title: PRO-cap from cardiac septum (ENCLB521ATF)

description:
https://www.encodeproject.org/experiments/ENCSR484CAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Septum of heart.
experiment encode accession: ENCSR484CAZ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB521ATF

source_name: Homo sapiens female adult (41 years) cardiac septum tissue

value: cardiac septum

value: tissue

value: DM:no; HTN:no; CAD:no

value: 41 year

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS104EPG at ENCODE; https://www.encodeproject.org/ENCBS104EPG/


title: PRO-cap from cardiac septum (ENCLB096ODA)

status: Public on Feb 28 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/ENCSR484CAZ/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Septum of heart.
experiment encode accession: ENCSR484CAZ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB096ODA

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

tag: biosample encode accession

tag: encode accession

tag: Sex

value: female

tag: health state

tag: dev stage

value: adult

tag: age

tag: lab

tag: source

tag: link


title: Flow-FISH CRISPR screen from K562 (ENCLB770YUQ)

description:
https://www.encodeproject.org/experiments/ENCSR609RED/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR609RED
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB770YUQ
size range: 200-210

library_source: genomic

molecule: genomic DNA

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

tag: line

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC

value: ENCBS543NBG at ENCODE; https://www.encodeproject.org/ENCBS543NBG/


title: PRO-cap from ovary (ENCLB653GXJ)

description:
https://www.encodeproject.org/experiments/ENCSR482XCK/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Ovary.
experiment encode accession: ENCSR482XCK
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB653GXJ

source_name: Homo sapiens female adult (53 years) ovary tissue

value: ovary

value: CHTN

value: ENCBS079YVX at ENCODE; https://www.encodeproject.org/ENCBS079YVX/


title: PRO-cap from ovary (ENCLB091DKJ)

description:
https://www.encodeproject.org/experiments/ENCSR482XCK/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Ovary.
experiment encode accession: ENCSR482XCK
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB091DKJ

value: tissue


title: proliferation CRISPR screen from WTC11 (ENCLB024BND)

description:
https://www.encodeproject.org/experiments/ENCSR482PHH/
***************
biological replicate number: 1
technical replicate number: 1
description: Cell survival-based CRISPR screen targeting genomic regions near MSH2, MSH6, MLH1, PMS2, PCNA and HPRT1 genes.
experiment encode accession: ENCSR482PHH
assay title: proliferation CRISPR screen
assembly: GRCh38
possible controls: ENCSR250ZWC
encode release date: 2020-12-08
lab: Yin Shen, UCSF
library encode accession: ENCLB024BND

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA) treated with 240 ng/mL tioguanine for 7 days

value: male

value: 30 year

tag: passage number

value: Yin Shen, UCSF

value: The Gladstone Stem Cell Core

tag: treatments

value: treatment_term_id:CHEBI:9555; treatment_term_name:tioguanine; treatment_type:chemical; duration:7; duration_units:day;

value: ENCBS037WBM at ENCODE; https://www.encodeproject.org/ENCBS037WBM/


title: STARR-seq from A549 (ENCLB064DWB)

description:
https://www.encodeproject.org/experiments/ENCSR261RMM/
***************
biological replicate number: 4
technical replicate number: 3
description:
experiment encode accession: ENCSR261RMM
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB064DWB
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line genetically modified (episome) using transient transfection treated with 1 uM Hydrocortisone (agonist) for 4 hours

extract_protocol:
general protocol: https://www.encodeproject.org/documents/c8891369-b036-4be1-b881-76ca3911151e/@@download/attachment/Reddy_Lab_WGSS_ENCODE_protocol.pdf
extraction method: Qiagen RNA extraction

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_name:Hydrocortisone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS702UMG at ENCODE; https://www.encodeproject.org/ENCBS702UMG/


title: Flow-FISH CRISPR screen from K562 (ENCLB668HHC)

description:
https://www.encodeproject.org/experiments/ENCSR609RED/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR609RED
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB668HHC
size range: 200-210

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC


title: proliferation CRISPR screen from WTC11 (ENCLB192YTQ)

description:
https://www.encodeproject.org/experiments/ENCSR482PHH/
***************
biological replicate number: 2
technical replicate number: 1
description: Cell survival-based CRISPR screen targeting genomic regions near MSH2, MSH6, MLH1, PMS2, PCNA and HPRT1 genes.
experiment encode accession: ENCSR482PHH
assay title: proliferation CRISPR screen
assembly: GRCh38
possible controls: ENCSR250ZWC
encode release date: 2020-12-08
lab: Yin Shen, UCSF
library encode accession: ENCLB192YTQ

value: male

value: ENCBS313EPD at ENCODE; https://www.encodeproject.org/ENCBS313EPD/


title: Flow-FISH CRISPR screen from K562 (ENCLB581XKQ)

description:
https://www.encodeproject.org/experiments/ENCSR609RED/
***************
biological replicate number: 3
technical replicate number: 2
description:
experiment encode accession: ENCSR609RED
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB581XKQ
size range: 200-210

value: ENCBS194VHJ at ENCODE; https://www.encodeproject.org/ENCBS194VHJ/


title: Flow-FISH CRISPR screen from K562 (ENCLB947TTQ)

description:
https://www.encodeproject.org/experiments/ENCSR609RED/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR609RED
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB947TTQ
size range: 200-210

value: ENCBS462WHN at ENCODE; https://www.encodeproject.org/ENCBS462WHN/


title: PRO-cap from jejunum (ENCLB423AZK)

description:
https://www.encodeproject.org/experiments/ENCSR255VLW/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Jejunum.
experiment encode accession: ENCSR255VLW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB423AZK

source_name: Homo sapiens female adult (59 years) jejunum tissue

value: jejunum

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS722JHP at ENCODE; https://www.encodeproject.org/ENCBS722JHP/


title: PRO-cap from jejunum (ENCLB285ZZB)

description:
https://www.encodeproject.org/experiments/ENCSR255VLW/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Jejunum.
experiment encode accession: ENCSR255VLW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB285ZZB

value: adult


title: PRO-cap from progenitor cell of endocrine pancreas (ENCLB136SJZ)

description:
https://www.encodeproject.org/experiments/ENCSR255MUU/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived pancreatic progenitor cells.
experiment encode accession: ENCSR255MUU
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB136SJZ

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein

value: ENCBS757CPW at ENCODE; https://www.encodeproject.org/ENCBS757CPW/


title: PRO-cap from upper lobe of left lung (ENCLB957UMM)

description:
https://www.encodeproject.org/experiments/ENCSR478DAN/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Upper lobe of left lung.
experiment encode accession: ENCSR478DAN
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB957UMM

source_name: Homo sapiens female adult (61 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: ENCBS559YGN at ENCODE; https://www.encodeproject.org/ENCBS559YGN/


title: PRO-cap from upper lobe of left lung (ENCLB956MKY)

description:
https://www.encodeproject.org/experiments/ENCSR478DAN/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Upper lobe of left lung.
experiment encode accession: ENCSR478DAN
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB956MKY

value: tissue


title: PRO-cap from progenitor cell of endocrine pancreas (ENCLB187PUY)

description:
https://www.encodeproject.org/experiments/ENCSR255MUU/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived pancreatic progenitor cells.
experiment encode accession: ENCSR255MUU
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB187PUY

value: Haiyuan Yu, Cornell

value: ENCBS731VJL at ENCODE; https://www.encodeproject.org/ENCBS731VJL/


title: proliferation CRISPR screen from WTC11 (ENCLB195KKR)

description:
https://www.encodeproject.org/experiments/ENCSR254SJU/
***************
biological replicate number: 2
technical replicate number: 1
description: Cell survival-based CRISPR screen targeting genomic regions near MSH2, MSH6, MLH1, PMS2, PCNA and HPRT1 genes.
experiment encode accession: ENCSR254SJU
assay title: proliferation CRISPR screen
assembly: GRCh38
possible controls: ENCSR427OPP
encode release date: 2020-12-08
lab: Yin Shen, UCSF
library encode accession: ENCLB195KKR

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using transduction, genetically modified using CRISPRi (sgRNA) treated with 160 ng/mL tioguanine for 7 days

value: cell line

value: male

value: 30 year

value: Yin Shen, UCSF

value: The Gladstone Stem Cell Core

value: treatment_term_id:CHEBI:9555; treatment_term_name:tioguanine; treatment_type:chemical; duration:7; duration_units:day;

value: ENCBS385UEE at ENCODE; https://www.encodeproject.org/ENCBS385UEE/


title: DNase-seq from heart left ventricle (ENCLB406BBD)

description:
https://www.encodeproject.org/experiments/ENCSR606QFW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR606QFW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB406BBD

source_name: Homo sapiens male adult (54 years) heart left ventricle tissue

value: heart left ventricle

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: adult

value: 54 year

value: John Stamatoyannopoulos, UW

value: Shin Lin

value: ENCBS571KFL at ENCODE; https://www.encodeproject.org/ENCBS571KFL/


title: DNase-seq from kidney (ENCLB167KNC)

description:
https://www.encodeproject.org/experiments/ENCSR604VIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR604VIY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB167KNC

source_name: Homo sapiens female adult (47 years) kidney tissue

value: kidney

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: Yiing Lin, MD, PhD

value: ENCBS201KPQ at ENCODE; https://www.encodeproject.org/ENCBS201KPQ/


title: DNase-seq from activated T-cell (ENCLB692NJU)

description:
https://www.encodeproject.org/experiments/ENCSR472LSL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR472LSL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB692NJU

source_name: Homo sapiens male adult (26 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: activated T-cell

value: primary cell

value: male

value: 26 year

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS405ZPY at ENCODE; https://www.encodeproject.org/ENCBS405ZPY/


title: Flow-FISH CRISPR screen from K562 (ENCLB624WXX)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB624WXX
size range: 200-210

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC

value: ENCBS489PUF at ENCODE; https://www.encodeproject.org/ENCBS489PUF/


title: PRO-cap from fallopian tube (ENCLB661AGP)

description:
https://www.encodeproject.org/experiments/ENCSR472ETC/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Fallopian tube.
experiment encode accession: ENCSR472ETC
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB661AGP

source_name: Homo sapiens female adult (46 years) fallopian tube tissue

value: fallopian tube

value: tissue

value: female

value: DM:no; HTN:no; CAD:no

value: 46 year

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS381HCL at ENCODE; https://www.encodeproject.org/ENCBS381HCL/


title: Flow-FISH CRISPR screen from K562 (ENCLB156ODD)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB156ODD
size range: 200-210

value: ENCBS188FGP at ENCODE; https://www.encodeproject.org/ENCBS188FGP/


title: Control CRISPR screen from WTC11 (ENCLB162EMV)

description:
https://www.encodeproject.org/experiments/ENCSR250ZWC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR250ZWC
assay title: Control CRISPR screen
assembly: GRCh38
encode release date: 2020-12-08
lab: Yin Shen, UCSF
library encode accession: ENCLB162EMV

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA)

value: male

value: 30 year

value: Yin Shen, UCSF

value: The Gladstone Stem Cell Core

value: ENCBS724UUB at ENCODE; https://www.encodeproject.org/ENCBS724UUB/


title: Flow-FISH CRISPR screen from K562 (ENCLB648EBX)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB648EBX
size range: 200-210

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Jesse Engreitz, Stanford


title: Flow-FISH CRISPR screen from K562 (ENCLB505IKJ)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB505IKJ
size range: 200-210

value: female

value: ATCC


title: PRO-cap from fallopian tube (ENCLB015ZXF)

description:
https://www.encodeproject.org/experiments/ENCSR472ETC/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Fallopian tube.
experiment encode accession: ENCSR472ETC
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB015ZXF

value: fallopian tube

value: tissue

value: DM:no; HTN:no; CAD:no

value: 46 year


title: proliferation CRISPR screen from WTC11 (ENCLB179AVL)

description:
https://www.encodeproject.org/experiments/ENCSR254SJU/
***************
biological replicate number: 1
technical replicate number: 1
description: Cell survival-based CRISPR screen targeting genomic regions near MSH2, MSH6, MLH1, PMS2, PCNA and HPRT1 genes.
experiment encode accession: ENCSR254SJU
assay title: proliferation CRISPR screen
assembly: GRCh38
possible controls: ENCSR427OPP
encode release date: 2020-12-08
lab: Yin Shen, UCSF
library encode accession: ENCLB179AVL

value: treatment_term_id:CHEBI:9555; treatment_term_name:tioguanine; treatment_type:chemical; duration:7; duration_units:day;

value: ENCBS292TTP at ENCODE; https://www.encodeproject.org/ENCBS292TTP/


title: PRO-cap from peripheral blood mononuclear cell (ENCLB491MCU)

description:
https://www.encodeproject.org/experiments/ENCSR250REI/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PBMCs.
experiment encode accession: ENCSR250REI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB491MCU

source_name: Homo sapiens peripheral blood mononuclear primary cell

value: peripheral blood mononuclear cell

value: primary cell

value: not collected

value: unknown

value: Haiyuan Yu, Cornell

value: Remi J. Creusot

value: ENCBS379BLO at ENCODE; https://www.encodeproject.org/ENCBS379BLO/


title: DNase-seq from activated T-cell (ENCLB919NAN)

description:
https://www.encodeproject.org/experiments/ENCSR472LSL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR472LSL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB919NAN

value: activated T-cell

value: male

value: adult

value: 26 year

value: John Stamatoyannopoulos, UW

value: Stemcell Technologies

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS131PVL at ENCODE; https://www.encodeproject.org/ENCBS131PVL/


title: Flow-FISH CRISPR screen from K562 (ENCLB268PMZ)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB268PMZ
size range: 200-210

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC

value: ENCBS489PUF at ENCODE; https://www.encodeproject.org/ENCBS489PUF/


title: Control CRISPR screen from WTC11 (ENCLB932JJU)

description:
https://www.encodeproject.org/experiments/ENCSR250ZWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR250ZWC
assay title: Control CRISPR screen
assembly: GRCh38
encode release date: 2020-12-08
lab: Yin Shen, UCSF
library encode accession: ENCLB932JJU

value: 30 year

value: Yin Shen, UCSF

value: The Gladstone Stem Cell Core

value: ENCBS979INT at ENCODE; https://www.encodeproject.org/ENCBS979INT/


title: Control CRISPR screen from glutamatergic neuron (ENCLB833XWL)

description:
https://www.encodeproject.org/experiments/ENCSR466IBU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR466IBU
assay title: Control CRISPR screen
assembly: GRCh38
encode release date: 2022-07-19
lab: Yin Shen, UCSF
library encode accession: ENCLB833XWL

source_name: Homo sapiens male adult (30 years) glutamatergic neuron in vitro differentiated cells genetically modified (insertion) using CRISPR (pgRNA) targeting H. sapiens FMR1, genetically modified (insertion) using transduction

value: glutamatergic neuron

value: in vitro differentiated cells

value: male

value: adult

value: Li Gan

value: ENCBS441ALJ at ENCODE; https://www.encodeproject.org/ENCBS441ALJ/


title: FACS CRISPR screen from WTC11 (ENCLB228GXC)

description:
https://www.encodeproject.org/experiments/ENCSR250ZBY/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR250ZBY
assay title: FACS CRISPR screen
assembly: GRCh38
possible controls: ENCSR900LDE
encode release date: 2022-07-19
lab: Yin Shen, UCSF
library encode accession: ENCLB228GXC

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR (pgRNA) targeting H. sapiens MECP2, genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (pgRNA)

value: cell line

value: ENCBS053PSR at ENCODE; https://www.encodeproject.org/ENCBS053PSR/


title: PRO-cap from osteocyte (ENCLB085QDX)

description:
https://www.encodeproject.org/experiments/ENCSR248SVP/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived osteocytes.
experiment encode accession: ENCSR248SVP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB085QDX

source_name: Homo sapiens female embryo (5 days) osteocyte in vitro differentiated cells

value: osteocyte

value: female

value: healthy

value: embryonic

value: 5 day

value: Haiyuan Yu, Cornell

value: Bradley Bernstein

value: ENCBS323ORD at ENCODE; https://www.encodeproject.org/ENCBS323ORD/


title: Flow-FISH CRISPR screen from K562 (ENCLB496RET)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB496RET
size range: 200-210

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

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC

value: ENCBS188FGP at ENCODE; https://www.encodeproject.org/ENCBS188FGP/


title: Control CRISPR screen from glutamatergic neuron (ENCLB253LZJ)

description:
https://www.encodeproject.org/experiments/ENCSR466IBU/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR466IBU
assay title: Control CRISPR screen
assembly: GRCh38
encode release date: 2022-07-19
lab: Yin Shen, UCSF
library encode accession: ENCLB253LZJ

value: glutamatergic neuron

value: in vitro differentiated cells

value: male

value: adult

value: 30 year

value: Yin Shen, UCSF

value: Li Gan

value: ENCBS592YLF at ENCODE; https://www.encodeproject.org/ENCBS592YLF/


title: FACS CRISPR screen from WTC11 (ENCLB449EIJ)

description:
https://www.encodeproject.org/experiments/ENCSR250ZBY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR250ZBY
assay title: FACS CRISPR screen
assembly: GRCh38
possible controls: ENCSR900LDE
encode release date: 2022-07-19
lab: Yin Shen, UCSF
library encode accession: ENCLB449EIJ

value: cell line

value: ENCBS597CSK at ENCODE; https://www.encodeproject.org/ENCBS597CSK/


title: PRO-cap from esophagus muscularis mucosa (ENCLB492IKM)

description:
https://www.encodeproject.org/experiments/ENCSR246YHR/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Esophagus muscularis mucosa.
experiment encode accession: ENCSR246YHR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB492IKM

source_name: Homo sapiens female adult (53 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: tissue

value: female

value: Haiyuan Yu, Cornell

value: GTEx

value: ENCBS189SWU at ENCODE; https://www.encodeproject.org/ENCBS189SWU/


title: Flow-FISH CRISPR screen from K562 (ENCLB612ENF)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB612ENF
size range: 200-210

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC

value: ENCBS188FGP at ENCODE; https://www.encodeproject.org/ENCBS188FGP/


title: Flow-FISH CRISPR screen from K562 (ENCLB116BUS)

description:
https://www.encodeproject.org/experiments/ENCSR602DUU/
***************
biological replicate number: 2
technical replicate number: 4
description:
experiment encode accession: ENCSR602DUU
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB116BUS
size range: 200-210

value: adult

value: ENCBS489PUF at ENCODE; https://www.encodeproject.org/ENCBS489PUF/


title: PRO-cap from esophagus muscularis mucosa (ENCLB614GEI)

description:
https://www.encodeproject.org/experiments/ENCSR246YHR/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Esophagus muscularis mucosa.
experiment encode accession: ENCSR246YHR
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB614GEI


title: perturbation followed by scRNA-seq from K562 (ENCLB761BDY)

description:
https://www.encodeproject.org/experiments/ENCSR464SPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR464SPV
assay title: perturbation followed by scRNA-seq
assembly: hg19
encode release date: 2023-01-06
lab: Tim Reddy, Duke
library encode accession: ENCLB761BDY

value: Tim Reddy, Duke

value: ENCBS538GQO at ENCODE; https://www.encodeproject.org/ENCBS538GQO/


title: PRO-cap from Karpas-422 (ENCLB489DAE)

description:
https://www.encodeproject.org/experiments/ENCSR245UIS/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in KARPAS-422.
experiment encode accession: ENCSR245UIS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB489DAE

source_name: Homo sapiens Karpas-422 cell line

value: cell line

value: human B cell non-Hodgkin's lymphoma

value: 72 year

value: Russell Ryan

value: ENCBS097KLE at ENCODE; https://www.encodeproject.org/ENCBS097KLE/


title: PRO-cap from peripheral blood mononuclear cell (ENCLB277EUH)

description:
https://www.encodeproject.org/experiments/ENCSR250REI/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PBMCs.
experiment encode accession: ENCSR250REI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB277EUH

value: peripheral blood mononuclear cell

value: primary cell

value: not collected

value: unknown

value: Haiyuan Yu, Cornell

value: Remi J. Creusot

value: ENCBS379BLO at ENCODE; https://www.encodeproject.org/ENCBS379BLO/


title: PRO-cap from osteocyte (ENCLB578ZUC)

description:
https://www.encodeproject.org/experiments/ENCSR248SVP/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived osteocytes.
experiment encode accession: ENCSR248SVP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB578ZUC

value: osteocyte

value: in vitro differentiated cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein

value: ENCBS832OLM at ENCODE; https://www.encodeproject.org/ENCBS832OLM/


title: PRO-cap from Karpas-422 (ENCLB354QXB)

description:
https://www.encodeproject.org/experiments/ENCSR245UIS/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in KARPAS-422.
experiment encode accession: ENCSR245UIS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB354QXB

value: cell line

value: human B cell non-Hodgkin's lymphoma

value: adult

value: 72 year

value: Russell Ryan

value: ENCBS291XTK at ENCODE; https://www.encodeproject.org/ENCBS291XTK/


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB065ZBC)

description:
https://www.encodeproject.org/experiments/ENCSR151MUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR151MUX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB065ZBC

source_name: Homo sapiens male adult (38 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours

value: primary cell

value: male

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour;

value: ENCBS391UMA at ENCODE; https://www.encodeproject.org/ENCBS391UMA/


title: Flow-FISH CRISPR screen from K562 (ENCLB769JMU)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 2
technical replicate number: 4
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB769JMU
size range: 200-210

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ATCC

value: ENCBS619VEU at ENCODE; https://www.encodeproject.org/ENCBS619VEU/


title: STARR-seq from A549 (ENCLB223WWC)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB223WWC
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

source_name: Homo sapiens A549 cell line genetically modified (episome) using transient transfection treated with 1 uM dexamethasone (agonist) for 4 hours

value: cell line

value: adult

value: 58 year

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS862FFO at ENCODE; https://www.encodeproject.org/ENCBS862FFO/


title: PRO-cap from psoas muscle (ENCLB940DWS)

description:
https://www.encodeproject.org/experiments/ENCSR245HPE/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Psoas muscle.
experiment encode accession: ENCSR245HPE
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB940DWS

source_name: Homo sapiens female adult (41 years) psoas muscle tissue

value: psoas muscle

value: tissue

value: DM:no; HTN:no; CAD:no

value: 41 year

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS533GIY at ENCODE; https://www.encodeproject.org/ENCBS533GIY/


title: STARR-seq from A549 (ENCLB721XHD)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB721XHD
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: male

value: ENCBS781ZYP at ENCODE; https://www.encodeproject.org/ENCBS781ZYP/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB635QRA)

description:
https://www.encodeproject.org/experiments/ENCSR601QTE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR601QTE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB635QRA

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with 100 ng/mL Interleukin-2 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 39 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS705OYO at ENCODE; https://www.encodeproject.org/ENCBS705OYO/


title: PRO-cap from psoas muscle (ENCLB381WJK)

description:
https://www.encodeproject.org/experiments/ENCSR245HPE/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Psoas muscle.
experiment encode accession: ENCSR245HPE
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB381WJK

value: psoas muscle

value: adult


title: STARR-seq from A549 (ENCLB215IMR)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB215IMR
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: cell line

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS906DTK at ENCODE; https://www.encodeproject.org/ENCBS906DTK/


title: Flow-FISH CRISPR screen from K562 (ENCLB091JSO)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB091JSO
size range: 200-210

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Jesse Engreitz, Stanford

value: ENCBS619VEU at ENCODE; https://www.encodeproject.org/ENCBS619VEU/


title: STARR-seq from A549 (ENCLB874BHJ)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 4
technical replicate number: 4
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB874BHJ
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: male

value: ENCBS781ZYP at ENCODE; https://www.encodeproject.org/ENCBS781ZYP/


title: Flow-FISH CRISPR screen from K562 (ENCLB266BUD)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB266BUD
size range: 200-210

value: female

value: ENCBS055GEB at ENCODE; https://www.encodeproject.org/ENCBS055GEB/


title: Flow-FISH CRISPR screen from K562 (ENCLB009NQD)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB009NQD
size range: 200-210


title: STARR-seq from A549 (ENCLB034UKB)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB034UKB
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: ENCBS862FFO at ENCODE; https://www.encodeproject.org/ENCBS862FFO/


title: STARR-seq from A549 (ENCLB538NRR)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 3
technical replicate number: 2
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB538NRR
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: ENCBS483MQT at ENCODE; https://www.encodeproject.org/ENCBS483MQT/


title: Flow-FISH CRISPR screen from K562 (ENCLB800INC)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB800INC
size range: 200-210

value: adult


title: STARR-seq from A549 (ENCLB220MOU)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 2
technical replicate number: 4
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB220MOU
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: cell line


title: STARR-seq from A549 (ENCLB939GTN)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB939GTN
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: 58 year


title: STARR-seq from A549 (ENCLB699VPG)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 3
technical replicate number: 3
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB699VPG
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: Tim Reddy, Duke


title: STARR-seq from A549 (ENCLB294SGK)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 4
technical replicate number: 2
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB294SGK
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: ATCC


title: STARR-seq from A549 (ENCLB616RHB)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB616RHB
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;


title: Flow-FISH CRISPR screen from K562 (ENCLB241KHH)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB241KHH
size range: 200-210


title: Flow-FISH CRISPR screen from K562 (ENCLB835OVQ)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB835OVQ
size range: 200-210


title: STARR-seq from A549 (ENCLB133HJV)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 3
technical replicate number: 4
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB133HJV
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg


title: STARR-seq from A549 (ENCLB598VZD)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 4
technical replicate number: 3
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB598VZD
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg


title: STARR-seq from A549 (ENCLB926FIK)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB926FIK
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: ENCBS906DTK at ENCODE; https://www.encodeproject.org/ENCBS906DTK/


title: Flow-FISH CRISPR screen from K562 (ENCLB724NVG)

description:
https://www.encodeproject.org/experiments/ENCSR601JKO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR601JKO
assay title: Flow-FISH CRISPR screen
assembly: hg19
encode release date: 2021-01-07
lab: Jesse Engreitz, Stanford
library encode accession: ENCLB724NVG
size range: 200-210

value: chronic myelogenous leukemia (CML)


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB634VLK)

description:
https://www.encodeproject.org/experiments/ENCSR600PWZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR600PWZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB634VLK

source_name: Homo sapiens male adult (42 years) stimulated activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL Interleukin-15 for 48 hours

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS558JOP at ENCODE; https://www.encodeproject.org/ENCBS558JOP/


title: PRO-cap from liver (ENCLB296JOG)

description:
https://www.encodeproject.org/experiments/ENCSR243MVI/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Liver.
experiment encode accession: ENCSR243MVI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB296JOG

source_name: Homo sapiens liver tissue

value: liver

value: tissue

value: not collected

value: unknown

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS547GTA at ENCODE; https://www.encodeproject.org/ENCBS547GTA/


title: STARR-seq from A549 (ENCLB795XFM)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB795XFM
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: cell line

value: male

value: adult

value: 58 year

value: Tim Reddy, Duke

value: ATCC

value: ENCBS483MQT at ENCODE; https://www.encodeproject.org/ENCBS483MQT/


title: STARR-seq from A549 (ENCLB175GZW)

description:
https://www.encodeproject.org/experiments/ENCSR459NUS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR459NUS
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR861AYG
encode release date: 2021-06-17
lab: Tim Reddy, Duke
library encode accession: ENCLB175GZW
size range: 900-1000
nucleic acid starting quantity: 75
nucleic acid starting quantity units: µg

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS906DTK at ENCODE; https://www.encodeproject.org/ENCBS906DTK/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB727NNE)

description:
https://www.encodeproject.org/experiments/ENCSR144JQL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR144JQL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB727NNE

source_name: Homo sapiens female adult (33 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-4 for 4 hours

value: primary cell

value: female

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS938UQT at ENCODE; https://www.encodeproject.org/ENCBS938UQT/


title: DNase-seq from stimulated activated CD4-positive, alpha-beta T cell (ENCLB361FSH)

description:
https://www.encodeproject.org/experiments/ENCSR600PWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR600PWZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB361FSH

value: 42 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS504IPS at ENCODE; https://www.encodeproject.org/ENCBS504IPS/


title: PRO-cap from gastrocnemius medialis (ENCLB184IYR)

description:
https://www.encodeproject.org/experiments/ENCSR235BZZ/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Gastrocnemius medialis.
experiment encode accession: ENCSR235BZZ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB184IYR

source_name: Homo sapiens female adult (53 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

value: tissue

value: adult

value: 53 year

value: Haiyuan Yu, Cornell

value: GTEx

value: ENCBS081ZOP at ENCODE; https://www.encodeproject.org/ENCBS081ZOP/


title: DNase-seq from activated B cell (ENCLB214UOH)

description:
https://www.encodeproject.org/experiments/ENCSR450TJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR450TJS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB214UOH

source_name: Homo sapiens male adult (45 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: primary cell

value: male

value: 45 year

value: Stemcell Technologies

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS824WBC at ENCODE; https://www.encodeproject.org/ENCBS824WBC/


title: PRO-cap from gastrocnemius medialis (ENCLB370BWX)

description:
https://www.encodeproject.org/experiments/ENCSR235BZZ/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Gastrocnemius medialis.
experiment encode accession: ENCSR235BZZ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB370BWX

value: female


title: DNase-seq from activated B cell (ENCLB415WCZ)

description:
https://www.encodeproject.org/experiments/ENCSR450TJS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR450TJS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB415WCZ

value: John Stamatoyannopoulos, UW

value: ENCBS610CQV at ENCODE; https://www.encodeproject.org/ENCBS610CQV/


title: DNase-seq from activated CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB034FFD)

description:
https://www.encodeproject.org/experiments/ENCSR146FHV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146FHV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB034FFD

source_name: Homo sapiens female adult (33 years) activated CD4-positive, CD25-positive, alpha-beta regulatory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours

value: 33 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:16; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS831SEE at ENCODE; https://www.encodeproject.org/ENCBS831SEE/


title: DNase-seq from T778 (ENCLB431VEV)

description:
https://www.encodeproject.org/experiments/ENCSR446MFK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR446MFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB431VEV

source_name: Homo sapiens T778 cell line

value: cell line

value: adult

value: 69 year

value: Garvan Institute

value: ENCBS431CKK at ENCODE; https://www.encodeproject.org/ENCBS431CKK/


title: PRO-cap from skeletal muscle tissue (ENCLB414UJI)

description:
https://www.encodeproject.org/experiments/ENCSR229XTQ/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Skeletal muscle of leg.
experiment encode accession: ENCSR229XTQ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB414UJI

source_name: Homo sapiens male adult (59 years) skeletal muscle tissue

value: skeletal muscle tissue

value: tissue

value: male

value: 59 year

value: Haiyuan Yu, Cornell

value: CHTN

value: ENCBS843ATN at ENCODE; https://www.encodeproject.org/ENCBS843ATN/


title: DNase-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB546CGA)

description:
https://www.encodeproject.org/experiments/ENCSR140EQO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR140EQO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB546CGA

source_name: Homo sapiens female adult (33 years) activated naive CD4-positive, alpha-beta T primary cell

value: primary cell

value: female

value: John Stamatoyannopoulos, UW

value: ENCBS115HCZ at ENCODE; https://www.encodeproject.org/ENCBS115HCZ/


title: PRO-cap from bronchus (ENCLB613ATQ)

description:
https://www.encodeproject.org/experiments/ENCSR233GRN/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Bronchus.
experiment encode accession: ENCSR233GRN
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB613ATQ

source_name: Homo sapiens female adult (68 years) bronchus tissue

value: bronchus

value: 68 year

value: ENCBS728SJT at ENCODE; https://www.encodeproject.org/ENCBS728SJT/


title: DNase-seq from HUDEP-2 (ENCLB891LXE)

description:
https://www.encodeproject.org/experiments/ENCSR139FTB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR139FTB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB891LXE

source_name: Homo sapiens HUDEP-2 cell line

value: cell line

value: adult

value: unknown

value: Riken BioResource Cell Bank

value: ENCBS983WCQ at ENCODE; https://www.encodeproject.org/ENCBS983WCQ/


title: DNase-seq from activated B cell (ENCLB377HZC)

description:
https://www.encodeproject.org/experiments/ENCSR450TJS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR450TJS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB377HZC

value: activated B cell

value: male

value: 45 year

value: Stemcell Technologies

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS004WAN at ENCODE; https://www.encodeproject.org/ENCBS004WAN/


title: PRO-cap from bronchus (ENCLB608VSW)

description:
https://www.encodeproject.org/experiments/ENCSR233GRN/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Bronchus.
experiment encode accession: ENCSR233GRN
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB608VSW

value: tissue

value: female

value: Haiyuan Yu, Cornell

value: CHTN


title: PRO-cap from skeletal muscle tissue (ENCLB880MLE)

description:
https://www.encodeproject.org/experiments/ENCSR229XTQ/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Skeletal muscle of leg.
experiment encode accession: ENCSR229XTQ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB880MLE

value: skeletal muscle tissue

value: 59 year

value: ENCBS843ATN at ENCODE; https://www.encodeproject.org/ENCBS843ATN/


title: proliferation CRISPR screen from K562 (ENCLB970MMU)

description:
https://www.encodeproject.org/experiments/ENCSR141ZPC/
***************
biological replicate number: 1
technical replicate number: 1
description: Tiling, Cas9/CRISPRk proliferation screen at the GATA1, MYB, and ZMYND8 loci
experiment encode accession: ENCSR141ZPC
assay title: proliferation CRISPR screen
assembly: GRCh38
encode release date: 2021-12-14
lab: Will Greenleaf, Stanford
library encode accession: ENCLB970MMU

source_name: Homo sapiens K562 cell line genetically modified (insertion) using transduction, genetically modified using CRISPR cutting (sgRNA) treated with 1 ug/mL Puromycin for 96 hours, 7 days post-nucleic acid delivery time

extract_protocol:
general protocol: https://www.encodeproject.org/documents/efd73756-33ac-41e4-839d-949c78bbc8f6/@@download/attachment/greenleaf_gata1_myb_zmynd8_crispr_screen_protocol.pdf
extraction method: QIAGEN DNeasy Blood & Tissue Kit

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Will Greenleaf, Stanford

value: Michael Bassik, Stanford

value: treatment_term_id:CHEBI:17939; treatment_term_name:Puromycin; treatment_type:chemical; duration:96; duration_units:hour;

value: ENCBS817QCK at ENCODE; https://www.encodeproject.org/ENCBS817QCK/


title: PRO-cap from endodermal cell (ENCLB816ANO)

description:
https://www.encodeproject.org/experiments/ENCSR443GRP/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived endodermal cells.
experiment encode accession: ENCSR443GRP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB816ANO

source_name: Homo sapiens female embryo (5 days) endodermal in vitro differentiated cells

value: endodermal cell

value: in vitro differentiated cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein

value: ENCBS781YES at ENCODE; https://www.encodeproject.org/ENCBS781YES/


title: DNase-seq from T778 (ENCLB203AOC)

description:
https://www.encodeproject.org/experiments/ENCSR446MFK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR446MFK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB203AOC

value: female

value: 69 year

value: John Stamatoyannopoulos, UW

value: Garvan Institute

value: ENCBS107DIL at ENCODE; https://www.encodeproject.org/ENCBS107DIL/


title: DNase-seq from HUDEP-2 (ENCLB718CNK)

description:
https://www.encodeproject.org/experiments/ENCSR139HUW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR139HUW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB718CNK

value: cell line

value: male

value: adult

value: unknown

value: Riken BioResource Cell Bank

value: ENCBS359ASF at ENCODE; https://www.encodeproject.org/ENCBS359ASF/


title: proliferation CRISPR screen from K562 (ENCLB659RSB)

description:
https://www.encodeproject.org/experiments/ENCSR138FGY/
***************
biological replicate number: 1
technical replicate number: 1
description: Tiling, dCas9/CRISPRd proliferation screen at the GATA1, MYB, and ZMYND8 loci
experiment encode accession: ENCSR138FGY
assay title: proliferation CRISPR screen
assembly: GRCh38
encode release date: 2021-12-14
lab: Will Greenleaf, Stanford
library encode accession: ENCLB659RSB

source_name: Homo sapiens K562 cell line genetically modified (insertion) using transduction, genetically modified using CRISPR dCas (sgRNA) treated with 1 ug/mL Puromycin for 96 hours, 21 days post-nucleic acid delivery time

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Will Greenleaf, Stanford

value: Michael Bassik, Stanford

value: treatment_term_id:CHEBI:17939; treatment_term_name:Puromycin; treatment_type:chemical; duration:96; duration_units:hour;

value: ENCBS004EUS at ENCODE; https://www.encodeproject.org/ENCBS004EUS/


title: proliferation CRISPR screen from K562 (ENCLB967MXO)

description:
https://www.encodeproject.org/experiments/ENCSR138FGY/
***************
biological replicate number: 2
technical replicate number: 1
description: Tiling, dCas9/CRISPRd proliferation screen at the GATA1, MYB, and ZMYND8 loci
experiment encode accession: ENCSR138FGY
assay title: proliferation CRISPR screen
assembly: GRCh38
encode release date: 2021-12-14
lab: Will Greenleaf, Stanford
library encode accession: ENCLB967MXO

value: female

value: ENCBS854UDL at ENCODE; https://www.encodeproject.org/ENCBS854UDL/


title: DNase-seq from activated B cell (ENCLB220HWW)

description:
https://www.encodeproject.org/experiments/ENCSR439ZKZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR439ZKZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB220HWW

source_name: Homo sapiens female adult (51 years) activated B primary cell treated with 1 ug/mL resiquimod for 48 hours, 10 ng/mL BAFF for 48 hours

value: activated B cell

value: primary cell

value: 51 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_id:CHEBI:36706; treatment_term_name:resiquimod; treatment_type:chemical; duration:48; duration_units:hour; treatment_term_id:UniProtKB:Q9Y275; treatment_term_name:BAFF; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS040KDF at ENCODE; https://www.encodeproject.org/ENCBS040KDF/


title: DNase-seq from activated B cell (ENCLB399SXJ)

description:
https://www.encodeproject.org/experiments/ENCSR439ZKZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR439ZKZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB399SXJ

value: adult

value: ENCBS069WJA at ENCODE; https://www.encodeproject.org/ENCBS069WJA/


title: DNase-seq from activated B cell (ENCLB295FYW)

description:
https://www.encodeproject.org/experiments/ENCSR439ZKZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR439ZKZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB295FYW

value: ENCBS499CSQ at ENCODE; https://www.encodeproject.org/ENCBS499CSQ/


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCLB404YRV)

description:
https://www.encodeproject.org/experiments/ENCSR436JXW/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic breast cancer to brain.
experiment encode accession: ENCSR436JXW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB404YRV

source_name: Homo sapiens female adult (72 years) Metastatic Breast Carcinoma in the Brain tissue

value: tissue

value: 72 year

value: Haiyuan Yu, Cornell

value: CHTN

value: ENCBS240WOG at ENCODE; https://www.encodeproject.org/ENCBS240WOG/


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCLB347NIO)

description:
https://www.encodeproject.org/experiments/ENCSR436JXW/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic breast cancer to brain.
experiment encode accession: ENCSR436JXW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB347NIO

value: female


title: PRO-cap from parotid gland (ENCLB045FDO)

description:
https://www.encodeproject.org/experiments/ENCSR431OQI/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Parotid gland.
experiment encode accession: ENCSR431OQI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB045FDO

source_name: Homo sapiens parotid gland tissue

value: parotid gland

value: not collected

value: unknown

value: Ahmed Mohyeldin

value: ENCBS010XSF at ENCODE; https://www.encodeproject.org/ENCBS010XSF/


title: PRO-cap from endothelial cell (ENCLB626IPE)

description:
https://www.encodeproject.org/experiments/ENCSR222JNI/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 derived endothelial cells.
experiment encode accession: ENCSR222JNI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB626IPE

source_name: Homo sapiens male adult (53 years) endothelial in vitro differentiated cells

value: endothelial cell

value: in vitro differentiated cells

value: male

value: 53 year

value: Bradley Bernstein

value: ENCBS451BGO at ENCODE; https://www.encodeproject.org/ENCBS451BGO/


title: DNase-seq from HUDEP-2 (ENCLB643ODR)

description:
https://www.encodeproject.org/experiments/ENCSR136SHW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136SHW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB643ODR

value: cell line

value: adult

value: John Stamatoyannopoulos, UW

value: Riken BioResource Cell Bank

value: ENCBS515FTN at ENCODE; https://www.encodeproject.org/ENCBS515FTN/


title: PRO-cap from endodermal cell (ENCLB768MNC)

description:
https://www.encodeproject.org/experiments/ENCSR443GRP/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in H9 derived endodermal cells.
experiment encode accession: ENCSR443GRP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB768MNC

value: endodermal cell

value: female

value: healthy

value: embryonic

value: 5 day

value: Haiyuan Yu, Cornell

value: ENCBS785TDE at ENCODE; https://www.encodeproject.org/ENCBS785TDE/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB937TMV)

description:
https://www.encodeproject.org/experiments/ENCSR136JHK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136JHK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB937TMV

source_name: Homo sapiens female adult (34 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 34 year

value: AllCells

value: ENCBS256ZXY at ENCODE; https://www.encodeproject.org/ENCBS256ZXY/


title: DNase-seq from T-helper 2 cell (ENCLB649MEE)

description:
https://www.encodeproject.org/experiments/ENCSR136URU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136URU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB649MEE

source_name: Homo sapiens male adult (56 years) T-helper 2 primary cell

value: T-helper 2 cell

value: male

value: 56 year

value: ENCBS692DUA at ENCODE; https://www.encodeproject.org/ENCBS692DUA/


title: PRO-cap from endothelial cell (ENCLB575KAA)

description:
https://www.encodeproject.org/experiments/ENCSR222JNI/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 derived endothelial cells.
experiment encode accession: ENCSR222JNI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB575KAA

value: endothelial cell

value: in vitro differentiated cells

value: adult

value: 53 year

value: Bradley Bernstein

value: ENCBS947AKF at ENCODE; https://www.encodeproject.org/ENCBS947AKF/


title: PRO-cap from thyroid gland (ENCLB957TZV)

description:
https://www.encodeproject.org/experiments/ENCSR431MXP/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Thyroid gland.
experiment encode accession: ENCSR431MXP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB957TZV

source_name: Homo sapiens female adult (51 years) thyroid gland tissue

value: thyroid gland

value: tissue

value: female

value: 51 year

value: Haiyuan Yu, Cornell

value: GTEx

value: ENCBS695NRD at ENCODE; https://www.encodeproject.org/ENCBS695NRD/


title: PRO-cap from parotid gland (ENCLB491CDA)

description:
https://www.encodeproject.org/experiments/ENCSR431OQI/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Parotid gland.
experiment encode accession: ENCSR431OQI
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB491CDA

value: parotid gland

value: not collected

value: unknown

value: Ahmed Mohyeldin

value: ENCBS010XSF at ENCODE; https://www.encodeproject.org/ENCBS010XSF/


title: DNase-seq from immature natural killer cell (ENCLB114CTX)

description:
https://www.encodeproject.org/experiments/ENCSR138CUE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR138CUE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB114CTX

source_name: Homo sapiens male adult (30 years) immature natural killer primary cell

value: immature natural killer cell

value: primary cell

value: male

value: 30 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS177PDP at ENCODE; https://www.encodeproject.org/ENCBS177PDP/


title: PRO-cap from left colon (ENCLB063BUP)

description:
https://www.encodeproject.org/experiments/ENCSR220OLX/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left colon.
experiment encode accession: ENCSR220OLX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB063BUP

source_name: Homo sapiens female adult (46 years) left colon tissue

value: left colon

value: tissue

value: female

value: DM:no; HTN:no; CAD:no

value: adult

value: 46 year

value: Michael Snyder

value: ENCBS671GUJ at ENCODE; https://www.encodeproject.org/ENCBS671GUJ/


title: PRO-cap from thyroid gland (ENCLB143SWF)

description:
https://www.encodeproject.org/experiments/ENCSR431MXP/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Thyroid gland.
experiment encode accession: ENCSR431MXP
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB143SWF

value: thyroid gland

value: 51 year

value: Haiyuan Yu, Cornell

value: GTEx

value: ENCBS695NRD at ENCODE; https://www.encodeproject.org/ENCBS695NRD/


title: PRO-cap from spleen (ENCLB371CCP)

description:
https://www.encodeproject.org/experiments/ENCSR219NJB/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Spleen.
experiment encode accession: ENCSR219NJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB371CCP

source_name: Homo sapiens female adult (61 years) spleen tissue

value: spleen

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: ENCBS452IFB at ENCODE; https://www.encodeproject.org/ENCBS452IFB/


title: PRO-cap from A549 (ENCLB272NEF)

description:
https://www.encodeproject.org/experiments/ENCSR219IHS/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Non-small cell adenocarcinoma cell line.
experiment encode accession: ENCSR219IHS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB272NEF

source_name: Homo sapiens A549 cell line

value: cell line

value: male

value: 58 year

value: ATCC

value: ENCBS563TRE at ENCODE; https://www.encodeproject.org/ENCBS563TRE/


title: PRO-cap from heart right ventricle (ENCLB249CWH)

description:
https://www.encodeproject.org/experiments/ENCSR219QKX/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Right ventricle of heart.
experiment encode accession: ENCSR219QKX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB249CWH

source_name: Homo sapiens male adult (40 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: DM:no; HTN:yes; CAD:no

value: adult

value: 40 year

value: ENCBS555EZC at ENCODE; https://www.encodeproject.org/ENCBS555EZC/


title: PRO-cap from left colon (ENCLB619UPL)

description:
https://www.encodeproject.org/experiments/ENCSR220OLX/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left colon.
experiment encode accession: ENCSR220OLX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB619UPL

value: left colon

value: female

value: DM:no; HTN:no; CAD:no

value: 46 year

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS671GUJ at ENCODE; https://www.encodeproject.org/ENCBS671GUJ/


title: DNase-seq from GOT3 (ENCLB281HHL)

description:
https://www.encodeproject.org/experiments/ENCSR218CZK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR218CZK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB281HHL

source_name: Homo sapiens GOT3 cell line

value: cell line

value: 76 year

value: John Stamatoyannopoulos, UW

value: Garvan Institute

value: ENCBS828PPD at ENCODE; https://www.encodeproject.org/ENCBS828PPD/


title: DNase-seq from natural killer cell (ENCLB190ZLE)

description:
https://www.encodeproject.org/experiments/ENCSR220XLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR220XLJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB190ZLE

source_name: Homo sapiens male adult (37 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: male

value: healthy

value: 37 year

value: Shelly Heimfeld

value: ENCBS504AAX at ENCODE; https://www.encodeproject.org/ENCBS504AAX/


title: STARR-seq from HepG2 (ENCLB197YVD)

description:
https://www.encodeproject.org/experiments/ENCSR135NXN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR135NXN
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR002ZDU
encode release date: 2020-06-11
lab: Kevin White, UChicago
library encode accession: ENCLB197YVD
fragmentation methods: shearing (generic)
size range: 200-600

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

value: hepatocellular carcinoma

value: child

value: 15 year

value: Kevin White, UChicago

value: ATCC

value: ENCBS155CUV at ENCODE; https://www.encodeproject.org/ENCBS155CUV/


title: PRO-cap from A549 (ENCLB035ZTH)

description:
https://www.encodeproject.org/experiments/ENCSR219IHS/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Non-small cell adenocarcinoma cell line.
experiment encode accession: ENCSR219IHS
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB035ZTH

value: cell line

value: adult

value: 58 year

value: Haiyuan Yu, Cornell

value: ENCBS226WXS at ENCODE; https://www.encodeproject.org/ENCBS226WXS/


title: STARR-seq from HepG2 (ENCLB459ABN)

description:
https://www.encodeproject.org/experiments/ENCSR135NXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR135NXN
assay title: STARR-seq
assembly: GRCh38
possible controls: ENCSR002ZDU
encode release date: 2020-06-11
lab: Kevin White, UChicago
library encode accession: ENCLB459ABN
fragmentation methods: shearing (generic)
size range: 200-600

value: ENCBS163FYM at ENCODE; https://www.encodeproject.org/ENCBS163FYM/


title: PRO-cap from heart right ventricle (ENCLB444QFA)

description:
https://www.encodeproject.org/experiments/ENCSR219QKX/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Right ventricle of heart.
experiment encode accession: ENCSR219QKX
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB444QFA

value: heart right ventricle

value: tissue

value: male

value: DM:no; HTN:yes; CAD:no

value: 40 year

value: Michael Snyder

value: ENCBS555EZC at ENCODE; https://www.encodeproject.org/ENCBS555EZC/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB440LQE)

description:
https://www.encodeproject.org/experiments/ENCSR136EXX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136EXX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB440LQE

source_name: Homo sapiens female adult (37 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 37 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: ENCBS292EOP at ENCODE; https://www.encodeproject.org/ENCBS292EOP/


title: DNase-seq from right lobe of liver (ENCLB912EQZ)

description:
https://www.encodeproject.org/experiments/ENCSR131KDD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR131KDD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB912EQZ

source_name: Homo sapiens female child (16 years) right lobe of liver tissue

value: right lobe of liver

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Shin Lin

value: ENCBS825OQZ at ENCODE; https://www.encodeproject.org/ENCBS825OQZ/


title: DNase-seq from right lobe of liver (ENCLB107ESZ)

description:
https://www.encodeproject.org/experiments/ENCSR131KDD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR131KDD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB107ESZ

value: tissue

value: ENCBS482IGT at ENCODE; https://www.encodeproject.org/ENCBS482IGT/


title: DNase-seq from K562 (ENCLB277CYH)

description:
https://www.encodeproject.org/experiments/ENCSR133YRZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133YRZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB277CYH

source_name: Homo sapiens K562 cell line

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: ATCC

value: ENCBS092NQM at ENCODE; https://www.encodeproject.org/ENCBS092NQM/


title: DNase-seq from GOT3 (ENCLB416NIL)

description:
https://www.encodeproject.org/experiments/ENCSR218CZK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR218CZK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB416NIL

value: female

value: 76 year

value: John Stamatoyannopoulos, UW

value: Garvan Institute

value: ENCBS182IPC at ENCODE; https://www.encodeproject.org/ENCBS182IPC/


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCLB711CEV)

description:
https://www.encodeproject.org/experiments/ENCSR216FUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic breast cancer to brain.
experiment encode accession: ENCSR216FUJ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB711CEV

source_name: Homo sapiens female adult (79 years) Metastatic Breast Carcinoma in the Brain tissue

value: 79 year

value: Haiyuan Yu, Cornell

value: CHTN

value: ENCBS333QSD at ENCODE; https://www.encodeproject.org/ENCBS333QSD/


title: DNase-seq from HCT116 (ENCLB489BGF)

description:
https://www.encodeproject.org/experiments/ENCSR216YZD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR216YZD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB489BGF

source_name: Homo sapiens HCT116 cell line

value: male

value: colorectal carcinoma

value: 48 year

value: Erez Aiden

value: ENCBS138QFQ at ENCODE; https://www.encodeproject.org/ENCBS138QFQ/


title: PRO-cap from Metastatic Breast Carcinoma in the Brain (ENCLB756VPO)

description:
https://www.encodeproject.org/experiments/ENCSR216FUJ/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Metastatic breast cancer to brain.
experiment encode accession: ENCSR216FUJ
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB756VPO

value: tissue

value: adult


title: PRO-cap from GM23338 (ENCLB269QPB)

description:
https://www.encodeproject.org/experiments/ENCSR215OJB/
***************
biological replicate number: 2
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 iPSCs via Sendai-viral Yamanaka factors.
experiment encode accession: ENCSR215OJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB269QPB

source_name: Homo sapiens GM23338 cell line

value: cell line

value: 53 year

value: Bradley Bernstein

value: ENCBS958MLZ at ENCODE; https://www.encodeproject.org/ENCBS958MLZ/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB753PCS)

description:
https://www.encodeproject.org/experiments/ENCSR130SOU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR130SOU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB753PCS

source_name: Homo sapiens male adult (42 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS130UYS at ENCODE; https://www.encodeproject.org/ENCBS130UYS/


title: PRO-cap from lower lobe of left lung (ENCLB493ZRN)

description:
https://www.encodeproject.org/experiments/ENCSR216UNW/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Lower lobe of left lung.
experiment encode accession: ENCSR216UNW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB493ZRN

source_name: Homo sapiens male adult (37 years) lower lobe of left lung tissue

value: lower lobe of left lung

value: male

value: 37 year

value: Haiyuan Yu, Cornell

value: Michael Snyder

value: ENCBS867JXK at ENCODE; https://www.encodeproject.org/ENCBS867JXK/


title: PRO-cap from GM23338 (ENCLB316BJL)

description:
https://www.encodeproject.org/experiments/ENCSR215OJB/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 iPSCs via Sendai-viral Yamanaka factors.
experiment encode accession: ENCSR215OJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB316BJL

value: adult

value: ENCBS229TZS at ENCODE; https://www.encodeproject.org/ENCBS229TZS/


title: DNase-seq from activated T-cell (ENCLB203WXU)

description:
https://www.encodeproject.org/experiments/ENCSR131CTE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR131CTE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB203WXU

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 50 U/mL Interleukin-2 for 4 hours

value: activated T-cell

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS204WXE at ENCODE; https://www.encodeproject.org/ENCBS204WXE/


title: PRO-cap from lower lobe of left lung (ENCLB360RCP)

description:
https://www.encodeproject.org/experiments/ENCSR216UNW/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Lower lobe of left lung.
experiment encode accession: ENCSR216UNW
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB360RCP

value: tissue


title: DNase-seq from activated T-cell (ENCLB285DSL)

description:
https://www.encodeproject.org/experiments/ENCSR131CTE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR131CTE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2025-09-20
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB285DSL

value: primary cell

value: ENCBS080HIJ at ENCODE; https://www.encodeproject.org/ENCBS080HIJ/


title: PRO-cap from GM23338 (ENCLB100EWJ)

description:
https://www.encodeproject.org/experiments/ENCSR215OJB/
***************
biological replicate number: 2
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 iPSCs via Sendai-viral Yamanaka factors.
experiment encode accession: ENCSR215OJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB100EWJ

value: cell line

value: 53 year

value: Bradley Bernstein

value: ENCBS958MLZ at ENCODE; https://www.encodeproject.org/ENCBS958MLZ/


title: PRO-cap from GM23338 (ENCLB505JSV)

description:
https://www.encodeproject.org/experiments/ENCSR215OJB/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in PGP-1 iPSCs via Sendai-viral Yamanaka factors.
experiment encode accession: ENCSR215OJB
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB505JSV

value: male


title: PRO-cap from heart left ventricle (ENCLB666IDS)

description:
https://www.encodeproject.org/experiments/ENCSR426RMA/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left ventricle of heart.
experiment encode accession: ENCSR426RMA
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB666IDS

source_name: Homo sapiens male adult (40 years) heart left ventricle tissue

value: heart left ventricle

value: DM:no; HTN:yes; CAD:no

value: 40 year

value: Haiyuan Yu, Cornell

value: ENCBS919EGV at ENCODE; https://www.encodeproject.org/ENCBS919EGV/


title: PRO-cap from heart left ventricle (ENCLB634JDM)

description:
https://www.encodeproject.org/experiments/ENCSR426RMA/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in Left ventricle of heart.
experiment encode accession: ENCSR426RMA
assay title: PRO-cap
assembly: GRCh38
encode release date: 2025-12-11
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB634JDM

value: adult

value: Michael Snyder