title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB988YMQ)

description:
https://www.encodeproject.org/experiments/ENCSR442SDV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR442SDV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB988YMQ

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 48 hours

value: primary cell

value: 33 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour;

value: ENCBS143WAD at ENCODE; https://www.encodeproject.org/ENCBS143WAD/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: Primary_ADC_cell_line_3

status: Public on Apr 27 2021

type: RNA

city: Oulu

first: Mervi

last: Kreus

address: Aapistie 5A

country: Finland

institute: University of Oulu

description: Gene expression data from stromal cells cultured from lung adenocarcinoma tumor tissue

hyb_protocol: GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450; fluidics script: FS450_0001.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 7G.

data_processing: Analysis of the microarray expression data was done using the R/Bioconductor through a graphical user interface, Chipster 3.12.5. Normalization was performed using custom chip description file for hgu133Aplus2. Intensity data were log2-transformed, and quantile normalized using robust multi-array average (RMA).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary pulmonary fibroblasts from Lung adenocarcinoma patient 3

label_protocol: Biotinylated cRNA were prepared with 3'IVT Express Kit and Affymetrix GeneChip® Hybridization, Wash and Stain Kit.

growth_protocol: Cells were plated at a density of 2000 cells/cm2 and grown for 72 hours.

extract_protocol: Total RNA was extracted using Qiagen Rneasy mini kit.

treatment_protocol: No additional treatments were applied to the cultured cell lines.

tag: tissue

value: Primary pulmonary fibroblasts

tag: age

tag: Sex

value: Male

tag: smoking status

value: Ex-smoker


title: DNase-seq from activated T-cell (ENCLB472MJN)

status: Public on Apr 22 2021

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/ENCSR223KKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR223KKX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB472MJN

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens female adult (33 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: activated T-cell

tag: biosample encode accession

value: female

tag: dev stage

value: adult

tag: lab

tag: source

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

tag: link

value: ENCBS123TAF at ENCODE; https://www.encodeproject.org/ENCBS123TAF/


title: DNase-seq from activated T-cell (ENCLB036IMM)

description:
https://www.encodeproject.org/experiments/ENCSR219KTW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR219KTW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB036IMM

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours

value: male

value: 38 year

value: ENCBS534SBH at ENCODE; https://www.encodeproject.org/ENCBS534SBH/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB907CBE)

description:
https://www.encodeproject.org/experiments/ENCSR692PKU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR692PKU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB907CBE

source_name: Homo sapiens male adult (38 years) effector memory CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: primary cell

value: John Stamatoyannopoulos, UW

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS958OIH at ENCODE; https://www.encodeproject.org/ENCBS958OIH/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB968IAS)

description:
https://www.encodeproject.org/experiments/ENCSR698VDM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR698VDM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB968IAS

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 50 U/mL Interleukin-2 for 4 hours

value: 42 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: ENCBS737BYZ at ENCODE; https://www.encodeproject.org/ENCBS737BYZ/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB885EJN)

description:
https://www.encodeproject.org/experiments/ENCSR696LPC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR696LPC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB885EJN

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS002SWL at ENCODE; https://www.encodeproject.org/ENCBS002SWL/


title: Primary_ADC_cell_line_1

source_name: Primary pulmonary fibroblasts from Lung adenocarcinoma patient 1

value: Primary pulmonary fibroblasts

value: Female

value: Non-smoker


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB744JIJ)

description:
https://www.encodeproject.org/experiments/ENCSR438USP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR438USP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB744JIJ

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

value: male

value: adult

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:P01375; treatment_term_name:TNF-alpha; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS703HIM at ENCODE; https://www.encodeproject.org/ENCBS703HIM/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB462IIH)

description:
https://www.encodeproject.org/experiments/ENCSR703AYZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR703AYZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-19
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB462IIH

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-4 for 24 hours

value: primary cell

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS777ZBQ at ENCODE; https://www.encodeproject.org/ENCBS777ZBQ/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB976YGI)

description:
https://www.encodeproject.org/experiments/ENCSR436JRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR436JRE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB976YGI

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

value: 20 year

value: Yijun Ruan, JAX

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

value: ENCBS316YKK at ENCODE; https://www.encodeproject.org/ENCBS316YKK/

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


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB174CUY)

description:
https://www.encodeproject.org/experiments/ENCSR965ZWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR965ZWZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB174CUY

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL TNF-alpha for 4 hours

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:P01375; treatment_term_name:TNF-alpha; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS643PKB at ENCODE; https://www.encodeproject.org/ENCBS643PKB/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from vagina (ENCLB724ZGL)

description:
https://www.encodeproject.org/experiments/ENCSR437AYW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR437AYW
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB724ZGL

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

value: vagina

value: tissue

value: female

value: adult

value: 53 year

value: Kristin Ardlie

value: ENCBS585SGJ at ENCODE; https://www.encodeproject.org/ENCBS585SGJ/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Human GM12878 combined data from Rao, Huntley et al., 2014

status: Public on Apr 23 2021

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
Rao_Huntley_et_al_2014_GM12878
Some libraries sequenced with Illumina HiSeq 2500

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (3D-DNA, Juicer)
Centromere position identification (repeat sequence mapping or structural analysis, 3D-DNA/JBAT)
Aggregate chromosome analysis (3D-DNA)
Variant calling (DRAGEN pipeline)
Chromosome-length variant phasing (3D-DNA)
Genome_build: In addition to those generate as part of the study, the following existing genome builds were used: GRCg6a (domestic chicken); Xla.v91 (African clawed frog); AaegL5.0 (Yellow fever mosquito), CpipJ3 (Southern domestic mosquito); Release_6_plus_ISO1_MT (fruit fly, with chromosome arms merged for ACA analysis resulting in Release_6_plus_ISO1_MT_merged); WBcel235 (C. elegans); sacCer3 (baker's yeast); arahy.Tifrunner.gnm2.J5K5 (ground nut); 161010_Chinese_Spring_v1.0_pseudomolecules (bread wheat).
Supplementary_files_format_and_content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary_files_format_and_content: hic: contact maps generated by aligning Hi-C data to corresponding chromosome-length reference sequences. In addition to standard contact maps generated for all genomic positions across chromosomes the uploaded files include ACA (aggregate chromosome analysis) maps and phasing contact maps representing interactions between positions on the genome that contain heterogyzous SNPs. For more details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: wig: tracks showing the alignment frequency of Hi-C reads from read pairs that contain centromere repeat-specifc sequences.
Supplementary_files_format_and_content: bedpe: Files describing the tentative position of centromeres in chromosome-length genome assemblies, identified either by mapping repeat sequences associated with the centromere or via analysis of the contact map for evidence of centromere-to-telomere folding axis. For details see Hoencamp et al., Supplement.
Supplementary_files_format_and_content: vcf.gz: Variants (specifically SNPs) identivied by the DRAGEN variant calling pipeline from aligning Hi-C data to chromosome-length references generated via Hi-C-guided assembly and phased using the 3D-DNA Hi-C-guided phasing module.

source_name: lymphoblastoid

extract_protocol:
Extraction protocol is described as part of the library construction protocol.
The Hi-C libraries were prepared following the in situ Hi-C strategy (Rao, Huntley et al., 2014). Briefly, cells or tissue were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. Afterward DNA was handled according to standard Illumina library construction protocol. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3 end. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on various Illumina instruments following the manufacturer's protocols. Fpr the tammar wallaby, a short insert-size PCR-free DNA-Seq library was prepared following the ClaSeek protocol.

value: lymphoblasts


title: ATAC-seq from gastrocnemius medialis (ENCLB194NLZ)

description:
https://www.encodeproject.org/experiments/ENCSR689SDA/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human gastrocnemius medialis
experiment encode accession: ENCSR689SDA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-06-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB194NLZ
size range: 150-250

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

value: gastrocnemius medialis

value: Michael Snyder, Stanford

value: ENCBS429IGV at ENCODE; https://www.encodeproject.org/ENCBS429IGV/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB048UTE)

description:
https://www.encodeproject.org/experiments/ENCSR688DKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR688DKY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB048UTE

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-4 for 1 hour

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:1; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS146MEO at ENCODE; https://www.encodeproject.org/ENCBS146MEO/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB928PUT)

description:
https://www.encodeproject.org/experiments/ENCSR688OIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR688OIJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB928PUT

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 48 hours, 100 ng/mL Interleukin-2 for 48 hours

value: female

value: adult

value: 33 year

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: ENCBS951QFW at ENCODE; https://www.encodeproject.org/ENCBS951QFW/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: ATAC-seq from testis (ENCLB258HLF)

description:
https://www.encodeproject.org/experiments/ENCSR210NKB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human testis
experiment encode accession: ENCSR210NKB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-06-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB258HLF
size range: 150-250

source_name: Homo sapiens testis tissue male adult (37 years)

value: testis

value: tissue

value: 37 year

value: ENCBS133MOQ at ENCODE; https://www.encodeproject.org/ENCBS133MOQ/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB639ROE)

description:
https://www.encodeproject.org/experiments/ENCSR207CQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR207CQH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB639ROE

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL Interleukin-12 subunit alpha for 48 hours, 100 ng/mL Interleukin-12 subunit beta for 48 hours

value: primary cell

value: male

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:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS783PCA at ENCODE; https://www.encodeproject.org/ENCBS783PCA/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB645ZBZ)

description:
https://www.encodeproject.org/experiments/ENCSR210JVF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR210JVF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB645ZBZ

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 1 hour, 100 ng/mL Interleukin-4 for 1 hour

value: female

value: John Stamatoyannopoulos, UW

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS736QNA at ENCODE; https://www.encodeproject.org/ENCBS736QNA/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB860DEN)

description:
https://www.encodeproject.org/experiments/ENCSR205ECC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR205ECC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB860DEN

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 48 hours, 100 ng/mL Interleukin-15 for 48 hours

value: adult

value: 33 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: ENCBS221UNT at ENCODE; https://www.encodeproject.org/ENCBS221UNT/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB025DHZ)

description:
https://www.encodeproject.org/experiments/ENCSR953UJL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR953UJL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB025DHZ

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours, 100 ng/mL Interleukin-12 subunit beta for 4 hours

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS079FSC at ENCODE; https://www.encodeproject.org/ENCBS079FSC/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB363HWT)

description:
https://www.encodeproject.org/experiments/ENCSR424MWH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR424MWH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB363HWT

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-21 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: description

value: 39 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:Q9HBE4; treatment_term_name:Interleukin-21; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS842AQJ at ENCODE; https://www.encodeproject.org/ENCBS842AQJ/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: ATAC-seq from breast epithelium (ENCLB957OSQ)

description:
https://www.encodeproject.org/experiments/ENCSR955JSO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human mammary gland
experiment encode accession: ENCSR955JSO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB957OSQ
size range: 150-250

source_name: Homo sapiens male adult (54 years) breast epithelium tissue

value: breast epithelium

value: tissue

value: male

value: 54 year

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS748DLA at ENCODE; https://www.encodeproject.org/ENCBS748DLA/


title: DNase-seq from activated T-cell (ENCLB427HRQ)

description:
https://www.encodeproject.org/experiments/ENCSR416QNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR416QNA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB427HRQ

source_name: Homo sapiens female adult (33 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: activated T-cell

value: female

value: adult

value: 33 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; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS766QIV at ENCODE; https://www.encodeproject.org/ENCBS766QIV/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB411NXI)

description:
https://www.encodeproject.org/experiments/ENCSR951MYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR951MYM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB411NXI

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour

value: primary cell

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour;

value: ENCBS723NNV at ENCODE; https://www.encodeproject.org/ENCBS723NNV/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB423EKJ)

description:
https://www.encodeproject.org/experiments/ENCSR679EFH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR679EFH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB423EKJ

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours

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

value: ENCBS705CAL at ENCODE; https://www.encodeproject.org/ENCBS705CAL/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB617QOU)

description:
https://www.encodeproject.org/experiments/ENCSR408GYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR408GYQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB617QOU
instrument models: Illumina HiSeq 4000,Illumina NextSeq 500

source_name: Homo sapiens female adult (37 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-17A for 4 hours

value: CD4-positive, alpha-beta T cell

value: 37 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:Q16552; treatment_term_name:Interleukin-17A; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS276SOD at ENCODE; https://www.encodeproject.org/ENCBS276SOD/

value: Derived from ENCODE donor ENCDO514TDF; https://www.encodeproject.org/ENCDO514TDF/


title: DNase-seq from T-helper 9 cell (ENCLB102CHD)

description:
https://www.encodeproject.org/experiments/ENCSR433WOV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR433WOV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB102CHD

source_name: Homo sapiens female adult (33 years) T-helper 9 primary cell treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours

value: T-helper 9 cell

value: female

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

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: ENCBS274LRN at ENCODE; https://www.encodeproject.org/ENCBS274LRN/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB155SGK)

description:
https://www.encodeproject.org/experiments/ENCSR950YTI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR950YTI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB155SGK

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, 50 U/mL Interleukin-2 for 4 hours

value: primary cell

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: ENCBS818CQE at ENCODE; https://www.encodeproject.org/ENCBS818CQE/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from gamma-delta T cell (ENCLB207OSA)

description:
https://www.encodeproject.org/experiments/ENCSR676GAW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR676GAW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB207OSA

source_name: Homo sapiens female adult (33 years) gamma-delta T primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: gamma-delta T cell

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS591QDH at ENCODE; https://www.encodeproject.org/ENCBS591QDH/


title: DNase-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB174QOX)

description:
https://www.encodeproject.org/experiments/ENCSR396EWH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR396EWH
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB174QOX

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

value: male

value: 43 year

value: Yijun Ruan, JAX

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

value: ENCBS620HRS at ENCODE; https://www.encodeproject.org/ENCBS620HRS/

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


title: ATAC-seq from excitatory neuron (ENCLB316BUG)

description:
https://www.encodeproject.org/experiments/ENCSR187VKR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR187VKR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-02-03
lab: Yin Shen, UCSF
library encode accession: ENCLB316BUG
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

source_name: Homo sapiens male adult (30 years) excitatory neuron in vitro differentiated cells genetically modified (insertion) using TALEN originated from WTC11

value: excitatory neuron

value: in vitro differentiated cells

value: adult

value: 30 year

value: Yin Shen, UCSF

value: Li Gan

value: ENCBS135UXG at ENCODE; https://www.encodeproject.org/ENCBS135UXG/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: DNase-seq from mesothelial cell of epicardium (ENCLB728ALH)

description:
https://www.encodeproject.org/experiments/ENCSR945KSP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR945KSP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB728ALH

source_name: Homo sapiens female embryo (5 days) mesothelial of epicardium in vitro differentiated cells

value: mesothelial cell of epicardium

value: WA09 derived epicardium (mesothelium)

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

tag: health state

value: healthy

value: ENCBS698CFG at ENCODE; https://www.encodeproject.org/ENCBS698CFG/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB149RMD)

description:
https://www.encodeproject.org/experiments/ENCSR940UEK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR940UEK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB149RMD

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-10 for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 39 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P22301; treatment_term_name:Interleukin-10; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS597KFJ at ENCODE; https://www.encodeproject.org/ENCBS597KFJ/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB431GLG)

description:
https://www.encodeproject.org/experiments/ENCSR943BCO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR943BCO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB431GLG

source_name: Homo sapiens male adult (38 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: male

value: adult

value: 38 year

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: ENCBS902BZH at ENCODE; https://www.encodeproject.org/ENCBS902BZH/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB418MMR)

description:
https://www.encodeproject.org/experiments/ENCSR669NQZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR669NQZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB418MMR

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-7 for 4 hours

value: female

value: 33 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P13232; treatment_term_name:Interleukin-7; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS884ZUR at ENCODE; https://www.encodeproject.org/ENCBS884ZUR/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: ATAC-seq from excitatory neuron (ENCLB066COW)

description:
https://www.encodeproject.org/experiments/ENCSR187VKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR187VKR
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-02-03
lab: Yin Shen, UCSF
library encode accession: ENCLB066COW
instrument models: Illumina HiSeq 4000,Illumina NovaSeq 6000

value: excitatory neuron

value: in vitro differentiated cells

value: 30 year

value: Yin Shen, UCSF

value: Li Gan

value: ENCBS583KRL at ENCODE; https://www.encodeproject.org/ENCBS583KRL/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: DNase-seq from sigmoid colon (ENCLB865DPH)

description:
https://www.encodeproject.org/experiments/ENCSR391YAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR391YAV
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865DPH

source_name: Homo sapiens male adult (54 years) sigmoid colon tissue

value: sigmoid colon

value: tissue

value: male

value: adult

value: 54 year

value: John Stamatoyannopoulos, UW

value: Kristin Ardlie

value: ENCBS402XYB at ENCODE; https://www.encodeproject.org/ENCBS402XYB/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB429XOW)

description:
https://www.encodeproject.org/experiments/ENCSR388NOI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR388NOI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB429XOW

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-17A for 1 hour

value: CD4-positive, alpha-beta T cell

value: primary cell

value: female

value: 39 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:Q16552; treatment_term_name:Interleukin-17A; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS948NAS at ENCODE; https://www.encodeproject.org/ENCBS948NAS/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB432FBG)

description:
https://www.encodeproject.org/experiments/ENCSR419CKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR419CKG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB432FBG

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-4 for 1 hour

value: 33 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS878OHR at ENCODE; https://www.encodeproject.org/ENCBS878OHR/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB178DNJ)

description:
https://www.encodeproject.org/experiments/ENCSR960EVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR960EVM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB178DNJ

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 48 hours, 100 ng/mL Interleukin-4 for 48 hours

value: adult

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS127NRQ at ENCODE; https://www.encodeproject.org/ENCBS127NRQ/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB530CBQ)

description:
https://www.encodeproject.org/experiments/ENCSR935HEI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR935HEI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB530CBQ

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: male

value: 20 year

value: Yijun Ruan, JAX

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS380JPF at ENCODE; https://www.encodeproject.org/ENCBS380JPF/

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


title: ATAC-seq from transverse colon (ENCLB091AYH)

description:
https://www.encodeproject.org/experiments/ENCSR386HAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human transverse colon
experiment encode accession: ENCSR386HAZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB091AYH
size range: 150-250

source_name: Homo sapiens transverse colon tissue female adult (51 year)

value: transverse colon

value: tissue

value: female

value: Michael Snyder, Stanford

value: 51 year

value: ENCBS360EPF at ENCODE; https://www.encodeproject.org/ENCBS360EPF/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: DNase-seq from H9 (ENCLB062OYL)

description:
https://www.encodeproject.org/experiments/ENCSR662RIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR662RIZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB062OYL

source_name: Homo sapiens H9 cell line

tag: line

value: cell line

value: H9 ES cells

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: healthy

value: ENCBS471SZK at ENCODE; https://www.encodeproject.org/ENCBS471SZK/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB865PHR)

description:
https://www.encodeproject.org/experiments/ENCSR180KMR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR180KMR
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865PHR

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 50 U/mL Interleukin-2 for 4 hours

value: primary cell

value: adult

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:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS737ISY at ENCODE; https://www.encodeproject.org/ENCBS737ISY/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: ATAC-seq from transverse colon (ENCLB018MKK)

description:
https://www.encodeproject.org/experiments/ENCSR668VCT/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human transverse colon
experiment encode accession: ENCSR668VCT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB018MKK
size range: 150-250

source_name: Homo sapiens transverse colon tissue male adult (37 years)

value: transverse colon

value: tissue

value: male

value: Michael Snyder, Stanford

value: 37 year

value: ENCBS572ESP at ENCODE; https://www.encodeproject.org/ENCBS572ESP/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB164CPC)

description:
https://www.encodeproject.org/experiments/ENCSR933VOY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933VOY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB164CPC

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours

value: 38 year

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

value: ENCBS535PDY at ENCODE; https://www.encodeproject.org/ENCBS535PDY/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB892SUF)

description:
https://www.encodeproject.org/experiments/ENCSR933HFM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933HFM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB892SUF

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-12 subunit alpha for 4 hours, 100 ng/mL Interleukin-12 subunit beta for 4 hours

value: primary cell

value: adult

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS086KJH at ENCODE; https://www.encodeproject.org/ENCBS086KJH/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB152LLE)

description:
https://www.encodeproject.org/experiments/ENCSR177GYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR177GYC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB152LLE

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 1 hour, 100 ng/mL Interleukin-2 for 1 hour

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

value: ENCBS113NST at ENCODE; https://www.encodeproject.org/ENCBS113NST/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB704THH)

description:
https://www.encodeproject.org/experiments/ENCSR175OHT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR175OHT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB704THH

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: male

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS239OGZ at ENCODE; https://www.encodeproject.org/ENCBS239OGZ/


title: DNase-seq from T-helper 1 cell (ENCLB746COG)

description:
https://www.encodeproject.org/experiments/ENCSR932OSG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR932OSG
assay title: DNase-seq
assembly: GRCh38
possible controls: ENCSR260UJJ
encode release date: 2020-09-25
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB746COG

source_name: Homo sapiens male adult (42 years) T-helper 1 primary cell treated with anti-CD3 and anti-CD28 coated beads for 16 hours, 50 U/mL Interleukin-2 for 16 hours

value: T-helper 1 cell

value: 42 year

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: ENCBS814RMF at ENCODE; https://www.encodeproject.org/ENCBS814RMF/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from effector memory CD4-positive, alpha-beta T cell (ENCLB686YNU)

description:
https://www.encodeproject.org/experiments/ENCSR173BJC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR173BJC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB686YNU

source_name: Homo sapiens male adult (42 years) effector memory CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: primary cell

value: adult

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS864MAM at ENCODE; https://www.encodeproject.org/ENCBS864MAM/


title: ATAC-seq from DND-41 (ENCLB946ZTU)

description:
https://www.encodeproject.org/experiments/ENCSR660WSB/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on human cell line DND-41
experiment encode accession: ENCSR660WSB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB946ZTU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens DND-41 cell line

value: cell line

value: child

value: 13 year

value: DSMZ

value: T-acute lymphoblastic leukemia (T-ALL; type III cortical)

value: ENCBS013RPN at ENCODE; https://www.encodeproject.org/ENCBS013RPN/

value: Derived from ENCODE donor ENCDO183AAA; https://www.encodeproject.org/ENCDO183AAA/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB776CTI)

description:
https://www.encodeproject.org/experiments/ENCSR173HPQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR173HPQ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB776CTI

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour

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:1; duration_units:hour;

value: ENCBS657ABO at ENCODE; https://www.encodeproject.org/ENCBS657ABO/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: ATAC-seq from DND-41 (ENCLB887BAP)

description:
https://www.encodeproject.org/experiments/ENCSR660WSB/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on human cell line DND-41
experiment encode accession: ENCSR660WSB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB887BAP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: male

value: ENCBS308ABW at ENCODE; https://www.encodeproject.org/ENCBS308ABW/


title: ATAC-seq from DND-41 (ENCLB169DQE)

description:
https://www.encodeproject.org/experiments/ENCSR660WSB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human cell line DND-41
experiment encode accession: ENCSR660WSB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB169DQE
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ENCBS167JGE at ENCODE; https://www.encodeproject.org/ENCBS167JGE/


title: DNase-seq from T-helper 1 cell (ENCLB917XRN)

description:
https://www.encodeproject.org/experiments/ENCSR384GGJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR384GGJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB917XRN

source_name: Homo sapiens male adult (38 years) T-helper 1 primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: T-helper 1 cell

value: primary cell

value: adult

value: 38 year

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS020KEB at ENCODE; https://www.encodeproject.org/ENCBS020KEB/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB977PJK)

description:
https://www.encodeproject.org/experiments/ENCSR171APM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR171APM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB977PJK

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 48 hours

value: female

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour;

value: ENCBS090AVS at ENCODE; https://www.encodeproject.org/ENCBS090AVS/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB577SMX)

description:
https://www.encodeproject.org/experiments/ENCSR167VIP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR167VIP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB577SMX

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 1 hour

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS869BMG at ENCODE; https://www.encodeproject.org/ENCBS869BMG/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB847CBB)

description:
https://www.encodeproject.org/experiments/ENCSR920JUM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR920JUM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB847CBB

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-4 for 1 hour

value: male

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS790TCU at ENCODE; https://www.encodeproject.org/ENCBS790TCU/


title: DNase-seq from activated T-cell (ENCLB446HQI)

description:
https://www.encodeproject.org/experiments/ENCSR660FSU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR660FSU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB446HQI

source_name: Homo sapiens female adult (33 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: 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: ENCBS679YMK at ENCODE; https://www.encodeproject.org/ENCBS679YMK/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB985TNI)

description:
https://www.encodeproject.org/experiments/ENCSR658NVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR658NVL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB985TNI

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL Interleukin-2 for 48 hours

value: primary cell

value: adult

value: 38 year

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: ENCBS159EWG at ENCODE; https://www.encodeproject.org/ENCBS159EWG/


title: ATAC-seq from NCI-H929 (ENCLB567EDU)

description:
https://www.encodeproject.org/experiments/ENCSR382LBS/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human cell line NCI-H929
experiment encode accession: ENCSR382LBS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB567EDU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens NCI-H929 cell line

value: cell line

value: female

value: 62 year

value: ATCC

value: IgAk myeloma

value: ENCBS952JSJ at ENCODE; https://www.encodeproject.org/ENCBS952JSJ/

value: Derived from ENCODE donor ENCDO220OYR; https://www.encodeproject.org/ENCDO220OYR/


title: ATAC-seq from NCI-H929 (ENCLB515ACH)

description:
https://www.encodeproject.org/experiments/ENCSR382LBS/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on human cell line NCI-H929
experiment encode accession: ENCSR382LBS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB515ACH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: John Stamatoyannopoulos, UW

value: ENCBS231ULS at ENCODE; https://www.encodeproject.org/ENCBS231ULS/


title: ATAC-seq from NCI-H929 (ENCLB065ROA)

description:
https://www.encodeproject.org/experiments/ENCSR382LBS/
***************
biological replicate number: 3
technical replicate number: 1
description: ATAC-seq on human cell line NCI-H929
experiment encode accession: ENCSR382LBS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB065ROA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ENCBS379IVU at ENCODE; https://www.encodeproject.org/ENCBS379IVU/


title: DNase-seq from stomach (ENCLB766ANJ)

description:
https://www.encodeproject.org/experiments/ENCSR163PKT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR163PKT
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB766ANJ

source_name: Homo sapiens male adult (54 years) stomach tissue

value: stomach

value: tissue

value: male

value: 54 year

value: Kristin Ardlie

value: ENCBS294WHX at ENCODE; https://www.encodeproject.org/ENCBS294WHX/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: DNase-seq from activated T-cell (ENCLB977GYY)

description:
https://www.encodeproject.org/experiments/ENCSR653OVF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR653OVF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB977GYY

source_name: Homo sapiens female adult (33 years) activated T-cell primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 50 U/mL Interleukin-2 for 1 hour

value: activated T-cell

value: primary cell

value: adult

value: 33 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS533QPZ at ENCODE; https://www.encodeproject.org/ENCBS533QPZ/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: ATAC-seq from thyroid gland (ENCLB721BMO)

description:
https://www.encodeproject.org/experiments/ENCSR914DTI/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human thyroid gland
experiment encode accession: ENCSR914DTI
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB721BMO
size range: 150-250

source_name: Homo sapiens female adult (53 years) thyroid gland tissue

value: thyroid gland

value: female

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS362EWE at ENCODE; https://www.encodeproject.org/ENCBS362EWE/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB634ZZX)

description:
https://www.encodeproject.org/experiments/ENCSR653ISV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR653ISV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB634ZZX

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 24 hours

value: John Stamatoyannopoulos, UW

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

value: ENCBS689GHV at ENCODE; https://www.encodeproject.org/ENCBS689GHV/


title: ATAC-seq from breast epithelium (ENCLB744SLA)

description:
https://www.encodeproject.org/experiments/ENCSR654UYP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human breast epithelium
experiment encode accession: ENCSR654UYP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB744SLA
size range: 150-250

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

value: breast epithelium

value: tissue

value: ENCBS114DQJ at ENCODE; https://www.encodeproject.org/ENCBS114DQJ/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB955BJS)

description:
https://www.encodeproject.org/experiments/ENCSR154NOT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154NOT
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB955BJS

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: primary cell

value: male

value: adult

value: 38 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS689OQH at ENCODE; https://www.encodeproject.org/ENCBS689OQH/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: ATAC-seq from right lobe of liver (ENCLB025PAH)

description:
https://www.encodeproject.org/experiments/ENCSR373TDL/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right lobe of liver
experiment encode accession: ENCSR373TDL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2016-10-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB025PAH
size range: 150-250

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: right lobe of liver

value: female

value: Michael Snyder, Stanford

value: 53 year

value: ENCBS904HZU at ENCODE; https://www.encodeproject.org/ENCBS904HZU/


title: DNase-seq from progenitor cell of endocrine pancreas (ENCLB511SSG)

description:
https://www.encodeproject.org/experiments/ENCSR169KNO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR169KNO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB511SSG

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: embryonic

value: 5 day

value: John Stamatoyannopoulos, UW

value: Bradley Bernstein

value: healthy

value: ENCBS103LFA at ENCODE; https://www.encodeproject.org/ENCBS103LFA/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB144BKI)

description:
https://www.encodeproject.org/experiments/ENCSR377CRU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR377CRU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB144BKI

source_name: Homo sapiens male adult (38 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-7 for 4 hours

value: primary cell

value: male

value: adult

value: 38 year

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:P13232; treatment_term_name:Interleukin-7; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS619ADC at ENCODE; https://www.encodeproject.org/ENCBS619ADC/


title: DNase-seq from omental fat pad (ENCLB498XTM)

description:
https://www.encodeproject.org/experiments/ENCSR154OUQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154OUQ
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB498XTM

source_name: Homo sapiens female adult (53 years) omental fat pad tissue

value: omental fat pad

value: tissue

value: female

value: 53 year

value: Kristin Ardlie

value: ENCBS299IZQ at ENCODE; https://www.encodeproject.org/ENCBS299IZQ/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB374ASB)

description:
https://www.encodeproject.org/experiments/ENCSR885AWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR885AWF
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB374ASB

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL TNF-alpha for 48 hours

value: 33 year

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P01375; treatment_term_name:TNF-alpha; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS975IPJ at ENCODE; https://www.encodeproject.org/ENCBS975IPJ/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB516AIM)

description:
https://www.encodeproject.org/experiments/ENCSR635VQU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR635VQU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB516AIM

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-4 for 4 hours

value: CD4-positive, alpha-beta T cell

value: primary cell

value: adult

value: 39 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS062QTX at ENCODE; https://www.encodeproject.org/ENCBS062QTX/

value: Derived from ENCODE donor ENCDO222BBW; https://www.encodeproject.org/ENCDO222BBW/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB146XHR)

description:
https://www.encodeproject.org/experiments/ENCSR881CRY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR881CRY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB146XHR

source_name: Homo sapiens female adult (33 years) 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: female

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: ENCBS133PNS at ENCODE; https://www.encodeproject.org/ENCBS133PNS/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB251YOU)

description:
https://www.encodeproject.org/experiments/ENCSR380TXB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR380TXB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB251YOU

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 24 hours, 100 ng/mL Interleukin-4 for 24 hours

value: 33 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS534XRZ at ENCODE; https://www.encodeproject.org/ENCBS534XRZ/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB020TNB)

description:
https://www.encodeproject.org/experiments/ENCSR642BXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR642BXP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB020TNB

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-12 subunit beta for 1 hour, Interleukin-12 subunit alpha for 1 hour

value: John Stamatoyannopoulos, UW

value: treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS949JRK at ENCODE; https://www.encodeproject.org/ENCBS949JRK/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB295MKF)

description:
https://www.encodeproject.org/experiments/ENCSR152FWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR152FWD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB295MKF

source_name: Homo sapiens female adult (39 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-15 for 4 hours

value: CD4-positive, alpha-beta T cell

value: primary cell

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS936LPB at ENCODE; https://www.encodeproject.org/ENCBS936LPB/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB012BZF)

description:
https://www.encodeproject.org/experiments/ENCSR152AVY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR152AVY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB012BZF

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 100 ng/mL Interleukin-23 for 1 hour, 100 ng/mL Interleukin-1b for 1 hour

value: male

value: adult

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:Q9NPF7; treatment_term_name:Interleukin-23; treatment_type:protein; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P01584; treatment_term_name:Interleukin-1b; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS709KIP at ENCODE; https://www.encodeproject.org/ENCBS709KIP/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from T-helper 1 cell (ENCLB461CYX)

description:
https://www.encodeproject.org/experiments/ENCSR635QIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR635QIZ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB461CYX

source_name: Homo sapiens female adult (33 years) T-helper 1 primary cell treated with 50 U/mL Interleukin-2 for 16 hours

value: T-helper 1 cell

value: female

value: AllCells

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:16; duration_units:hour;

value: ENCBS956LFD at ENCODE; https://www.encodeproject.org/ENCBS956LFD/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from astrocyte (ENCLB028WFL)

description:
https://www.encodeproject.org/experiments/ENCSR146KFX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146KFX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-02-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB028WFL

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

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS687IRK at ENCODE; https://www.encodeproject.org/ENCBS687IRK/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB224ESX)

description:
https://www.encodeproject.org/experiments/ENCSR144NXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR144NXI
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB224ESX

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

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: ENCBS864TAX at ENCODE; https://www.encodeproject.org/ENCBS864TAX/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB040YCB)

description:
https://www.encodeproject.org/experiments/ENCSR874DUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR874DUP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB040YCB

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 50 U/mL Interleukin-2 for 4 hours

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:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS876MUC at ENCODE; https://www.encodeproject.org/ENCBS876MUC/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB751TNH)

description:
https://www.encodeproject.org/experiments/ENCSR889YWJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889YWJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB751TNH

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL Interleukin-15 for 48 hours

value: 38 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: ENCBS364YTK at ENCODE; https://www.encodeproject.org/ENCBS364YTK/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB288YJC)

description:
https://www.encodeproject.org/experiments/ENCSR634ZYB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR634ZYB
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB288YJC

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours, 100 ng/mL Interleukin-23 for 4 hours, 100 ng/mL Interleukin-1b for 4 hours

value: female

value: 33 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour; treatment_term_id:UniProtKB:Q9NPF7; treatment_term_name:Interleukin-23; treatment_type:protein; duration:4; duration_units:hour; treatment_term_id:UniProtKB:P01584; treatment_term_name:Interleukin-1b; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS650VZK at ENCODE; https://www.encodeproject.org/ENCBS650VZK/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from stomach (ENCLB297PPR)

description:
https://www.encodeproject.org/experiments/ENCSR641ZPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR641ZPF
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2017-10-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB297PPR

source_name: Homo sapiens female adult (51 years) stomach tissue

value: stomach

value: tissue

value: adult

value: 51 year

value: Kristin Ardlie

value: ENCBS329RLP at ENCODE; https://www.encodeproject.org/ENCBS329RLP/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB298XXR)

description:
https://www.encodeproject.org/experiments/ENCSR141RSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR141RSN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB298XXR

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS755ACM at ENCODE; https://www.encodeproject.org/ENCBS755ACM/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB762PVH)

description:
https://www.encodeproject.org/experiments/ENCSR363LUK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR363LUK
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB762PVH

source_name: Homo sapiens female adult (26 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-15 for 1 hour

value: CD4-positive, alpha-beta T cell

value: female

value: 26 year

value: John Stamatoyannopoulos, UW

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS438ROI at ENCODE; https://www.encodeproject.org/ENCBS438ROI/

value: Derived from ENCODE donor ENCDO134JGU; https://www.encodeproject.org/ENCDO134JGU/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB258SYI)

description:
https://www.encodeproject.org/experiments/ENCSR139PLJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR139PLJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-23
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB258SYI

source_name: Homo sapiens male adult (42 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 1 hour, 50 U/mL Interleukin-2 for 1 hour

value: adult

value: 42 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:1; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:1; duration_units:hour;

value: ENCBS708MEP at ENCODE; https://www.encodeproject.org/ENCBS708MEP/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB819MJR)

description:
https://www.encodeproject.org/experiments/ENCSR134CIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR134CIY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB819MJR

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 48 hours, 50 U/mL Interleukin-2 for 48 hours

value: primary cell

value: 33 year

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:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS267KBL at ENCODE; https://www.encodeproject.org/ENCBS267KBL/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from regulatory T cell (ENCLB877HAJ)

description:
https://www.encodeproject.org/experiments/ENCSR133OSO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR133OSO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB877HAJ

source_name: Homo sapiens female adult (33 years) 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: regulatory T cell

value: female

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: ENCBS606MDK at ENCODE; https://www.encodeproject.org/ENCBS606MDK/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB942XUA)

description:
https://www.encodeproject.org/experiments/ENCSR860IDO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR860IDO
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB942XUA

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

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS940OED at ENCODE; https://www.encodeproject.org/ENCBS940OED/


title: blood_Ciswomen_pretreatment_rep1 [CV26]

type: genomic

city: A Coruña

first: Rosa

last: Fernandez

state: None / N/A

address: Campus Elviña

department: Psychology

country: Spain

institute: University of A Coruña

description:
203717910049_R05C01
CV26
Cis women

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
DNA quality checks, data normalization, and statistical filters were performed with the Partek® Genomics Suite® v7.19.1018 Methylation Module.
Average Beta

source_name: blood, cis, pre treatment

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNAs were extracted from peripheral blood samples using the DNeasy Blood & Tissue Kit from Qiagen.

value: blood

tag: gender

tag: birth sex

value: 24 years

tag: population

value: Caucasian

tag: treatment


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB775DCP)

description:
https://www.encodeproject.org/experiments/ENCSR884ODJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR884ODJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB775DCP

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 48 hours, 100 ng/mL Interleukin-12 subunit alpha for 48 hours, 100 ng/mL Interleukin-12 subunit beta for 48 hours

value: male

value: adult

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:48; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:48; duration_units:hour;

value: ENCBS044RQV at ENCODE; https://www.encodeproject.org/ENCBS044RQV/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB508YOY)

description:
https://www.encodeproject.org/experiments/ENCSR124PXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR124PXN
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB508YOY

source_name: Homo sapiens female adult (33 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 4 hours

value: primary cell

value: 33 year

value: AllCells

value: ENCBS852VFV at ENCODE; https://www.encodeproject.org/ENCBS852VFV/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: DNase-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB324UJD)

description:
https://www.encodeproject.org/experiments/ENCSR130HIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR130HIE
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB324UJD

source_name: Homo sapiens male adult (38 years) activated CD8-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL Interleukin-7 for 24 hours

value: John Stamatoyannopoulos, UW

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P13232; treatment_term_name:Interleukin-7; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS776QLD at ENCODE; https://www.encodeproject.org/ENCBS776QLD/


title: DNase-seq from CD4-positive, alpha-beta T cell (ENCLB820LYN)

description:
https://www.encodeproject.org/experiments/ENCSR883WDW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR883WDW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB820LYN
instrument models: Illumina HiSeq 4000,Illumina NextSeq 500

source_name: Homo sapiens female adult (37 years) CD4-positive, alpha-beta T primary cell treated with Interleukin-6 for 4 hours

value: CD4-positive, alpha-beta T cell

value: female

value: 37 year

value: Shelly Heimfeld

value: treatment_term_id:UniProtKB:P05231; treatment_term_name:Interleukin-6; treatment_type:protein; duration:4; duration_units:hour;

value: ENCBS469XWH at ENCODE; https://www.encodeproject.org/ENCBS469XWH/

value: Derived from ENCODE donor ENCDO514TDF; https://www.encodeproject.org/ENCDO514TDF/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB234RZR)

description:
https://www.encodeproject.org/experiments/ENCSR147QLU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR147QLU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB234RZR

source_name: Homo sapiens male adult (38 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 100 ng/mL TNF-alpha for 24 hours

value: male

value: adult

value: 38 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P01375; treatment_term_name:TNF-alpha; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS441DTK at ENCODE; https://www.encodeproject.org/ENCBS441DTK/


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCLB035QCP)

description:
https://www.encodeproject.org/experiments/ENCSR121BSW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121BSW
assay title: DNase-seq
assembly: GRCh38
encode release date: 2020-10-06
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB035QCP

value: primary cell

value: 33 year

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:4; duration_units:hour;

value: ENCBS286HWS at ENCODE; https://www.encodeproject.org/ENCBS286HWS/