://www.encodeproject.org/experiments/ENCSR739VGY/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR739VGY
assay title: MPRA
possible controls: ENCSR278KFS
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB749AZI
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: ENCBS967VOI at ENCODE; https://www.encodeproject.org/ENCBS967VOI/


title: DNase-seq from substantia nigra (ENCLB971OMW)

description:
https://www.encodeproject.org/experiments/ENCSR355WIW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR355WIW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB971OMW

value: substantia nigra

value: female

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS938JRW at ENCODE; https://www.encodeproject.org/ENCBS938JRW/


title: Control MPRA from HepG2 (ENCLB815SSG)

description:
https://www.encodeproject.org/experiments/ENCSR730SAC/
***************
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 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: ENCLB815SSG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS170XWN at ENCODE; https://www.encodeproject.org/ENCBS170XWN/