title: MPRA from HepG2 (ENCLB010RYK)

description:
https://www.encodeproject.org/experiments/ENCSR281FRP/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT enhancer, using 3' to 5' direction.
experiment encode accession: ENCSR281FRP
assay title: MPRA
possible controls: ENCSR730SAC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB010RYK
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: DNase-seq from amygdala (ENCLB300VRC)

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/ENCSR165TAZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR165TAZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB300VRC

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: tissue

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: unknown

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS247GKQ at ENCODE; https://www.encodeproject.org/ENCBS247GKQ/


title: PUMCH tumor 25

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 Cy29

source_name: lung adenocarcinoma

label_protocol: Standard Illumina protocol

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

tag: tissue

value: lung adenocarcinoma

tag: tumor stage

value: II

tag: age at diagnosis

value: Male


title: PUMCH tumor 24

description: genomic DNA from LUAD

label: Cy3 and Cy28

value: III

value: Female


title: PUMCH tumor 29

description: genomic DNA from LUAD

label: Cy3 and Cy33


title: DNase-seq from caudate nucleus (ENCLB365POF)

description:
https://www.encodeproject.org/experiments/ENCSR163CXS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR163CXS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB365POF

source_name: Homo sapiens female adult caudate nucleus tissue

value: caudate nucleus

value: ENCBS610ZBK at ENCODE; https://www.encodeproject.org/ENCBS610ZBK/


title: PUMCH tumor 23

description: genomic DNA from LUAD

label: Cy3 and Cy27

value: I


title: MPRA from HepG2 (ENCLB387ZSU)

description:
https://www.encodeproject.org/experiments/ENCSR281FRP/
***************
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: ENCSR281FRP
assay title: MPRA
possible controls: ENCSR730SAC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB387ZSU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

library_source: transcriptomic

molecule: total RNA

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

tag: line

value: cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PUMCH tumor 22

description: genomic DNA from LUAD

label: Cy3 and Cy26


title: Control MPRA from HepG2 (ENCLB728NPD)

description:
https://www.encodeproject.org/experiments/ENCSR293DMS/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the F9 promoter.
experiment encode accession: ENCSR293DMS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB728NPD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: PUMCH tumor 21

description: genomic DNA from LUAD

label: Cy3 and Cy25

value: lung adenocarcinoma


title: PUMCH tumor 19

description: genomic DNA from LUAD

label: Cy3 and Cy23


title: Control MPRA from HepG2 (ENCLB718JIR)

description:
https://www.encodeproject.org/experiments/ENCSR278KFS/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR278KFS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB718JIR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: PUMCH tumor 20

description: genomic DNA from LUAD

label: Cy3 and Cy24


title: PUMCH tumor 18

description: genomic DNA from LUAD

label: Cy3 and Cy22

value: Male


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB822YUF)

description:
https://www.encodeproject.org/experiments/ENCSR160PPK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR160PPK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB822YUF

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS949FTN at ENCODE; https://www.encodeproject.org/ENCBS949FTN/


title: PUMCH tumor 16

description: genomic DNA from LUAD

label: Cy3 and Cy20

value: I

value: Female


title: PUMCH tumor 17

description: genomic DNA from LUAD

label: Cy3 and Cy21


title: PUMCH tumor 14

description: genomic DNA from LUAD

label: Cy3 and Cy18

value: II


title: MPRA from HaCaT (ENCLB808LNT)

description:
https://www.encodeproject.org/experiments/ENCSR270PHO/
***************
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: ENCSR270PHO
assay title: MPRA
possible controls: ENCSR849FAC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB808LNT
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: male

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

value: 65 year

value: Nadav Ahituv, UCSF

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


title: PUMCH tumor 12

description: genomic DNA from LUAD

label: Cy3 and Cy16

value: lung adenocarcinoma


title: DNase-seq from anterior cingulate cortex (ENCLB104FBC)

description:
https://www.encodeproject.org/experiments/ENCSR157UQY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157UQY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB104FBC

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

value: tissue

value: ENCBS574JTH at ENCODE; https://www.encodeproject.org/ENCBS574JTH/


title: MPRA from HaCaT (ENCLB381EGJ)

description:
https://www.encodeproject.org/experiments/ENCSR270PHO/
***************
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: ENCSR270PHO
assay title: MPRA
possible controls: ENCSR849FAC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB381EGJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: adult

value: ATCC

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


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB826PWH)

description:
https://www.encodeproject.org/experiments/ENCSR160PPK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR160PPK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB826PWH

value: dorsolateral prefrontal cortex

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS158ZUZ at ENCODE; https://www.encodeproject.org/ENCBS158ZUZ/


title: PUMCH tumor 13

description: genomic DNA from LUAD

label: Cy3 and Cy17

value: I

value: Female


title: MPRA from HaCaT (ENCLB005JTR)

description:
https://www.encodeproject.org/experiments/ENCSR270PHO/
***************
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: ENCSR270PHO
assay title: MPRA
possible controls: ENCSR849FAC
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB005JTR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: HaCaT

value: cell line

value: male

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

value: 65 year

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


title: DNase-seq from cerebellum (ENCLB029ICP)

description:
https://www.encodeproject.org/experiments/ENCSR156BWT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR156BWT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB029ICP

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: female

value: ENCBS885DMW at ENCODE; https://www.encodeproject.org/ENCBS885DMW/


title: PUMCH tumor 11

description: genomic DNA from LUAD

label: Cy3 and Cy15

value: lung adenocarcinoma


title: PUMCH tumor 10

description: genomic DNA from LUAD

label: Cy3 and Cy14

value: Male


title: PUMCH tumor 9

description: genomic DNA from LUAD

label: Cy3 and Cy13

value: III


title: PUMCH tumor 8

description: genomic DNA from LUAD

label: Cy3 and Cy12


title: PUMCH tumor 15

description: genomic DNA from LUAD

label: Cy3 and Cy19


title: Control MPRA from HepG2 (ENCLB601HVC)

description:
https://www.encodeproject.org/experiments/ENCSR278KFS/
***************
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: ENCSR278KFS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB601HVC
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from hypothalamus (ENCLB856ZVA)

description:
https://www.encodeproject.org/experiments/ENCSR148TWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR148TWM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB856ZVA

source_name: Homo sapiens female adult hypothalamus tissue

value: hypothalamus

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS623CUQ at ENCODE; https://www.encodeproject.org/ENCBS623CUQ/


title: Control MPRA from HepG2 (ENCLB044FSE)

description:
https://www.encodeproject.org/experiments/ENCSR278KFS/
***************
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: ENCSR278KFS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB044FSE
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

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


title: PUMCH tumor 7

description: genomic DNA from LUAD

label: Cy3 and Cy11

value: lung adenocarcinoma

value: Female


title: MPRA from HepG2 (ENCLB148XBH)

description:
https://www.encodeproject.org/experiments/ENCSR259LFO/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR259LFO
assay title: MPRA
possible controls: ENCSR542KWX
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB148XBH
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

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


title: DNase-seq from putamen (ENCLB863FRF)

description:
https://www.encodeproject.org/experiments/ENCSR147XZQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147XZQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB863FRF

source_name: Homo sapiens female adult putamen tissue

value: putamen

value: tissue

value: female

value: ENCBS305PUH at ENCODE; https://www.encodeproject.org/ENCBS305PUH/


title: PUMCH tumor 6

description: genomic DNA from LUAD

label: Cy3 and Cy10

value: I


title: MPRA from HepG2 (ENCLB698LRS)

description:
https://www.encodeproject.org/experiments/ENCSR259LFO/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR259LFO
assay title: MPRA
possible controls: ENCSR542KWX
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB698LRS
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PUMCH tumor 4

description: genomic DNA from LUAD

label: Cy3 and Cy8

value: III

value: Male


title: MPRA from HepG2 (ENCLB877JUQ)

description:
https://www.encodeproject.org/experiments/ENCSR259LFO/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the pGL4.23 vector upstream of a minimal promoter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the SORT1 enhancer.
experiment encode accession: ENCSR259LFO
assay title: MPRA
possible controls: ENCSR542KWX
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB877JUQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: ENCBS316VVP at ENCODE; https://www.encodeproject.org/ENCBS316VVP/


title: DNase-seq from hypothalamus (ENCLB043UPP)

description:
https://www.encodeproject.org/experiments/ENCSR144RDG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR144RDG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB043UPP

value: hypothalamus

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS424ZXK at ENCODE; https://www.encodeproject.org/ENCBS424ZXK/


title: MPRA from HepG2 (ENCLB985NKW)

description:
https://www.encodeproject.org/experiments/ENCSR255GVC/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR255GVC
assay title: MPRA
assembly: hg19
possible controls: ENCSR932ZCL
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB985NKW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: hepatocellular carcinoma

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


title: DNase-seq from substantia nigra (ENCLB583FSA)

description:
https://www.encodeproject.org/experiments/ENCSR143VEP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR143VEP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB583FSA

source_name: Homo sapiens male adult substantia nigra tissue

value: substantia nigra

value: tissue

value: ENCBS250HMW at ENCODE; https://www.encodeproject.org/ENCBS250HMW/


title: PUMCH tumor 3

description: genomic DNA from LUAD

label: Cy3 and Cy7

value: lung adenocarcinoma

value: I

value: Female


title: PUMCH tumor 2

description: genomic DNA from LUAD

label: Cy3 and Cy6

value: III


title: DNase-seq from hypothalamus (ENCLB332BXE)

description:
https://www.encodeproject.org/experiments/ENCSR148TWM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR148TWM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB332BXE

value: female

value: ENCBS800XNV at ENCODE; https://www.encodeproject.org/ENCBS800XNV/


title: PTPN11 Y279C, Day 26 Fibrosa VICs

city: New York

first: Clifford

middle: Z.

last: Liu

state: NY

address: 1470 Madison Ave, Hess 8-301

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Sample 11

library_source: transcriptomic single cell

data_processing:
Sequencing was performed in paired-end mode on NovaSeq instrument (Illumina) to a target depth of 50,000-100,000 reads per cell. Sequencing data was aligned and quantified with Cell Ranger Single-Cell Software Suite (v7.1.0, 10X Genomics).
Assembly: GRCh38 reference genome
Supplementary files format and content: Processed Cell Ranger files are outputted as filtered or unfiltered (raw), with each set consisting of a "barcodes.tsv.gz", "features.tsv.gz", and "matrix.mtx.gz" files.

source_name: iPSC differentiated

extract_protocol:
Gel-bead in emulsions (GEMs) were generated on the Chromium controller sample chip (10X Genomics) using live cell samples with an input of ~10,000 cells. Barcoded cDNA was then extracted from the GEMs by post-GEM RT-cleanup and amplified for 12 cycles.
Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the maufacturer's protocol. Libraries were quantified with Bioanalyzer (Agilent) and QuBit (ThermoFisher) analysis.

value: iPSC differentiated

tag: cell line

tag: cell type

value: Valvular Interstitial Cells

tag: genotype


title: PUMCH tumor 1

description: genomic DNA from LUAD

label: Cy3 and Cy5


title: PTPN11 N308D, Day 26 Fibrosa VICs

description: Library name: Sample 8


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB808LAF)

description:
https://www.encodeproject.org/experiments/ENCSR141HQJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR141HQJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB808LAF

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: adult

value: unknown

value: ENCBS285WVB at ENCODE; https://www.encodeproject.org/ENCBS285WVB/


title: MPRA from WTC11 (ENCLB553CIN)

description:
https://www.encodeproject.org/experiments/ENCSR244FWB/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential WTC11 enhancers and promoters of protein-coding genes.
experiment encode accession: ENCSR244FWB
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR653CPO
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB553CIN
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: cell line

value: male

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from WTC11 (ENCLB096RIQ)

description:
https://www.encodeproject.org/experiments/ENCSR244FWB/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential WTC11 enhancers and promoters of protein-coding genes.
experiment encode accession: ENCSR244FWB
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR653CPO
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB096RIQ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: DNase-seq from hypothalamus (ENCLB716WVE)

description:
https://www.encodeproject.org/experiments/ENCSR143CJJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR143CJJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB716WVE

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: tissue

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS460YUH at ENCODE; https://www.encodeproject.org/ENCBS460YUH/


title: PTPN11 N308D, Day 26 Spongiosa VICs

description: Library name: Sample 9

value: iPSC differentiated

value: Valvular Interstitial Cells


title: PUMCH tumor 5

description: genomic DNA from LUAD

label: Cy3 and Cy9

value: lung adenocarcinoma

value: I

value: Male


title: DNase-seq from amygdala (ENCLB019LOP)

description:
https://www.encodeproject.org/experiments/ENCSR141UWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR141UWM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB019LOP

value: amygdala

value: female

value: adult

value: unknown

value: ENCBS245XPI at ENCODE; https://www.encodeproject.org/ENCBS245XPI/


title: DNase-seq from cerebellum (ENCLB516UGU)

description:
https://www.encodeproject.org/experiments/ENCSR137NDN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR137NDN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB516UGU

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: male

value: ENCBS682PAF at ENCODE; https://www.encodeproject.org/ENCBS682PAF/


title: MPRA from WTC11 (ENCLB508BFJ)

description:
https://www.encodeproject.org/experiments/ENCSR244FWB/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential WTC11 enhancers and promoters of protein-coding genes.
experiment encode accession: ENCSR244FWB
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR653CPO
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB508BFJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HepG2 (ENCLB219LBZ)

description:
https://www.encodeproject.org/experiments/ENCSR255GVC/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR255GVC
assay title: MPRA
assembly: hg19
possible controls: ENCSR932ZCL
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB219LBZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: RAF1 S257L, Day 26 Spongiosa VICs

description: Library name: Sample 6

value: iPSC differentiated

value: Valvular Interstitial Cells


title: PTPN11 N308D, Day 14 Endocardial

description: Library name: Sample 7

value: Endocardial


title: DNase-seq from amygdala (ENCLB732DQT)

description:
https://www.encodeproject.org/experiments/ENCSR136FJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136FJS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB732DQT

source_name: Homo sapiens male adult amygdala tissue

value: amygdala

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS861MXE at ENCODE; https://www.encodeproject.org/ENCBS861MXE/


title: MPRA from HepG2 (ENCLB950LVT)

description:
https://www.encodeproject.org/experiments/ENCSR215YXA/
***************
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: ENCSR215YXA
assay title: MPRA
assembly: hg19
possible controls: ENCSR752EIG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB950LVT
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: Nadav Ahituv, UCSF

value: ENCBS709WHM at ENCODE; https://www.encodeproject.org/ENCBS709WHM/


title: PTPN11 Y279C, Day 14 Endocardial

description: Library name: Sample 10


title: MPRA from HepG2 (ENCLB960GEO)

description:
https://www.encodeproject.org/experiments/ENCSR255GVC/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements and barcodes cloned into the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR255GVC
assay title: MPRA
assembly: hg19
possible controls: ENCSR932ZCL
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB960GEO
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: ATCC

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


title: DNase-seq from substantia nigra (ENCLB843LEI)

description:
https://www.encodeproject.org/experiments/ENCSR135UCR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR135UCR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB843LEI

source_name: Homo sapiens female adult substantia nigra tissue

value: substantia nigra

value: female

value: ENCBS028ASQ at ENCODE; https://www.encodeproject.org/ENCBS028ASQ/


title: DNase-seq from cerebellum (ENCLB116EJT)

description:
https://www.encodeproject.org/experiments/ENCSR136ECA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136ECA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB116EJT

value: cerebellum

value: tissue

value: ENCBS311PXY at ENCODE; https://www.encodeproject.org/ENCBS311PXY/


title: MPRA from HepG2 (ENCLB536YAW)

description:
https://www.encodeproject.org/experiments/ENCSR215YXA/
***************
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: ENCSR215YXA
assay title: MPRA
assembly: hg19
possible controls: ENCSR752EIG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB536YAW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: 15 year

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


title: WT (unedited control), Day 26 Fibrosa VICs

description: Library name: Sample 2

value: iPSC differentiated

value: Valvular Interstitial Cells

value: WT (Control)


title: WT (unedited control), Day 14 Endocardial

description: Library name: Sample 1

value: Endocardial


title: RAF1 S257L, Day 26 Fibrosa VICs

description: Library name: Sample 5


title: RAF1 S257L, Day 14 Endocardial

description: Library name: Sample 4


title: WT (unedited control), Day 26 Spongiosa VICs

description: Library name: Sample 3


title: CART19_VX800_CD8_D03

city: Chicago

first: James

last: LaBelle

state: IL

address: 900 East 57th Street, KCBD 5122

institute: University of Chicago

description:
Library name: CART19_VX800_CD8_D03
JL-NA-1s-12

data_processing:
End-to-end read processing was applied using nf-core/rnaseq
Assembly: GRCh38
Supplementary files format and content: Tab delimited text file with gene counts: salmon.merged.gene_counts.tsv
Supplementary files format and content: tab delimited text file with TPM normalized gene counts: salmon.merged.gene_tpm.tsv

molecule: polyA RNA

source_name: Lymphocytes

growth_protocol: Cells were grown in culture for 13 days with complete RPMI with a 1:1 cell:bead ratio with anti-CD3/CD28 dynabeads and 500U/mL recombinant IL-2. Cells were incubated in a 5% CO2 incubator at 37.0°C.

extract_protocol:
RNA extraction
RNA was quantified via the Qubit RNA HS Assay Kit (Invitrogen, Q32852), and quality-assessed for integrity via High Sensitivity RNA ScreenTape (Agilent, 5067-5579). 500 ng high-quality RNA with a RIN score > 7 of each sample was used for library preparation using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760S). Libraries were prepared according to manufacturer protocols. All libraries were quantified via the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851), quality-checked for fragment sizes via High Sensitivity D5000 ScreenTapes (Agilent, 5067-5592), pooled, and sequenced (Illumina, NovaSeq X).

treatment_protocol: Cells were treated with either 0.1% DMSO or 800nM venetoclax on days 2,5,6,7,8,9,10 of the growth period

value: Lymphocytes

value: CD8+ CAR T-cells

tag: treatment

value: 800nM Venetoclax


title: CART19_VX800_CD8_D02

description:
Library name: CART19_VX800_CD8_D02
JL-NA-1s-11


title: CART19_VX800_CD8_D01

description:
Library name: CART19_VX800_CD8_D01
JL-NA-1s-10


title: MPRA from HepG2 (ENCLB341HPF)

description:
https://www.encodeproject.org/experiments/ENCSR215YXA/
***************
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: ENCSR215YXA
assay title: MPRA
assembly: hg19
possible controls: ENCSR752EIG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB341HPF
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

tag: biosample encode accession

value: male

value: hepatocellular carcinoma

value: child

value: Nadav Ahituv, UCSF

value: ATCC

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


title: PTPN11 Y279C, Day 26 Spongiosa VICs

description: Library name: Sample 12


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB652AMH)

description:
https://www.encodeproject.org/experiments/ENCSR134TVI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR134TVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB652AMH

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

value: C1 segment of cervical spinal cord

value: tissue

tag: encode accession

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS661VXG at ENCODE; https://www.encodeproject.org/ENCBS661VXG/


title: CART19_DMSO_CD8_D03

description:
Library name: CART19_DMSO_CD8_D03
JL-NA-1s-09

value: Lymphocytes

value: 0.1% DMSO


title: CART19_DMSO_CD8_D02

description:
Library name: CART19_DMSO_CD8_D02
JL-NA-1s-08

value: CD8+ CAR T-cells


title: CART19_DMSO_CD8_D01

description:
Library name: CART19_DMSO_CD8_D01
JL-NA-1s-07


title: CART19_VX800_CD4_D03

description:
Library name: CART19_VX800_CD4_D03
JL-NA-1s-06

value: CD4+ CAR T-cells

value: 800nM Venetoclax


title: MPRA from HepG2 (ENCLB218THX)

description:
https://www.encodeproject.org/experiments/ENCSR208DGH/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR208DGH
assay title: MPRA
assembly: hg19
possible controls: ENCSR335DOI
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB218THX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

tag: Sex

value: male

value: hepatocellular carcinoma

value: 15 year

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


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB492JVI)

description:
https://www.encodeproject.org/experiments/ENCSR134TVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR134TVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB492JVI

value: C1 segment of cervical spinal cord

tag: dev stage

value: ENCBS451VZY at ENCODE; https://www.encodeproject.org/ENCBS451VZY/


title: CART19_VX800_CD4_D01

description:
Library name: CART19_VX800_CD4_D01
JL-NA-1s-04


title: CART19_VX800_CD4_D02

description:
Library name: CART19_VX800_CD4_D02
JL-NA-1s-05


title: MPRA from HepG2 (ENCLB987IYU)

description:
https://www.encodeproject.org/experiments/ENCSR208DGH/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR208DGH
assay title: MPRA
assembly: hg19
possible controls: ENCSR335DOI
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB987IYU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: child

tag: age

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HepG2 (ENCLB292ZLX)

description:
https://www.encodeproject.org/experiments/ENCSR215YXA/
***************
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: ENCSR215YXA
assay title: MPRA
assembly: hg19
possible controls: ENCSR752EIG
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB292ZLX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

tag: lab

value: ENCBS223TAZ at ENCODE; https://www.encodeproject.org/ENCBS223TAZ/


title: CART19_DMSO_CD4_D03

description:
Library name: CART19_DMSO_CD4_D03
JL-NA-1s-03

value: Lymphocytes


title: DNase-seq from anterior cingulate cortex (ENCLB288JSA)

description:
https://www.encodeproject.org/experiments/ENCSR135EKC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR135EKC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB288JSA

value: anterior cingulate cortex

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

tag: source

value: Kristin Ardlie

value: ENCBS672EUT at ENCODE; https://www.encodeproject.org/ENCBS672EUT/


title: MPRA from HepG2 (ENCLB316CYF)

description:
https://www.encodeproject.org/experiments/ENCSR208DGH/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the ORI (STARR-seq lacking a minimal promoter) vector, with both elements and barcodes cloned into the 3' UTR. Tested in the same batch as ORI_b2, using primers around the full element and barcode to circumvent the possible detection of artifacts emerging from transcription initiation internal to the upstream element.
experiment encode accession: ENCSR208DGH
assay title: MPRA
assembly: hg19
possible controls: ENCSR335DOI
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB316CYF
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: 15 year

tag: link

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


title: CART19_DMSO_CD4_D02

description:
Library name: CART19_DMSO_CD4_D02
JL-NA-1s-02

tag: tissue

value: CD4+ CAR T-cells

value: 0.1% DMSO


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB101FCU)

description:
https://www.encodeproject.org/experiments/ENCSR134TVI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR134TVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB101FCU

value: C1 segment of cervical spinal cord

value: ENCBS702WEJ at ENCODE; https://www.encodeproject.org/ENCBS702WEJ/


title: MPRA from K562 (ENCLB720QMU)

description:
https://www.encodeproject.org/experiments/ENCSR203UFY/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR203UFY
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR897BXT
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB720QMU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from nucleus accumbens (ENCLB393VFW)

description:
https://www.encodeproject.org/experiments/ENCSR132UYU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR132UYU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB393VFW

source_name: Homo sapiens female adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS219JBW at ENCODE; https://www.encodeproject.org/ENCBS219JBW/


title: CART19_DMSO_CD4_D01

description:
Library name: CART19_DMSO_CD4_D01
JL-NA-1s-01

value: Lymphocytes

value: CD4+ CAR T-cells


title: MPRA from K562 (ENCLB300NVP)

description:
https://www.encodeproject.org/experiments/ENCSR203UFY/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR203UFY
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR897BXT
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB300NVP
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

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


title: MDA-MB-231-WT-2

city: hyderabad

first: Ramesh

last: Ummanni

state: Telangana

address: Tarnaka

department: Applied Biology

country: India

institute: CSIR-Indian Institute of Chemical Technology

description: Library name: Sample2

data_processing:
Adapter sequences and low-quality bases were trimmed using Trim Galore v0.6.6.
Clean reads were aligned to the human genome (GRCh38/hg38) using STAR v2.7.9a.
Gene-level counts were obtained with HTSeq-count v0.13.5.
Low-expression genes (<10 total reads across all samples) were filtered out.
Counts were normalized using DESeq2 rlog transformation
Assembly: Homo sapiens reference genome GRCh38 (hg38)
Supplementary files format and content: CSV files include raw counts for each Sample

source_name: Breast

growth_protocol: MDA-MB-231 parental cells and its resistant derivatives MDA-MB-231/DREVE and MAD-MB-231/DRRIDA were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. RNA integrity and quality were assessed using the Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Parental MDA-MB-231 cells received no drug treatment. Resistant derivatives were continuously cultured in the presence of either 20 µM everolimus (MDA-MB-231/DREVE) or 30 µM ridaforolimus (MDA-MB-231/DRRIDA) for several months to establish stable resistance prior to RNA extraction

value: Breast

value: TNBC,Mesenchymal Stem like

tag: phenotype

value: Wild type

value: DMSO


title: DNase-seq from cerebellum (ENCLB202MAH)

description:
https://www.encodeproject.org/experiments/ENCSR132DSW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR132DSW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB202MAH

value: cerebellum

value: male

value: ENCBS893TMT at ENCODE; https://www.encodeproject.org/ENCBS893TMT/


title: MDA-MB-231-DR_RIDA-2

description: Library name: Sample6

value: Ridaforolimus Resistant

value: Ridaforolimus 30µM


title: MDA-MB-231-DR_RIDA-1

description: Library name: Sample5


title: DNase-seq from nucleus accumbens (ENCLB478LOU)

description:
https://www.encodeproject.org/experiments/ENCSR129UPE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR129UPE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB478LOU

value: nucleus accumbens

value: tissue

value: female

value: adult

value: unknown

value: ENCBS077SPX at ENCODE; https://www.encodeproject.org/ENCBS077SPX/


title: MDA-MB-231-DR_EVE-2

description: Library name: Sample4

value: Everolimus Resistant

value: Everolimus 20µM


title: MPRA from K562 (ENCLB492ZGU)

description:
https://www.encodeproject.org/experiments/ENCSR203UFY/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test potential HepG2, K562, and WTC11 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR203UFY
assay title: MPRA
assembly: GRCh38
possible controls: ENCSR897BXT
encode release date: 2023-12-21
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB492ZGU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HepG2 (ENCLB646XKW)

description:
https://www.encodeproject.org/experiments/ENCSR202CHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR202CHZ
assay title: MPRA
assembly: hg19
possible controls: ENCSR990ZAU
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB646XKW
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

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


title: MDA-MB-231-WT-1

description: Library name: Sample1

value: Breast

value: TNBC,Mesenchymal Stem like

value: Wild type

value: DMSO


title: MDA-MB-231-DR_EVE-1

description: Library name: Sample3

value: Everolimus Resistant


title: DNase-seq from nucleus accumbens (ENCLB710FXQ)

description:
https://www.encodeproject.org/experiments/ENCSR128PGE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR128PGE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB710FXQ

source_name: Homo sapiens male adult nucleus accumbens tissue

value: nucleus accumbens

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS636KSG at ENCODE; https://www.encodeproject.org/ENCBS636KSG/


title: MPRA from HepG2 (ENCLB040URD)

description:
https://www.encodeproject.org/experiments/ENCSR202CHZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR202CHZ
assay title: MPRA
assembly: hg19
possible controls: ENCSR990ZAU
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB040URD
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: Nadav Ahituv, UCSF

value: ATCC

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


title: MPRA from HepG2 (ENCLB918KZJ)

description:
https://www.encodeproject.org/experiments/ENCSR202CHZ/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned upstream of the reporter's minimal promoter, with barcode located in the 3' UTR of a reporter in a lentiviral vector, using a mutant integrase to prevent genomic integration. One of nine methods testing element activity in parallel.
experiment encode accession: ENCSR202CHZ
assay title: MPRA
assembly: hg19
possible controls: ENCSR990ZAU
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB918KZJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: hepatocellular carcinoma

value: child

value: 15 year

value: ENCBS837XYC at ENCODE; https://www.encodeproject.org/ENCBS837XYC/


title: DNase-seq from nucleus accumbens (ENCLB937AYX)

description:
https://www.encodeproject.org/experiments/ENCSR127BQL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR127BQL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB937AYX

value: ENCBS881KFN at ENCODE; https://www.encodeproject.org/ENCBS881KFN/


title: MPRA from HEL (ENCLB775TIH)

description:
https://www.encodeproject.org/experiments/ENCSR200LXA/
***************
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: ENCSR200LXA
assay title: MPRA
possible controls: ENCSR769LVZ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB775TIH
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: ENCBS137CKZ at ENCODE; https://www.encodeproject.org/ENCBS137CKZ/


title: DNase-seq from cerebellum (ENCLB075MKB)

description:
https://www.encodeproject.org/experiments/ENCSR132DSW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR132DSW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB075MKB

value: cerebellum

value: tissue

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: ENCBS893XZS at ENCODE; https://www.encodeproject.org/ENCBS893XZS/


title: DNase-seq from amygdala (ENCLB223XWZ)

description:
https://www.encodeproject.org/experiments/ENCSR126ZZQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR126ZZQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB223XWZ

source_name: Homo sapiens female adult amygdala tissue

value: amygdala

value: female

value: Kristin Ardlie

value: ENCBS231EGS at ENCODE; https://www.encodeproject.org/ENCBS231EGS/


title: MPRA from HEL (ENCLB999TLG)

description:
https://www.encodeproject.org/experiments/ENCSR200LXA/
***************
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: ENCSR200LXA
assay title: MPRA
possible controls: ENCSR769LVZ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB999TLG
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: Nadav Ahituv, UCSF

value: ATCC

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


title: DNase-seq from nucleus accumbens (ENCLB500HAU)

description:
https://www.encodeproject.org/experiments/ENCSR125FPU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125FPU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB500HAU

value: nucleus accumbens

value: ENCBS305UFW at ENCODE; https://www.encodeproject.org/ENCBS305UFW/


title: thoracic aorta rep4

type: RNA

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
gene expression data of adult mouse thoracic aorta
5902-Aorta 09062010 P4

hyb_protocol: A mixture of purified and fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse Gene 1.0 ST arrays followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.34.0) of Bioconductor. Expression values are represented on a log2-scale.

label: biotin

organism: Mus musculus

source_name: thoracic aorta

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 500 pg of total RNA was amplified and converted to single-stranded antisense cDNA using the NuGEN WT-Ovation Pico RNA Amplification System v1.0. Subsequently, the anti-sense cDNA was converted to the sense orientation using the NuGEN WT-Ovation Exon Module. cDNA was fragmented  and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2. All steps were carried out according to the manufacturers protocol (NuGEN).

growth_protocol: Cells were isolated from tissues directly in RNA lysis buffer without culturing them.

extract_protocol: Thoracic aorta and vena cava from Tie2-GFP mice were dissected out, pooled and placed in ice-cold MCDB131 medium (Gibco). Excess fat and contaminating tissue surrounding the vessels were removed and vessels were cut into small pieces prior to incubation in ice-cold PBS containing 2 mg/mL crude collagenase extract (Roche) at 37°C until fully dissociated. Digests were repeatedly shaken, filtered through a 100 µm nylon mesh (BD Biosciences) and spun down (600 g, 7 minutes). Arterial and venous single cell suspensions were then resuspended in PBS supplemented with 1% bovine serum albumin (BSA) and run through a FACS AriaTM device (Beckton Dickinson) to sort the endothelial (GFP+) cell fraction. Cells were collected in RNA lysis buffer. RNA was extracted using the RNeasy minikit (Qiagen). The quality and purity of the RNA samples was analysed with a Bioanalyser 2100.

treatment_protocol: Cells were isolated from untreated mice.

value: thoracic aorta

tag: analysed cell fraction

value: GFP positive

tag: developmental stage

value: adult (8-12 weeks old)


title: DNase-seq from nucleus accumbens (ENCLB940DDE)

description:
https://www.encodeproject.org/experiments/ENCSR127BQL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR127BQL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB940DDE

value: tissue

value: adult

value: unknown

value: ENCBS874HPN at ENCODE; https://www.encodeproject.org/ENCBS874HPN/


title: snATAC-seq from heart (ENCLB513ZTV)

description:
https://www.encodeproject.org/experiments/ENCSR890TGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR890TGR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB513ZTV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (73 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

tag: note

value: Homo sapiens heart tissue

value: female

value: embryonic

value: 73 day

value: Michael Snyder, Stanford

tag: subcellular fraction term name

value: nucleus

value: BDRL

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS539UEJ at ENCODE; https://www.encodeproject.org/ENCBS539UEJ/


title: vena cava rep3

description:
gene expression data of adult mouse vena cava
17.03 VC P2-17032010

source_name: vena cava

value: vena cava

tag: genotype


title: snATAC-seq from liver (ENCLB340MGH)

description:
https://www.encodeproject.org/experiments/ENCSR825WYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR825WYQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB340MGH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (45 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

tag: biosample encode accession

value: Homo sapiens liver tissue?

value: male

tag: health state

value: healthy

value: 45 year

value: Yiing Lin, MD, PhD

value: ENCBS475QWU at ENCODE; https://www.encodeproject.org/ENCBS475QWU/


title: MPRA from HEL (ENCLB358FAJ)

description:
https://www.encodeproject.org/experiments/ENCSR200LXA/
***************
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: ENCSR200LXA
assay title: MPRA
possible controls: ENCSR769LVZ
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB358FAJ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

tag: line

value: HEL

value: cell line

tag: encode accession

tag: Sex

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

value: adult

value: 30 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS194CGU at ENCODE; https://www.encodeproject.org/ENCBS194CGU/


title: Control MPRA from K562 (ENCLB402CFM)

description:
https://www.encodeproject.org/experiments/ENCSR186NQR/
***************
biological replicate number: 3
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR186NQR
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB402CFM
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

tag: age

value: 53 year

tag: lab

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


title: vena cava rep5

description:
gene expression data of adult mouse vena cava
5912-Vena Cava 18062010 P4

tag: tissue

value: vena cava

value: GFP positive

value: adult (8-12 weeks old)


title: snATAC-seq from heart (ENCLB790EOO)

description:
https://www.encodeproject.org/experiments/ENCSR805DID/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR805DID
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB790EOO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (127 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: tissue

value: Homo sapiens heart tissue

value: embryonic

value: 127 day

value: Michael Snyder, Stanford

value: nucleus

tag: source

value: BDRL

value: not applicable

tag: link

value: ENCBS869CTV at ENCODE; https://www.encodeproject.org/ENCBS869CTV/


title: thoracic aorta rep2

description:
gene expression data of adult mouse thoracic aorta
15.03 A P2-15032010

value: thoracic aorta

tag: analysed cell fraction

tag: developmental stage


title: DNase-seq from putamen (ENCLB694DEE)

description:
https://www.encodeproject.org/experiments/ENCSR120MHH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR120MHH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB694DEE

source_name: Homo sapiens male adult putamen tissue

value: putamen

value: male

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS590RNA at ENCODE; https://www.encodeproject.org/ENCBS590RNA/


title: vena cava rep2

description:
gene expression data of adult mouse vena cava
15.03 VC P2-15032010

value: vena cava

value: GFP positive

value: adult (8-12 weeks old)


title: snATAC-seq from heart (ENCLB011MIF)

description:
https://www.encodeproject.org/experiments/ENCSR715JSZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR715JSZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB011MIF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male embryo (94 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: tissue

tag: note

value: Homo sapiens heart tissue

value: embryonic

value: 94 day

tag: subcellular fraction term name

value: ENCBS104EDP at ENCODE; https://www.encodeproject.org/ENCBS104EDP/


title: Control MPRA from K562 (ENCLB858YYP)

description:
https://www.encodeproject.org/experiments/ENCSR186NQR/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR186NQR
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB858YYP
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: ENCBS220LJR at ENCODE; https://www.encodeproject.org/ENCBS220LJR/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB657AQH)

description:
https://www.encodeproject.org/experiments/ENCSR159GVI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR159GVI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB657AQH

source_name: Homo sapiens male adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: male

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS602CGY at ENCODE; https://www.encodeproject.org/ENCBS602CGY/


title: Control MPRA from K562 (ENCLB295SZU)

description:
https://www.encodeproject.org/experiments/ENCSR186NQR/
***************
biological replicate number: 2
technical replicate number: 1
description: Elements cloned into the lentiMPRA vector upstream of a minimal promoter, with barcode located in the 5' UTR of the reporter. Elements test K562 enhancers and promoters of all protein-coding genes.
experiment encode accession: ENCSR186NQR
assay title: Control MPRA
encode release date: 2021-09-01
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB295SZU
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: DNase-seq from amygdala (ENCLB448PHB)

description:
https://www.encodeproject.org/experiments/ENCSR115LHB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR115LHB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB448PHB

value: amygdala

value: tissue

value: ENCBS819SVJ at ENCODE; https://www.encodeproject.org/ENCBS819SVJ/


title: snATAC-seq from liver (ENCLB543EXO)

description:
https://www.encodeproject.org/experiments/ENCSR659ANG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR659ANG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB543EXO
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (31 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: Homo sapiens liver tissue?

value: healthy

value: 31 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS856BWW at ENCODE; https://www.encodeproject.org/ENCBS856BWW/


title: snATAC-seq from liver (ENCLB695SXF)

description:
https://www.encodeproject.org/experiments/ENCSR650BBI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR650BBI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB695SXF
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (51 years) liver tissue, preserved by flash-freezing nuclear fraction

tag: biosample encode accession

value: female

value: adult

value: 51 year

value: ENCBS330QQM at ENCODE; https://www.encodeproject.org/ENCBS330QQM/


title: vena cava rep4

description:
gene expression data of adult mouse vena cava
5904-Vena Cava 09062010 P4

value: vena cava

tag: genotype

value: GFP positive

value: adult (8-12 weeks old)


title: DNase-seq from Ammon's horn (ENCLB336BYO)

description:
https://www.encodeproject.org/experiments/ENCSR117RUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR117RUZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB336BYO

source_name: Homo sapiens female adult Ammon's horn tissue

value: Ammon's horn

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS421YJO at ENCODE; https://www.encodeproject.org/ENCBS421YJO/


title: thoracic aorta rep1

description:
gene expression data of adult mouse thoracic aorta
A P2-24022010

value: thoracic aorta


title: thoracic aorta rep5

description:
gene expression data of adult mouse thoracic aorta
5910-Aorta 18062010 P4


title: DNase-seq from nucleus accumbens (ENCLB872FWF)

description:
https://www.encodeproject.org/experiments/ENCSR113ZKW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR113ZKW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB872FWF

value: nucleus accumbens

value: ENCBS063GVP at ENCODE; https://www.encodeproject.org/ENCBS063GVP/


title: snATAC-seq from liver (ENCLB025VSY)

description:
https://www.encodeproject.org/experiments/ENCSR552QVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR552QVU
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB025VSY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (18 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: Homo sapiens liver tissue?

value: male

tag: health state

value: healthy

value: 18 year

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: not applicable

value: ENCBS882OYS at ENCODE; https://www.encodeproject.org/ENCBS882OYS/


title: Control MPRA from K562 (ENCLB283DYX)

description:
https://www.encodeproject.org/experiments/ENCSR166BQV/
***************
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: ENCSR166BQV
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB283DYX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

tag: line

value: cell line

tag: encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: thoracic aorta rep3

description:
gene expression data of adult mouse thoracic aorta
17.03 A P2-17032010

value: thoracic aorta

value: GFP positive

value: adult (8-12 weeks old)


title: snATAC-seq from liver (ENCLB100CRC)

description:
https://www.encodeproject.org/experiments/ENCSR594BJF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR594BJF
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB100CRC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (33 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: tissue

value: Homo sapiens liver tissue?

tag: Sex

value: healthy

tag: dev stage

value: 33 year

value: ENCBS748WBD at ENCODE; https://www.encodeproject.org/ENCBS748WBD/


title: snATAC-seq from liver (ENCLB537FRW)

description:
https://www.encodeproject.org/experiments/ENCSR497ZST/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR497ZST
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB537FRW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (35 years) liver tissue, preserved by flash-freezing nuclear fraction

value: male

tag: age

value: 35 year

tag: lab

value: Michael Snyder, Stanford

value: nucleus

value: Yiing Lin, MD, PhD

value: not applicable

value: ENCBS538HCO at ENCODE; https://www.encodeproject.org/ENCBS538HCO/


title: Control MPRA from K562 (ENCLB500WNR)

description:
https://www.encodeproject.org/experiments/ENCSR166BQV/
***************
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: ENCSR166BQV
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB500WNR
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Nadav Ahituv, UCSF

tag: source

value: ATCC

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


title: DNase-seq from Ammon's horn (ENCLB711SKV)

description:
https://www.encodeproject.org/experiments/ENCSR110MYS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR110MYS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB711SKV

value: Ammon's horn

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

tag: link

value: ENCBS601MQQ at ENCODE; https://www.encodeproject.org/ENCBS601MQQ/


title: STARR-seq from K562 (ENCLB521MHS)

description:
https://www.encodeproject.org/experiments/ENCSR312UQM/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR312UQM
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR886XNQ
encode release date: 2023-03-21
lab: Tim Reddy, Duke
library encode accession: ENCLB521MHS
size range: >200

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

value: Tim Reddy, Duke

value: ENCBS322MIG at ENCODE; https://www.encodeproject.org/ENCBS322MIG/


title: Control MPRA from K562 (ENCLB665EZV)

description:
https://www.encodeproject.org/experiments/ENCSR166BQV/
***************
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: ENCSR166BQV
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB665EZV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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


title: DNase-seq from cerebellum (ENCLB187ARJ)

description:
https://www.encodeproject.org/experiments/ENCSR109OTE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR109OTE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB187ARJ

source_name: Homo sapiens male adult cerebellum tissue

value: cerebellum

value: male

value: ENCBS909ZHU at ENCODE; https://www.encodeproject.org/ENCBS909ZHU/


title: snATAC-seq from heart (ENCLB003DXD)

description:
https://www.encodeproject.org/experiments/ENCSR515SNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515SNH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB003DXD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (84 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: Homo sapiens heart tissue

value: female

value: embryonic

value: 84 day

value: Michael Snyder, Stanford

value: nucleus

value: BDRL

value: not applicable

value: ENCBS835WTE at ENCODE; https://www.encodeproject.org/ENCBS835WTE/


title: vena cava rep1

description:
gene expression data of adult mouse vena cava
VC P2 -24022010

tag: tissue

value: vena cava

tag: analysed cell fraction

value: GFP positive

value: adult (8-12 weeks old)


title: STARR-seq from K562 (ENCLB930QDD)

description:
https://www.encodeproject.org/experiments/ENCSR312UQM/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR312UQM
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR886XNQ
encode release date: 2023-03-21
lab: Tim Reddy, Duke
library encode accession: ENCLB930QDD
size range: >200

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS366IDN at ENCODE; https://www.encodeproject.org/ENCBS366IDN/


title: Control MPRA from HepG2 (ENCLB995TBZ)

description:
https://www.encodeproject.org/experiments/ENCSR118NBQ/
***************
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: ENCSR118NBQ
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB995TBZ
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

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

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

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


title: STARR-seq from K562 (ENCLB840PQJ)

description:
https://www.encodeproject.org/experiments/ENCSR312UQM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR312UQM
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR886XNQ
encode release date: 2023-03-21
lab: Tim Reddy, Duke
library encode accession: ENCLB840PQJ
size range: >200

value: female

value: ENCBS417PWP at ENCODE; https://www.encodeproject.org/ENCBS417PWP/


title: DNase-seq from dorsolateral prefrontal cortex (ENCLB267ADH)

description:
https://www.encodeproject.org/experiments/ENCSR108KVV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR108KVV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB267ADH

source_name: Homo sapiens female adult dorsolateral prefrontal cortex tissue

value: dorsolateral prefrontal cortex

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS907GOK at ENCODE; https://www.encodeproject.org/ENCBS907GOK/


title: DNase-seq from C1 segment of cervical spinal cord (ENCLB321HUM)

description:
https://www.encodeproject.org/experiments/ENCSR106LXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR106LXV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB321HUM

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

value: C1 segment of cervical spinal cord

value: adult

value: ENCBS355FLR at ENCODE; https://www.encodeproject.org/ENCBS355FLR/


title: snATAC-seq from heart (ENCLB037GRI)

description:
https://www.encodeproject.org/experiments/ENCSR282FAK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR282FAK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB037GRI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (120 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

tag: note

value: Homo sapiens heart tissue

value: embryonic

value: 120 day

value: Michael Snyder, Stanford

value: nucleus

value: BDRL

value: not applicable

value: ENCBS788CMM at ENCODE; https://www.encodeproject.org/ENCBS788CMM/


title: snATAC-seq from liver (ENCLB303IXE)

description:
https://www.encodeproject.org/experiments/ENCSR118PUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR118PUH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB303IXE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (41 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

value: tissue

value: Homo sapiens liver tissue?

value: male

value: healthy

value: 41 year

tag: subcellular fraction term name

value: Yiing Lin, MD, PhD

value: ENCBS227ZRJ at ENCODE; https://www.encodeproject.org/ENCBS227ZRJ/


title: Control MPRA from HepG2 (ENCLB969XGK)

description:
https://www.encodeproject.org/experiments/ENCSR118NBQ/
***************
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: ENCSR118NBQ
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB969XGK
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: ENCBS551EAN at ENCODE; https://www.encodeproject.org/ENCBS551EAN/


title: snATAC-seq from heart (ENCLB935NNA)

description:
https://www.encodeproject.org/experiments/ENCSR306FRQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306FRQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB935NNA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male embryo (59 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: Homo sapiens heart tissue

value: embryonic

value: 59 day

value: Michael Snyder, Stanford

value: nucleus

value: BDRL

tag: collection date

value: not applicable

value: ENCBS092RCN at ENCODE; https://www.encodeproject.org/ENCBS092RCN/


title: STARR-seq from K562 (ENCLB227ACX)

description:
https://www.encodeproject.org/experiments/ENCSR312UQM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR312UQM
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR886XNQ
encode release date: 2023-03-21
lab: Tim Reddy, Duke
library encode accession: ENCLB227ACX
size range: >200

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Tim Reddy, Duke

value: ENCBS655ORZ at ENCODE; https://www.encodeproject.org/ENCBS655ORZ/


title: Control MPRA from HepG2 (ENCLB480QYV)

description:
https://www.encodeproject.org/experiments/ENCSR118NBQ/
***************
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: ENCSR118NBQ
assay title: Control MPRA
encode release date: 2021-02-19
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB480QYV
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS468GLN at ENCODE; https://www.encodeproject.org/ENCBS468GLN/


title: DNase-seq from cerebellum (ENCLB924ZBV)

description:
https://www.encodeproject.org/experiments/ENCSR106CAP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR106CAP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB924ZBV

source_name: Homo sapiens female adult cerebellum tissue

value: cerebellum

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS140GCT at ENCODE; https://www.encodeproject.org/ENCBS140GCT/


title: snATAC-seq from heart (ENCLB465WGY)

description:
https://www.encodeproject.org/experiments/ENCSR024TGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR024TGD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB465WGY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male embryo (103 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: Homo sapiens heart tissue

value: embryonic

value: 103 day

value: Michael Snyder, Stanford

value: nucleus

value: BDRL

value: not applicable

tag: geographic location

value: ENCBS452UFQ at ENCODE; https://www.encodeproject.org/ENCBS452UFQ/


title: snATAC-seq from liver (ENCLB115HIZ)

description:
https://www.encodeproject.org/experiments/ENCSR074DOR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR074DOR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2023-03-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB115HIZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (39 years) liver tissue, preserved by flash-freezing nuclear fraction

value: liver

tag: biosample encode accession

value: Homo sapiens liver tissue?

value: female

value: healthy

value: adult

value: 39 year

value: Yiing Lin, MD, PhD

value: ENCBS509PYF at ENCODE; https://www.encodeproject.org/ENCBS509PYF/


title: snATAC-seq from heart (ENCLB628HGI)

description:
https://www.encodeproject.org/experiments/ENCSR004IAY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004IAY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2024-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB628HGI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female embryo (105 days) heart tissue, preserved by flash-freezing nuclear fraction

value: heart

value: tissue

value: 105 day

value: ENCBS534KHU at ENCODE; https://www.encodeproject.org/ENCBS534KHU/


title: snATAC-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB013KIP)

description:
https://www.encodeproject.org/experiments/ENCSR810IIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR810IIV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB013KIP
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (43 years) stimulated activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads, 10 ng/mL Interleukin-2 nuclear fraction

value: primary cell

value: male

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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

value: ENCBS111IJY at ENCODE; https://www.encodeproject.org/ENCBS111IJY/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: Control MPRA from HepG2 (ENCLB362BPY)

description:
https://www.encodeproject.org/experiments/ENCSR092XKS/
***************
biological replicate number: 1
technical replicate number: 1
description: Elements cloned into the pGL4.11 vector upstream of the reporter, with barcode located in the 3' UTR of the reporter. Elementas are generated by error-prone PCR of the LDLR promoter.
experiment encode accession: ENCSR092XKS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB362BPY
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

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


title: Control MPRA from HepG2 (ENCLB874LME)

description:
https://www.encodeproject.org/experiments/ENCSR092XKS/
***************
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: ENCSR092XKS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB874LME
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

tag: line

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


title: DNase-seq from cerebellum (ENCLB378RGB)

description:
https://www.encodeproject.org/experiments/ENCSR106CAP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR106CAP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB378RGB

value: cerebellum

value: tissue

tag: encode accession

value: female

value: adult

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS769IYS at ENCODE; https://www.encodeproject.org/ENCBS769IYS/


title: snATAC-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB480TJO)

description:
https://www.encodeproject.org/experiments/ENCSR600UDB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR600UDB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB480TJO
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (43 years) stimulated activated naive CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads, 10 ng/mL Interleukin-2 nuclear fraction

value: primary cell

tag: Sex

value: male

value: 43 year

value: Yijun Ruan, JAX

value: nucleus

value: AllCells

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

value: ENCBS759ZHR at ENCODE; https://www.encodeproject.org/ENCBS759ZHR/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: DNase-seq from anterior cingulate cortex (ENCLB288BJO)

description:
https://www.encodeproject.org/experiments/ENCSR102ZXS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR102ZXS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB288BJO

source_name: Homo sapiens male adult anterior cingulate cortex tissue

value: anterior cingulate cortex

tag: dev stage

value: ENCBS373VDB at ENCODE; https://www.encodeproject.org/ENCBS373VDB/


title: Control MPRA from HepG2 (ENCLB313JJX)

description:
https://www.encodeproject.org/experiments/ENCSR092XKS/
***************
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: ENCSR092XKS
assay title: Control MPRA
encode release date: 2022-10-11
lab: Nadav Ahituv, UCSF
library encode accession: ENCLB313JJX
fragmentation methods: chemical (Illumina TruSeq)
size range: 10-20

value: cell line

value: hepatocellular carcinoma

value: child

tag: age

value: 15 year

value: Nadav Ahituv, UCSF

value: ATCC

value: ENCBS533EDQ at ENCODE; https://www.encodeproject.org/ENCBS533EDQ/


title: snATAC-seq from activated CD4-positive, alpha-beta T cell (ENCLB312SWK)

description:
https://www.encodeproject.org/experiments/ENCSR569ZMI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR569ZMI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB312SWK
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (20 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads, 10 ng/mL Interleukin-2 nuclear fraction

value: primary cell

value: male

value: adult

value: 20 year

tag: lab

value: ENCBS631HVS at ENCODE; https://www.encodeproject.org/ENCBS631HVS/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: snATAC-seq from activated CD8-positive, alpha-beta T cell (ENCLB151QQZ)

description:
https://www.encodeproject.org/experiments/ENCSR472HFJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR472HFJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB151QQZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads , 10 ng/mL Interleukin-2 nuclear fraction

value: 21 year

value: Yijun Ruan, JAX

tag: source

value: AllCells

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

value: nucleus

value: ENCBS501DVY at ENCODE; https://www.encodeproject.org/ENCBS501DVY/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: DNase-seq from hypothalamus (ENCLB271FLB)

description:
https://www.encodeproject.org/experiments/ENCSR101JUF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101JUF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB271FLB

source_name: Homo sapiens male adult hypothalamus tissue

value: hypothalamus

value: tissue

value: unknown

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

tag: link

value: ENCBS214PXQ at ENCODE; https://www.encodeproject.org/ENCBS214PXQ/