title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB897KPF)

description:
https://www.encodeproject.org/experiments/ENCSR976RUD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR976RUD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR239ZVK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB897KPF

value: adult


title: Histone ChIP-seq from middle frontal area 46 (ENCLB418MPZ)

status: Public on Jul 22 2022

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/ENCSR157MPY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR157MPY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR993YSN
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB418MPZ
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (89 years) with Alzheimer's disease; middle frontal area 46 tissue

tag: antibody

value: middle frontal area 46

value: tissue

tag: biosample encode accession

tag: age

value: 89 year

tag: Sex

value: female

tag: dev stage

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Rush University

tag: link

value: ENCBS748EGF at ENCODE; https://www.encodeproject.org/ENCBS748EGF/

value: Derived from ENCODE donor ENCDO843TIL; https://www.encodeproject.org/ENCDO843TIL/


title: WT (LB, 50 mM maltose) vs. WT (LB)-rep1

type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

description: Biological replicate 1 of 3

hyb_protocol: Gene expression changes were compared using self-made PCR-product based DNA microarrays (Lange et al. 2003), custom-made DNA microarrays with 70-mer oligonucleotides obtained from Operon Biotechnologies (Cologne, Germany) or custom-made 4x44K 60mer DNA microarrays from Agilent Technologies (Waldbronn, Germany). Hybridization of mixtures of Cy3- and Cy5-labelled cDNA on the arrays and washing of the arrays were performed as described by Frunzke et al. 2008, Polen & Wendisch 2003, and Vogt et al. 2014.

scan_protocol: The fluorescence of DNA microarrays was determined at 532 nm (Cy2-dUTP) and 635 nm (Cy5-dUTP) at 5 or 10 µm resolution with a GenePix 4000B laser scanner and GenePix Pro Software (Molecular Devices, Sunnyvale, USA).

data_processing: The raw results were saved as GPR-files and processed and normalized using the BioConductor R packages limma and marray (http://www.bioconductor.org). For further analysis, loess-normalized data were saved in the in-house DNA microarray database (Polen et al. 2004) including detailed information about each experiment following MIAME standards (Brazma et al. 2009). Normalized ratios of medians reflecting the relative mRNA level were filtered for a signal-to-noise ratio ((F635Median/B635Median) or (F532Median/B532Median)) higher than 3. Statistical analysis for calculation of p-values was performed with a paired Student´s t-test comparing relative RNA levels for a gene to the relative RNA levels of all other genes in the replicates.

molecule: total RNA

organism: Corynebacterium glutamicum

source_name: wild type

label_protocol: Equal amounts of RNA (15-30 µg) were used for random hexamer primed synthesis of fluorescently labelled cDNA using the nucleotide analogous Cy3-dUTP or Cy5-dUTP (GE Healthcare, Eindhoven, Netherlands).

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen, Hilden, Germany) or as described by Wendisch et al. 2001.

tag: condition

value: WT harvested during exponential growth phase, LB maltose, date of experiment:2004-09

value: WT harvested during exponential growth phase, OD 5, LB, date of experiment:2004-09


title: WT (4% maltose) vs. WT (4% glucose)-rep2

description: Biological replicate 2 of 3

value: WT harvested during exponential growth phase, CGXII maltose, date of experiment:2002-09/2002-10

value: WT harvested during exponential growth phase, OD 5, CGXII glucose, date of experiment:2002-09/2002-10


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB774BOB)

description:
https://www.encodeproject.org/experiments/ENCSR976IRR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR976IRR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774BOB

source_name: Homo sapiens male adult (35 years) CD4-positive naive resting alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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

value: ENCBS266XPE at ENCODE; https://www.encodeproject.org/ENCBS266XPE/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: Mint-ChIP-seq from natural killer cell (ENCLB580PEJ)

description:
https://www.encodeproject.org/experiments/ENCSR374XMP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR374XMP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB580PEJ

source_name: Homo sapiens female adult (41 years) natural killer primary cell treated with 100 ng/mL Interleukin-18 for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-15 for...

value: natural killer cell

value: 41 year

value: female

value: adult

value: John Stamatoyannopoulos

value: treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS492DTF at ENCODE; https://www.encodeproject.org/ENCBS492DTF/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: Mint-ChIP-seq from natural killer cell (ENCLB599TYM)

description:
https://www.encodeproject.org/experiments/ENCSR374XMP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR374XMP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB599TYM

value: Bradley Bernstein, Broad

value: ENCBS623MIU at ENCODE; https://www.encodeproject.org/ENCBS623MIU/


title: Mint-ChIP-seq from natural killer cell (ENCLB130NBR)

description:
https://www.encodeproject.org/experiments/ENCSR374XMP/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR374XMP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB130NBR

value: primary cell


description:
WT PnrdH::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

data_processing:
The raw results were saved as GPR-files and processed and normalized using the BioConductor R packages limma and marray (http://www.bioconductor.org). For further analysis, loess-normalized data were saved in the in-house DNA microarray database (Polen et al. 2004) including detailed information about each experiment following MIAME standards (Brazma et al. 2009). Normalized ratios of medians reflecting the relative mRNA level were filtered for a signal-to-noise ratio ((F635Median/B635Median) or (F532Median/B532Median)) higher than 3. Statistical analysis for calculation of p-values was performed with a paired Student´s t-test comparing relative RNA levels for a gene to the relative RNA levels of all other genes in the replicates.
All listed GAL files are included in a tar archive on the SERIES record. The 'ID' field of the GAL files includes the Biomax IDs. A supplementary file provides the CG IDs for the Biomax IDs.

source_name: WT PnrdH::Ptuf PctaE::Ptuf PctaC::Ptuf

tag: genotype

value: promoter exchange

value: WT PnrdH::Ptuf PctaE::Ptuf PctaC::Ptuf harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02


title: WT (10 min heatshock, 50°C) vs. WT-rep1

description: Biological replicate 1 of 3

value: WT harvest 10 min after cultivation at 50°C, CGXII glucose, date of experiment:2002-03/2003-04

value: WT harvested during exponential growth phase, OD 5, CGXII glucose, date of experiment:2002-03/2003-04


title: WT (4% maltose) vs. WT (4% glucose)-rep1

description: Biological replicate 1 of 3

value: WT harvested during exponential growth phase, CGXII maltose, date of experiment:2002-09/2002-10


title: WT (10 min heatshock, 50°C) vs. WT-rep3

description: Biological replicate 3 of 3


description:
WT PnrdH::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB213UOY)

description:
https://www.encodeproject.org/experiments/ENCSR388HWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR388HWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR569JUB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB213UOY

source_name: Homo sapiens male adult (36 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: 36 year

value: male

value: ENCBS793QJH at ENCODE; https://www.encodeproject.org/ENCBS793QJH/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: WT (10 min heatshock, 50°C) vs. WT-rep2

description: Biological replicate 2 of 3


title: Mint-ChIP-seq from Calu3 (ENCLB137TLI)

description:
https://www.encodeproject.org/experiments/ENCSR976GAB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR976GAB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB137TLI

source_name: Homo sapiens Calu3 cell line

tag: line

value: cell line

value: 25 year

tag: health state

value: Lung adenocarcinoma

value: adult

value: Mats Ljungman

value: ENCBS827USO at ENCODE; https://www.encodeproject.org/ENCBS827USO/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: Histone ChIP-seq from spleen (ENCLB407JZC)

description:
https://www.encodeproject.org/experiments/ENCSR761LTB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR761LTB
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR749YQP
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB407JZC
size range: 200-600

source_name: Homo sapiens female adult (41 years) spleen tissue, preserved by flash-freezing

value: spleen

value: tissue

value: female

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

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS248EXJ at ENCODE; https://www.encodeproject.org/ENCBS248EXJ/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB814IAF)

description:
https://www.encodeproject.org/experiments/ENCSR976IRR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR976IRR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB814IAF

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS266XPE at ENCODE; https://www.encodeproject.org/ENCBS266XPE/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


description:
WT PnrdH::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: promoter exchange

value: WT PnrdH::Ptuf PctaE::Ptuf PctaC::Ptuf harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02


description:
WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep1
Biological replicate 1 of 4
original platform:
GPL17304

source_name: WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf

value: WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05/2012-05

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05/2012-05


title: WT (4% maltose) vs. WT (4% glucose)-rep3

description: Biological replicate 3 of 3

value: WT harvested during exponential growth phase, CGXII maltose, date of experiment:2002-09/2002-10

value: WT harvested during exponential growth phase, OD 5, CGXII glucose, date of experiment:2002-09/2002-10


description:
WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep4
Biological replicate 4 of 4
original platform:
GPL17304


title: Histone ChIP-seq from middle frontal area 46 (ENCLB755SSX)

description:
https://www.encodeproject.org/experiments/ENCSR157MPY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR157MPY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR993YSN
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB755SSX
size range: 200-600

value: middle frontal area 46

value: tissue

value: 89 year

value: female

value: adult

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS748EGF at ENCODE; https://www.encodeproject.org/ENCBS748EGF/

value: Derived from ENCODE donor ENCDO843TIL; https://www.encodeproject.org/ENCDO843TIL/


title: Mint-ChIP-seq from natural killer cell (ENCLB443AOJ)

description:
https://www.encodeproject.org/experiments/ENCSR374XMP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR374XMP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB443AOJ

value: natural killer cell

value: primary cell

value: 41 year

value: John Stamatoyannopoulos

value: treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS623MIU at ENCODE; https://www.encodeproject.org/ENCBS623MIU/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: Mint-ChIP-seq from Caco-2 (ENCLB996RHK)

description:
https://www.encodeproject.org/experiments/ENCSR971UMG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR971UMG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR662AMW
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB996RHK

source_name: Homo sapiens Caco-2 cell line

value: cell line

value: 72 year

value: male

value: colorectal adenocarcinoma

value: Mats Ljungman

value: ENCBS257JWV at ENCODE; https://www.encodeproject.org/ENCBS257JWV/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: Mint-ChIP-seq from endodermal cell (ENCLB848REK)

description:
https://www.encodeproject.org/experiments/ENCSR758YNR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR758YNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB848REK
fragmentation methods: none

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

value: endodermal cell

value: in vitro differentiated cells

tag: description

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/

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


description:
WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep3
Biological replicate 3 of 4
original platform:
GPL17304

value: promoter exchange

value: WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05/2012-05

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05/2012-05


description:
WT PctaD::Ptuf PctaE::Ptuf PctaC::Ptuf vs. WT-rep2
Biological replicate 2 of 4
original platform:
GPL17304


title: WT PatpB::Ptuf vs. WT-rep3

description:
WT PatpB::Ptuf vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL17304

source_name: WT PatpB::Ptuf

value: WT PatpB::Ptuf harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05


title: WT PatpB::Ptuf vs. WT-rep2

description:
WT PatpB::Ptuf vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL17304


title: Mint-ChIP-seq from endodermal cell (ENCLB976QWK)

description:
https://www.encodeproject.org/experiments/ENCSR758YNR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR758YNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB976QWK
fragmentation methods: none

value: endodermal cell

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB943PGW)

description:
https://www.encodeproject.org/experiments/ENCSR968XKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR968XKX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR111BQQ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB943PGW

source_name: Homo sapiens male adult (38 years) CD4-positive, CD25-positive, alpha-beta regulatory T primary cell

value: primary cell

value: 38 year

value: male

value: adult

value: John Stamatoyannopoulos

value: ENCBS879HBS at ENCODE; https://www.encodeproject.org/ENCBS879HBS/

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


title: WT PatpB::Ptuf vs. WT-rep1

description:
WT PatpB::Ptuf vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL17304


title: Mint-ChIP-seq from Calu3 (ENCLB336TDI)

description:
https://www.encodeproject.org/experiments/ENCSR976GAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR976GAB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB336TDI

value: cell line

value: 25 year

value: Lung adenocarcinoma

value: Bradley Bernstein, Broad

value: Mats Ljungman

value: ENCBS827USO at ENCODE; https://www.encodeproject.org/ENCBS827USO/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB304OQG)

description:
https://www.encodeproject.org/experiments/ENCSR968XKX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR968XKX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR111BQQ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB304OQG


title: TF ChIP-seq from middle frontal area 46 (ENCLB567HDW)

description:
https://www.encodeproject.org/experiments/ENCSR374PKX/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue male adult (83 years)
experiment encode accession: ENCSR374PKX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR772LYM
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB567HDW
size range: 200-600

source_name: Homo sapiens male adult (83 years) middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: 83 year

value: Rush University

value: ENCBS485UEI at ENCODE; https://www.encodeproject.org/ENCBS485UEI/

value: Derived from ENCODE donor ENCDO736YJH; https://www.encodeproject.org/ENCDO736YJH/


title: Mint-ChIP-seq from Caco-2 (ENCLB161NED)

description:
https://www.encodeproject.org/experiments/ENCSR971UMG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971UMG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR662AMW
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB161NED

value: 72 year

value: male

value: colorectal adenocarcinoma

value: adult

value: ENCBS257JWV at ENCODE; https://www.encodeproject.org/ENCBS257JWV/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: TF ChIP-seq from middle frontal area 46 (ENCLB355JVW)

description:
https://www.encodeproject.org/experiments/ENCSR374PKX/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue male adult (83 years)
experiment encode accession: ENCSR374PKX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR772LYM
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB355JVW
size range: 200-600

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from endodermal cell (ENCLB817VBY)

description:
https://www.encodeproject.org/experiments/ENCSR758YNR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR758YNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB817VBY
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB101ZHI)

description:
https://www.encodeproject.org/experiments/ENCSR965WYA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR965WYA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR212ZBB
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB101ZHI

source_name: Homo sapiens male adult (50 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: 50 year

value: John Stamatoyannopoulos

value: ENCBS552ZBM at ENCODE; https://www.encodeproject.org/ENCBS552ZBM/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: MV-Leu55 vs. WT-rep3

description:
MV-Leu55 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL17304

value: production strain MV-Leu55

value: MV-Leu55 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: MV-Leu55 vs. MV-Leu20-rep1

description:
MV-Leu55 vs. MV-Leu20-rep1
Biological replicate 1 of 3
original platform:
GPL17304

value: production strain MV-Leu20

value: MV-Leu20 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: Mint-ChIP-seq from T-cell (ENCLB579IAI)

description:
https://www.encodeproject.org/experiments/ENCSR374DFV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR374DFV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB579IAI

source_name: Homo sapiens female adult (21 years) T-cell primary cell

value: T-cell

value: 21 year

value: female

value: adult

value: Bradley Bernstein, Broad

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: MV-Leu55 vs. MV-Leu20-rep2

description:
MV-Leu55 vs. MV-Leu20-rep2
Biological replicate 2 of 3
original platform:
GPL17304


title: Mint-ChIP-seq from stimulated activated memory B cell (ENCLB402ONV)

description:
https://www.encodeproject.org/experiments/ENCSR563XBT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR563XBT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR655TYY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB402ONV

source_name: Homo sapiens male adult (40 years) stimulated activated memory B primary cell treated with 1ug/mL anti-CD40 for 72 hours, 100 ng/mL Interleukin-4 for 72 hours, 10ug/mL anti-IgM for 72 hours

value: stimulated activated memory B cell

value: primary cell

value: 40 year

value: male

value: treatment_term_name:anti-CD40; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-IgM; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS619HZC at ENCODE; https://www.encodeproject.org/ENCBS619HZC/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: MV-Leu55 vs. WT-rep1

description:
MV-Leu55 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL17304

value: production strain MV-Leu55

value: MV-Leu55 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: MV-Leu55 ∆ilvE vs. MV-Leu55-rep2

description:
MV-Leu55 ∆ilvE vs. MV-Leu55-rep2
Biological replicate 2 of 2
original platform:
GPL17304

source_name: MV-Leu55 ∆ilvE

value: production strain MV-Leu55 deletion mutant

value: MV-Leu55 delta_ilvE harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: Mint-ChIP-seq from endodermal cell (ENCLB123AFB)

description:
https://www.encodeproject.org/experiments/ENCSR758YNR/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR758YNR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB123AFB
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

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


title: MV-Leu55 ∆ilvE vs. MV-Leu55-rep1

description:
MV-Leu55 ∆ilvE vs. MV-Leu55-rep1
Biological replicate 1 of 2
original platform:
GPL17304


title: MV-Leu55 vs. MV-Leu20-rep3

description:
MV-Leu55 vs. MV-Leu20-rep3
Biological replicate 3 of 3
original platform:
GPL17304

value: production strain MV-Leu20

value: MV-Leu20 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: MV-Leu20 ∆ilvE vs. MV-Leu20-rep2

description:
MV-Leu20 ∆ilvE vs. MV-Leu20-rep2
Biological replicate 2 of 3
original platform:
GPL17304

source_name: MV-Leu20 ∆ilvE

value: production strain MV-Leu20 deletion mutant

value: MV-Leu20 delta_ilvE harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: MV-Leu20 ∆ilvE vs. WT-rep4

description:
MV-Leu20 ∆ilvE vs. WT-rep4
Biological replicate 4 of 4
original platform:
GPL17304

value: wild type

value: WT harvested during late exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: MV-Leu20 ∆ilvE vs. WT-rep3

description:
MV-Leu20 ∆ilvE vs. WT-rep3
Biological replicate 3 of 4
original platform:
GPL17304


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB070WFP)

description:
https://www.encodeproject.org/experiments/ENCSR965WYA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR965WYA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR212ZBB
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB070WFP

value: primary cell

value: 50 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS552ZBM at ENCODE; https://www.encodeproject.org/ENCBS552ZBM/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: Mint-ChIP-seq from T-cell (ENCLB473CIE)

description:
https://www.encodeproject.org/experiments/ENCSR374DFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR374DFV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB473CIE

value: T-cell

value: 21 year

value: female

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB523HJW)

description:
https://www.encodeproject.org/experiments/ENCSR561MDN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR561MDN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR173UJQ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB523HJW

source_name: Homo sapiens male adult (51 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: 51 year

value: Charles Lee

value: ENCBS409NZS at ENCODE; https://www.encodeproject.org/ENCBS409NZS/

value: Derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: MV-Leu20 ∆ilvE vs. MV-Leu20-rep3

description:
MV-Leu20 ∆ilvE vs. MV-Leu20-rep3
Biological replicate 3 of 3
original platform:
GPL17304

value: production strain MV-Leu20 deletion mutant

value: MV-Leu20 delta_ilvE harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06

value: production strain MV-Leu20

value: MV-Leu20 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: MV-Leu55 vs. WT-rep2

description:
MV-Leu55 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL17304

value: production strain MV-Leu55

value: MV-Leu55 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB146JWI)

description:
https://www.encodeproject.org/experiments/ENCSR963EAC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR963EAC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB146JWI

source_name: Homo sapiens with multiple sclerosis; CD4-positive, CD25-positive, alpha-beta regulatory T primary cell, preserved by cryopreservation

value: primary cell

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS781DHR at ENCODE; https://www.encodeproject.org/ENCBS781DHR/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB290QQK)

description:
https://www.encodeproject.org/experiments/ENCSR963EAC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR963EAC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB290QQK


title: MV-Leu20 ∆ilvE vs. WT-rep1

description:
MV-Leu20 ∆ilvE vs. WT-rep1
Biological replicate 1 of 4
original platform:
GPL17304

value: production strain MV-Leu20 deletion mutant

source_name: WT

value: WT harvested during late exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: JVO1 ∆fkpA (35°C) vs. JVO1 (35°C)-rep2

description:
JVO1 ∆fkpA (35°C) vs. JVO1 (35°C)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: JVO1 ∆fkpA (35°C)

value: production strain JVO1

value: JVO1 delta_fkpA harvested during exponential growth phase, CGXII glucose 35°C, date of experiment:2011-10, GEO:GSE65294

source_name: JVO1 (35°C)

value: JVO1 harvested during exponential growth phase, CGXII glucose 35°C, date of experiment:2011-10, GEO:GSE65294


title: TF ChIP-seq from Caco-2 (ENCLB399LXO)

description:
https://www.encodeproject.org/experiments/ENCSR961IOA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR961IOA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR436HPW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB399LXO
size range: 200-600

value: CTCF

value: cell line

value: 72 year

value: male

value: colorectal adenocarcinoma

value: adult

value: Mats Ljungman

value: ENCBS202UKI at ENCODE; https://www.encodeproject.org/ENCBS202UKI/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: MV-Leu20 ∆ilvE vs. MV-Leu20-rep1

description:
MV-Leu20 ∆ilvE vs. MV-Leu20-rep1
Biological replicate 1 of 3
original platform:
GPL17304

value: MV-Leu20 delta_ilvE harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06

value: production strain MV-Leu20

value: MV-Leu20 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: Mint-ChIP-seq from T-helper 17 cell (ENCLB343LES)

description:
https://www.encodeproject.org/experiments/ENCSR560ONA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR560ONA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR104DYP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB343LES

source_name: Homo sapiens male adult (50 years) T-helper 17 primary cell

value: T-helper 17 cell

value: primary cell

value: 50 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS720LKW at ENCODE; https://www.encodeproject.org/ENCBS720LKW/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: Control ChIP-seq from middle frontal area 46 (ENCLB894IEE)

description:
https://www.encodeproject.org/experiments/ENCSR373OML/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR373OML
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB894IEE
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) with Alzheimer's disease; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS270KUL at ENCODE; https://www.encodeproject.org/ENCBS270KUL/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: Mint-ChIP-seq from stimulated activated memory B cell (ENCLB385SYO)

description:
https://www.encodeproject.org/experiments/ENCSR563XBT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR563XBT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR655TYY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385SYO

value: stimulated activated memory B cell

value: 40 year

value: male

value: adult

value: treatment_term_name:anti-CD40; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-IgM; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS619HZC at ENCODE; https://www.encodeproject.org/ENCBS619HZC/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: Control ChIP-seq from middle frontal area 46 (ENCLB360OMY)

description:
https://www.encodeproject.org/experiments/ENCSR373OML/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR373OML
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB360OMY
size range: 200-600

value: Bradley Bernstein, Broad


title: TF ChIP-seq from Caco-2 (ENCLB757WNF)

description:
https://www.encodeproject.org/experiments/ENCSR961IOA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR961IOA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR436HPW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB757WNF
size range: 200-600

source_name: Homo sapiens Caco-2 cell line

value: CTCF

value: cell line

value: 72 year

value: colorectal adenocarcinoma

value: Mats Ljungman

value: ENCBS202UKI at ENCODE; https://www.encodeproject.org/ENCBS202UKI/

value: Derived from ENCODE donor ENCDO000ACR; https://www.encodeproject.org/ENCDO000ACR/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB738UMJ)

description:
https://www.encodeproject.org/experiments/ENCSR561MDN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR561MDN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR173UJQ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB738UMJ

value: CD14-positive monocyte

value: primary cell

value: 51 year

value: Charles Lee

value: ENCBS409NZS at ENCODE; https://www.encodeproject.org/ENCBS409NZS/

value: Derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: 901_DelAro4-4clpc mufasO pMKEX2-STSah (OD 5)-rep3

description:
DelAro4-4clpc mufasO pMKEX2-STSah (OD 5, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (OD 5)-rep3
Biological replicate 3 of 3
original platform:
GPL28615

value: production strain DelAro4-4clpc mufasO pMKEX2-STSah

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during exponential growth phase, CGXII glucose 5 mM coumaric acid 1 mM IPTG, date of experiment:2019-04/2019-05

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during exponential growth phase, CGXII glucose, date of experiment:2019-04/2019-05


title: 900_DelAro4-4clpc mufasO pMKEX2-STSah (OD 5)-rep2

description:
DelAro4-4clpc mufasO pMKEX2-STSah (OD 5, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (OD 5)-rep2
Biological replicate 2 of 3
original platform:
GPL28615


title: 898_DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep4

description:
DelAro4-4clpc mufasO pMKEX2-STSah (48 hours, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep 4
Biological replicate 4 of 4
original platform:
GPL28615

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 48 h, CGXII glucose 5 mM coumaric acid 1 mM IPTG, date of experiment:2019-02

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 48 h, CGXII glucose, date of experiment:2019-02/2019-04


title: JVO1 ∆fkpA (35°C) vs. JVO1 (35°C)-rep1

description:
JVO1 ∆fkpA (35°C) vs. JVO1 (35°C)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: production strain JVO1

value: JVO1 delta_fkpA harvested during exponential growth phase, CGXII glucose 35°C, date of experiment:2011-10, GEO:GSE65294

value: JVO1 harvested during exponential growth phase, CGXII glucose 35°C, date of experiment:2011-10, GEO:GSE65294


title: Control Mint-ChIP-seq from T-cell (ENCLB191QQB)

description:
https://www.encodeproject.org/experiments/ENCSR367LFV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR367LFV
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB191QQB

value: T-cell

value: 21 year

value: female

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: Control Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB780MSP)

description:
https://www.encodeproject.org/experiments/ENCSR368JDN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR368JDN
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB780MSP

source_name: Homo sapiens male adult (33 years) stimulated activated effector memory CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, 100 ng/mL Interleukin-1...

value: primary cell

value: 33 year

value: male

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS523QRO at ENCODE; https://www.encodeproject.org/ENCBS523QRO/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: 894_DelAro4-4clpc mufasO pMKEX2-STSah (24 hours)-rep2

description:
DelAro4-4clpc mufasO pMKEX2-STSah (24 hours, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (24 hours)-rep2
Biological replicate 2 of 2
original platform:
GPL28615

value: production strain DelAro4-4clpc mufasO pMKEX2-STSah

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 24 h, CGXII glucose 5 mM coumaric acid 1 mM IPTG, date of experiment:2019-02

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 24 h, date of experiment:2019-02


title: 899_DelAro4-4clpc mufasO pMKEX2-STSah (OD 5)-rep1

description:
DelAro4-4clpc mufasO pMKEX2-STSah (OD 5, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (OD 5)-rep1
Biological replicate 1 of 3
original platform:
GPL28615

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during exponential growth phase, CGXII glucose 5 mM coumaric acid 1 mM IPTG, date of experiment:2019-04/2019-05

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during exponential growth phase, CGXII glucose, date of experiment:2019-04/2019-05


title: Control Mint-ChIP-seq from Calu3 (ENCLB557QBC)

description:
https://www.encodeproject.org/experiments/ENCSR372VUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR372VUZ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB557QBC

source_name: Homo sapiens Calu3 cell line

value: cell line

value: 25 year

value: Lung adenocarcinoma

value: Mats Ljungman

value: ENCBS827USO at ENCODE; https://www.encodeproject.org/ENCBS827USO/

value: Derived from ENCODE donor ENCDO109DGE; https://www.encodeproject.org/ENCDO109DGE/


title: Control Mint-ChIP-seq from Calu3 (ENCLB741MJY)

description:
https://www.encodeproject.org/experiments/ENCSR372VUZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR372VUZ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB741MJY

value: adult

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from T-helper 17 cell (ENCLB487RPA)

description:
https://www.encodeproject.org/experiments/ENCSR560ONA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR560ONA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR104DYP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB487RPA

value: T-helper 17 cell

value: primary cell

value: 50 year

value: male

value: John Stamatoyannopoulos

value: ENCBS720LKW at ENCODE; https://www.encodeproject.org/ENCBS720LKW/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: 896_DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep2

description:
DelAro4-4clpc mufasO pMKEX2-STSah (48 hours, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep 2
Biological replicate 2 of 4
original platform:
GPL28615

value: production strain DelAro4-4clpc mufasO pMKEX2-STSah

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 48 h, CGXII glucose 5 mM coumaric acid 1 mM IPTG, date of experiment:2019-02

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 48 h, CGXII glucose, date of experiment:2019-02/2019-04


title: 897_DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep3

description:
DelAro4-4clpc mufasO pMKEX2-STSah (48 hours, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep 3
Biological replicate 3 of 4
original platform:
GPL28615


title: 893_DelAro4-4clpc mufasO pMKEX2-STSah (24 hours)-rep1

description:
DelAro4-4clpc mufasO pMKEX2-STSah (24 hours, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (24 hours)-rep1
Biological replicate 1 of 2
original platform:
GPL28615

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 24 h, CGXII glucose 5 mM coumaric acid 1 mM IPTG, date of experiment:2019-02

value: DelAro4-4clpc mufasO pMKEX2-STSah harvested during stationary growth phase after 24 h, date of experiment:2019-02


title: Mint-ChIP-seq from MCF 10A (ENCLB182LFB)

description:
https://www.encodeproject.org/experiments/ENCSR362VGZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR362VGZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182LFB

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: 36 year

value: female

value: fibrocystic disease

value: Mats Ljungman

value: ENCBS654ZDZ at ENCODE; https://www.encodeproject.org/ENCBS654ZDZ/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: MV-Leu20 ∆ilvE vs. WT-rep2

description:
MV-Leu20 ∆ilvE vs. WT-rep2
Biological replicate 2 of 4
original platform:
GPL17304

value: production strain MV-Leu20 deletion mutant

value: MV-Leu20 delta_ilvE harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06

value: wild type

value: WT harvested during late exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06


title: 895_DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep1

description:
DelAro4-4clpc mufasO pMKEX2-STSah (48 hours, 5 mM coumaric acid, 1 mM IPTG) vs. DelAro4-4clpc mufasO pMKEX2-STSah (48 hours)-rep 1
Biological replicate 1 of 4
original platform:
GPL28615

value: production strain DelAro4-4clpc mufasO pMKEX2-STSah


description:
DM1800 ∆prpC12 PgltA::pdapA (L1) vs. DM1800 ∆prpC12-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: DM1800 ∆prpC12 PgltA::pdapA (L1)

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (L1) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

source_name: DM1800 ∆prpC12

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-12/2009-01


title: Control Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB020YQZ)

description:
https://www.encodeproject.org/experiments/ENCSR368JDN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR368JDN
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB020YQZ

value: primary cell

value: 33 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS523QRO at ENCODE; https://www.encodeproject.org/ENCBS523QRO/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB291AER)

description:
https://www.encodeproject.org/experiments/ENCSR360XNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR360XNZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB291AER

source_name: Homo sapiens male adult (35 years) CD4-positive naive resting alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS266XPE at ENCODE; https://www.encodeproject.org/ENCBS266XPE/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: Control Mint-ChIP-seq from T-cell (ENCLB474EOW)

description:
https://www.encodeproject.org/experiments/ENCSR367LFV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367LFV
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB474EOW

source_name: Homo sapiens female adult (21 years) T-cell primary cell

value: T-cell

value: 21 year

value: female

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB304CPB)

description:
https://www.encodeproject.org/experiments/ENCSR360XNZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR360XNZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB304CPB

value: primary cell

value: male

value: adult


description:
DM1800 ∆lysEG pEKEx2-cadA vs. DM1800 pEKEx3-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: DM1800 ∆lysEG pEKEx2-cadA

value: production strain DM1800 deletion mutant + overexpression

value: DM1800 delta_lysEG pEKEx2-cadA harvested during exponential growth phase, CGXII glucose, date of experiment:2009-05

source_name: DM1800 pEKEx3

value: DM1800 pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-05


title: Mint-ChIP-seq from stimulated activated memory B cell (ENCLB813EHD)

description:
https://www.encodeproject.org/experiments/ENCSR559MYU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR559MYU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR655TYY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813EHD

source_name: Homo sapiens male adult (40 years) stimulated activated memory B primary cell treated with 1ug/mL anti-CD40 for 72 hours, 100 ng/mL Interleukin-4 for 72 hours, 10ug/mL anti-IgM for 72 hours

value: stimulated activated memory B cell

value: 40 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: treatment_term_name:anti-CD40; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-IgM; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS619HZC at ENCODE; https://www.encodeproject.org/ENCBS619HZC/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: Mint-ChIP-seq from MCF 10A (ENCLB029LAM)

description:
https://www.encodeproject.org/experiments/ENCSR362VGZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR362VGZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB029LAM

value: MCF 10A

value: cell line

value: 36 year

value: fibrocystic disease

value: Mats Ljungman

value: ENCBS654ZDZ at ENCODE; https://www.encodeproject.org/ENCBS654ZDZ/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


description:
DM1800 ∆prpC12 PgltA::pdapA (L1) vs. DM1800 ∆prpC12-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (L1) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-12/2009-01


title: TF ChIP-seq from middle frontal area 46 (ENCLB435ZCV)

description:
https://www.encodeproject.org/experiments/ENCSR757DFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR757DFT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB435ZCV
size range: 200-600

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: adult

value: Rush University

value: ENCBS270KUL at ENCODE; https://www.encodeproject.org/ENCBS270KUL/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: Histone ChIP-seq from upper lobe of right lung (ENCLB129CGN)

description:
https://www.encodeproject.org/experiments/ENCSR958TSO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR958TSO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR750BQT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB129CGN
size range: 200-600

source_name: Homo sapiens male adult (60 years) upper lobe of right lung tissue

value: upper lobe of right lung

value: 60 year

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS339XRG at ENCODE; https://www.encodeproject.org/ENCBS339XRG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


description:
DM1800 ∆lysEG pEKEx2-cadA vs. DM1800 pEKEx3-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: production strain DM1800 deletion mutant + overexpression

value: DM1800 delta_lysEG pEKEx2-cadA harvested during exponential growth phase, CGXII glucose, date of experiment:2009-05

value: DM1800 pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-05


title: Histone ChIP-seq from heart left ventricle (ENCLB424KST)

description:
https://www.encodeproject.org/experiments/ENCSR958QNE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR958QNE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB424KST
size range: 200-600

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

value: heart left ventricle

value: tissue

value: 54 year

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

value: ENCBS115UFJ at ENCODE; https://www.encodeproject.org/ENCBS115UFJ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: TF ChIP-seq from middle frontal area 46 (ENCLB047HZP)

description:
https://www.encodeproject.org/experiments/ENCSR757DFT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR757DFT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047HZP
size range: 200-600

value: CTCF

value: middle frontal area 46

value: 90 or above year

value: female

value: adult

value: Rush University

value: ENCBS270KUL at ENCODE; https://www.encodeproject.org/ENCBS270KUL/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


description:
DM1800 ∆prpC12 PgltA::pdapA (A16) vs. DM1800 ∆prpC12-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: DM1800 ∆prpC12 PgltA::pdapA (A16)

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (A16) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-12


title: Histone ChIP-seq from upper lobe of right lung (ENCLB246UDL)

description:
https://www.encodeproject.org/experiments/ENCSR958TSO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR958TSO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR750BQT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB246UDL
size range: 200-600

value: upper lobe of right lung

value: 60 year

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS339XRG at ENCODE; https://www.encodeproject.org/ENCBS339XRG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


description:
DM1800 ∆prpC12 PgltA::pdapA (A16) vs. DM1800 ∆prpC12-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: production strain DM1800 deletion mutant


description:
DM1800 ∆prpC12 PgltA::pdapA (A14) vs. DM1800 ∆prpC12-rep4
Biological replicate 4 of 4
original platform:
GPL15451

source_name: DM1800 ∆prpC12 PgltA::pdapA (A14)

value: DM1800 delta_prpC12 PgltA::pdapA (A14) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01


description:
DM1800 ∆prpC12 PgltA::pdapA (C17) vs. DM1800 ∆prpC12-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: DM1800 ∆prpC12 PgltA::pdapA (C17)

value: DM1800 delta_prpC12 PgltA::pdapA (C7) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-11


title: Histone ChIP-seq from heart left ventricle (ENCLB345ZTE)

description:
https://www.encodeproject.org/experiments/ENCSR958QNE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR958QNE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB345ZTE
size range: 200-600

value: heart left ventricle

value: tissue

value: adult

value: 54 year

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

value: ENCBS115UFJ at ENCODE; https://www.encodeproject.org/ENCBS115UFJ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Mint-ChIP-seq from stimulated activated memory B cell (ENCLB572SDC)

description:
https://www.encodeproject.org/experiments/ENCSR559MYU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR559MYU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR655TYY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572SDC

value: stimulated activated memory B cell

value: primary cell

value: 40 year

value: male

value: John Stamatoyannopoulos

value: treatment_term_name:anti-CD40; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-IgM; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS619HZC at ENCODE; https://www.encodeproject.org/ENCBS619HZC/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


description:
DM1800 ∆prpC12 PgltA::pdapA (A16) vs. DM1800 ∆prpC12-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (A16) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-12


description:
DM1800 ∆prpC12 PgltA::pdapA (A14) vs. DM1800 ∆prpC12-rep3
Biological replicate 3 of 4
original platform:
GPL15451

value: DM1800 delta_prpC12 PgltA::pdapA (A14) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: production strain DM1800 deletion mutant

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01


description:
DM1800 ∆prpC12 PgltA::pdapA (A14) vs. DM1800 ∆prpC12-rep2
Biological replicate 2 of 4
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB885QHL)

description:
https://www.encodeproject.org/experiments/ENCSR957EOR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR957EOR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB885QHL

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS087RNX at ENCODE; https://www.encodeproject.org/ENCBS087RNX/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


description:
DM1933 (anaerob) vs. DM1933 (aerob)-rep2
Biological replicate 2 of 4
original platform:
GPL15451

source_name: DM1933 (anaerob)

value: production strain DM1933

value: DM1933 harvested during exponential growth phase after anaerobic cultivation, CGXII glucose, date of experiment:2012-05

source_name: DM1933 (aerob)

value: DM1933 harvested during exponential growth, CGXII glucose, date of experiment:2012-05


description:
DM1800 ∆prpC12 PgltA::pdapA (L1) vs. DM1800 ∆prpC12-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (L1) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-12/2009-01


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB330APX)

description:
https://www.encodeproject.org/experiments/ENCSR146KCI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR146KCI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB330APX

source_name: Homo sapiens male adult (48 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: male

value: John Stamatoyannopoulos

value: ENCBS684ANF at ENCODE; https://www.encodeproject.org/ENCBS684ANF/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB217XBY)

description:
https://www.encodeproject.org/experiments/ENCSR146KCI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146KCI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB217XBY

value: 48 year

value: adult


description:
DM1800 ∆prpC12 PgltA::pdapA (A14) vs. DM1800 ∆prpC12-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: DM1800 delta_prpC12 PgltA::pdapA (A14) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: production strain DM1800 deletion mutant

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01


title: Cg43 vs. WT-rep2

description:
Cg43 vs. WT-rep2
Biological replicate 2 of 2
original platform:
GPL22561

value: production strain Cg43

value: Cg43 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB990DLH)

description:
https://www.encodeproject.org/experiments/ENCSR559KWT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on naive thymus-derived CD4-positive, alpha-beta T cell originated from naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR559KWT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR521SOP
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB990DLH
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell, preserved by cryopreservation

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: TF ChIP-seq from middle frontal area 46 (ENCLB649CKT)

description:
https://www.encodeproject.org/experiments/ENCSR755WXO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR755WXO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR846OTK
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB649CKT
size range: 200-600

source_name: Homo sapiens female adult (89 years) with Alzheimer's disease; middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: 89 year

value: female

value: Rush University

value: ENCBS647UCT at ENCODE; https://www.encodeproject.org/ENCBS647UCT/

value: Derived from ENCODE donor ENCDO853VGZ; https://www.encodeproject.org/ENCDO853VGZ/


title: TF ChIP-seq from middle frontal area 46 (ENCLB271FPU)

description:
https://www.encodeproject.org/experiments/ENCSR755WXO/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR755WXO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR846OTK
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB271FPU
size range: 200-600

value: adult


title: Mint-ChIP-seq from HCT116 (ENCLB763MFW)

description:
https://www.encodeproject.org/experiments/ENCSR957EOR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR957EOR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB763MFW

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: Erez Aiden

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS087RNX at ENCODE; https://www.encodeproject.org/ENCBS087RNX/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


description:
DM1933 (anaerob) vs. DM1933 (aerob)-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: production strain DM1933

value: DM1933 harvested during exponential growth phase after anaerobic cultivation, CGXII glucose, date of experiment:2012-05

value: DM1933 harvested during exponential growth, CGXII glucose, date of experiment:2012-05


description:
DM1933 (anaerob) vs. DM1933 (aerob)-rep4
Biological replicate 4 of 4
original platform:
GPL15451


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB380SYO)

description:
https://www.encodeproject.org/experiments/ENCSR559KWT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on naive thymus-derived CD4-positive, alpha-beta T cell originated from naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR559KWT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR521SOP
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB380SYO
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

value: CD4+ naive CD3+ CD4+ CD8- CD45RA+ CD45RO- nonTreg

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Mint-ChIP-seq from HCT116 (ENCLB900LSN)

description:
https://www.encodeproject.org/experiments/ENCSR954TNC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR954TNC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR933ZIE
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB900LSN

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: ENCBS169OGM at ENCODE; https://www.encodeproject.org/ENCBS169OGM/


description:
DM1800 ∆prpC12 PgltA::pdapA (C17) vs. DM1800 ∆prpC12-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (C7) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

source_name: DM1800 ∆prpC12

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-11


description:
BOL-3 (aerob) vs. BOL-2 (microaerob)-rep3
Biological replicate 3 of 4
original platform:
GPL15451

source_name: BOL-3 (aerob)

value: production strain BOL-2

value: BOL-2 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-12

source_name: BOL-2 (microaerob)

value: BOL-2 harvested during exponential growth phase after cultivation under microaerobic conditions, CGXII glucose, date of experiment:2012-12


title: Cg43 vs. WT-rep1

description:
Cg43 vs. WT-rep1
Biological replicate 1 of 2
original platform:
GPL22561

value: production strain Cg43

value: Cg43 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05


title: Mint-ChIP-seq from HCT116 (ENCLB942XUM)

description:
https://www.encodeproject.org/experiments/ENCSR954TNC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954TNC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR933ZIE
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB942XUM

value: Bradley Bernstein, Broad

value: Erez Aiden

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


description:
BOL-3 (anaerob) vs. BOL-3 (microaerob)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: BOL-3 (anaerob)

value: production strain BOL-3

value: BOL-3 harvested during exponential growth phase after cultivation under anaerob conditions for 60 min, CGXII glucose, date of experiment:2012-12

source_name: BOL-3 (microaerob)

value: BOL-3 harvested during exponential growth phase after cultivation under microaerobic conditions for 60 min, CGXII glucose, date of experiment:2012-12


description:
BOL-3 (aerob) vs. BOL-2 (microaerob)-rep2
Biological replicate 2 of 4
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB981LAW)

description:
https://www.encodeproject.org/experiments/ENCSR558CXM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR558CXM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB981LAW

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS403YHB at ENCODE; https://www.encodeproject.org/ENCBS403YHB/


title: Mint-ChIP-seq from stimulated activated CD8-positive, alpha-beta T cell (ENCLB251AZU)

description:
https://www.encodeproject.org/experiments/ENCSR754RSP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR754RSP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR651JZJ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251AZU

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

value: primary cell

value: 21 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: ENCBS387CPR at ENCODE; https://www.encodeproject.org/ENCBS387CPR/

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


description:
DM1933 (anaerob) vs. DM1933 (aerob)-rep3
Biological replicate 3 of 4
original platform:
GPL15451

value: production strain DM1933

value: DM1933 harvested during exponential growth phase after anaerobic cultivation, CGXII glucose, date of experiment:2012-05

value: DM1933 harvested during exponential growth, CGXII glucose, date of experiment:2012-05


description:
BOL-3 (aerob) vs. BOL-2 (microaerob)-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: production strain BOL-2

value: BOL-2 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-12

value: BOL-2 harvested during exponential growth phase after cultivation under microaerobic conditions, CGXII glucose, date of experiment:2012-12


title: Mint-ChIP-seq from stimulated activated CD8-positive, alpha-beta T cell (ENCLB262PYB)

description:
https://www.encodeproject.org/experiments/ENCSR754RSP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR754RSP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR651JZJ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB262PYB

value: male


title: Mint-ChIP-seq from HCT116 (ENCLB042WFU)

description:
https://www.encodeproject.org/experiments/ENCSR558CXM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR558CXM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB042WFU

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Mint-ChIP-seq from memory B cell (ENCLB888CAB)

description:
https://www.encodeproject.org/experiments/ENCSR144ADG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR144ADG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB888CAB

source_name: Homo sapiens male adult (40 years) memory B primary cell

value: memory B cell

value: primary cell

value: 40 year

value: John Stamatoyannopoulos

value: ENCBS880QZN at ENCODE; https://www.encodeproject.org/ENCBS880QZN/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


description:
DM1800 ∆prpC12 PgltA::pdapA (C17) vs. DM1800 ∆prpC12-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: DM1800 ∆prpC12 PgltA::pdapA (C17)

value: production strain DM1800 deletion mutant + promoter exchange

value: DM1800 delta_prpC12 PgltA::pdapA (C7) harvested during exponential growth phase, CGXII glucose, date of experiment:2009-01

value: DM1800 delta_prpC12 harvested during exponential growth phase, CGXII glucose, date of experiment:2008-11


title: Mint-ChIP-seq from memory B cell (ENCLB703OCP)

description:
https://www.encodeproject.org/experiments/ENCSR144ADG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR144ADG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB703OCP

value: male


description:
BOL-3 (aerob) vs. BOL-2 (microaerob)-rep4
Biological replicate 4 of 4
original platform:
GPL15451

value: production strain BOL-2

value: BOL-2 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-12

value: BOL-2 harvested during exponential growth phase after cultivation under microaerobic conditions, CGXII glucose, date of experiment:2012-12


description:
BOL-3 (anaerob) vs. BOL-3 (microaerob)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: production strain BOL-3

value: BOL-3 harvested during exponential growth phase after cultivation under anaerob conditions for 60 min, CGXII glucose, date of experiment:2012-12

value: BOL-3 harvested during exponential growth phase after cultivation under microaerobic conditions for 60 min, CGXII glucose, date of experiment:2012-12


title: Histone ChIP-seq from upper lobe of right lung (ENCLB780AQF)

description:
https://www.encodeproject.org/experiments/ENCSR954JMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954JMZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR750BQT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB780AQF
size range: 200-600

source_name: Homo sapiens male adult (60 years) upper lobe of right lung tissue

value: upper lobe of right lung

value: tissue

value: 60 year

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS339XRG at ENCODE; https://www.encodeproject.org/ENCBS339XRG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: BOL-3 (anaerob) vs. BOL-3 (aerob)-rep3

description:
BOL-3 (anaerob) vs. BOL-3 (aerob)-rep3
Biological replicate 3 of 4
original platform:
GPL15451

value: BOL-3 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-12


title: BOL-3 (anaerob) vs. BOL-3 (aerob)-rep2

description:
BOL-3 (anaerob) vs. BOL-3 (aerob)-rep2
Biological replicate 2 of 4
original platform:
GPL15451


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB889KKZ)

description:
https://www.encodeproject.org/experiments/ENCSR753YVA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR753YVA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR414ZUR
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB889KKZ

source_name: Homo sapiens male adult (36 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

value: primary cell

value: 36 year

value: male

value: John Stamatoyannopoulos

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS253TXN at ENCODE; https://www.encodeproject.org/ENCBS253TXN/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB609SOX)

description:
https://www.encodeproject.org/experiments/ENCSR753YVA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR753YVA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR414ZUR
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB609SOX


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB743NYF)

description:
https://www.encodeproject.org/experiments/ENCSR556MTN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR556MTN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB743NYF

source_name: Homo sapiens male adult (35 years) CD4-positive naive resting alpha-beta T primary cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS417NZZ at ENCODE; https://www.encodeproject.org/ENCBS417NZZ/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB281ZDD)

description:
https://www.encodeproject.org/experiments/ENCSR358BNI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR358BNI
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB281ZDD

source_name: Homo sapiens male adult (48 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: 48 year

value: adult

value: Bradley Bernstein, Broad

value: ENCBS684ANF at ENCODE; https://www.encodeproject.org/ENCBS684ANF/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: Chassis C1 vs. MB001-rep4

description:
Chassis C1 vs. MB001-rep4
Biological replicate 4 of 4
original platform:
GPL22561

source_name: Chassis C1

value: MB001(DE3) deletion mutant

value: Chassis C1 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-06, GEO:GSE88717

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-06, GEO:GSE88717


title: Chassis C1 vs. MB001-rep2

description:
Chassis C1 vs. MB001-rep2
Biological replicate 2 of 4
original platform:
GPL22561


description:
MB001(DE3) (200 µg kasugamycin, 30 min) vs. MB001(DE3)-rep3
Biological replicate 3 of 6
original platform:
GPL28615

source_name: MB001(DE3) (200 µg kasugamycin, 30 min)

value: MB001(DE3) harvested during exponential growth phase 30 min after addition of 200 µg kasugamycin, CGXII glucose, date of experiment:2018-09

value: MB001(DE3) harvested during exponential growth phase, CGXII glucose, date of experiment:2018-09


title: BOL-3 (anaerob) vs. BOL-3 (aerob)-rep1

description:
BOL-3 (anaerob) vs. BOL-3 (aerob)-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: production strain BOL-3

value: BOL-3 harvested during exponential growth phase after cultivation under anaerob conditions for 60 min, CGXII glucose, date of experiment:2012-12

value: BOL-3 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-12


description:
MB001(DE3) (200 µg kasugamycin, 30 min) vs. MB001(DE3)-rep4
Biological replicate 4 of 6
original platform:
GPL28615


description:
MB001(DE3) (200 µg kasugamycin, 30 min) vs. MB001(DE3)-rep6
Biological replicate 6 of 6
original platform:
GPL28615


title: Chassis C1 vs. MB001-rep1

description:
Chassis C1 vs. MB001-rep1
Biological replicate 1 of 4
original platform:
GPL22561


description:
MB001(DE3) (200 µg kasugamycin, 30 min) vs. MB001(DE3)-rep5
Biological replicate 5 of 6
original platform:
GPL28615


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB947KXE)

description:
https://www.encodeproject.org/experiments/ENCSR556MTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR556MTN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB947KXE

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX


title: Control ChIP-seq from upper lobe of right lung (ENCLB404KSN)

description:
https://www.encodeproject.org/experiments/ENCSR750BQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR750BQT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB404KSN
size range: 200-600

value: upper lobe of right lung

value: tissue

value: 60 year

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: Shin Lin

value: ENCBS339XRG at ENCODE; https://www.encodeproject.org/ENCBS339XRG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: Histone ChIP-seq from heart right ventricle (ENCLB562IYM)

description:
https://www.encodeproject.org/experiments/ENCSR953NFS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR953NFS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR597PTH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562IYM
size range: 200-600

source_name: Homo sapiens male adult (55 years) heart right ventricle tissue

value: heart right ventricle

value: 55 year

value: ischemic (EF 25% LVEDD 6.9; RV normal size, moderate dysfunction)

value: adult

value: Bradley Bernstein, Broad

value: ENCBS377GPP at ENCODE; https://www.encodeproject.org/ENCBS377GPP/

value: Derived from ENCODE donor ENCDO439CAZ; https://www.encodeproject.org/ENCDO439CAZ/


title: Histone ChIP-seq from heart right ventricle (ENCLB725KBC)

description:
https://www.encodeproject.org/experiments/ENCSR953NFS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR953NFS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR597PTH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB725KBC
size range: 200-600

value: male


title: Chassis C1 vs. MB001-rep3

description:
Chassis C1 vs. MB001-rep3
Biological replicate 3 of 4
original platform:
GPL22561

value: MB001(DE3) deletion mutant

value: Chassis C1 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-06, GEO:GSE88717

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-06, GEO:GSE88717


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB109CYV)

description:
https://www.encodeproject.org/experiments/ENCSR358BNI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR358BNI
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB109CYV

value: primary cell

value: 48 year

value: John Stamatoyannopoulos

value: ENCBS684ANF at ENCODE; https://www.encodeproject.org/ENCBS684ANF/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: Histone ChIP-seq from upper lobe of right lung (ENCLB375DIY)

description:
https://www.encodeproject.org/experiments/ENCSR954JMZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR954JMZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR750BQT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB375DIY
size range: 200-600

value: upper lobe of right lung

value: tissue

value: 60 year

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: Shin Lin

value: ENCBS339XRG at ENCODE; https://www.encodeproject.org/ENCBS339XRG/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: Control Mint-ChIP-seq from IgD-negative memory B cell (ENCLB760MPW)

description:
https://www.encodeproject.org/experiments/ENCSR737MLQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR737MLQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB760MPW

source_name: Homo sapiens IgD-negative memory B primary cell, preserved by cryopreservation

value: IgD-negative memory B cell

value: B memory CD3- CD14- CD19+ CD27+ IgD-

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS793OUV at ENCODE; https://www.encodeproject.org/ENCBS793OUV/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


description:
MB001(DE3) (200 µg kasugamycin, 30 min) vs. MB001(DE3)-rep2
Biological replicate 2 of 6
original platform:
GPL28615

value: MB001(DE3) harvested during exponential growth phase 30 min after addition of 200 µg kasugamycin, CGXII glucose, date of experiment:2018-09

value: MB001(DE3) harvested during exponential growth phase, CGXII glucose, date of experiment:2018-09


description:
MB001(DE3) (200 µg kasugamycin, 10 min) vs. MB001(DE3)-rep6
Biological replicate 6 of 6
original platform:
GPL28615

source_name: MB001(DE3) (200 µg kasugamycin, 10 min)

value: MB001(DE3) harvested during exponential growth phase 10 min after addition of 200 µg kasugamycin, CGXII glucose, date of experiment:2018-09


description:
MB001(DE3) (200 µg kasugamycin, 30 min) vs. MB001(DE3)-rep1
Biological replicate 1 of 6
original platform:
GPL28615