title: Mint-ChIP-seq from natural killer cell (ENCLB548TDY)

description:
https://www.encodeproject.org/experiments/ENCSR870XPB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR870XPB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548TDY

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: primary cell

value: 41 year

value: female

value: adult

value: Bradley Bernstein, Broad

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: ∆acnR (4% glucose, 40 mM glutamate, 500 µM FeSO4) vs. ∆acnR (4% glucose, 40 mM glutamate)-rep3

status: Public on Jul 22 2022

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 3 of 5

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: deletion mutant

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: delta_acn harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-01

source_name: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-03


title: ∆acnR (4% glucose, 40 mM glutamate, 500 µM FeSO4) vs. ∆acnR (4% glucose, 40 mM glutamate)-rep1

description: Biological replicate 1 of 5

value: WT harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-01


title: Mint-ChIP-seq from natural killer cell (ENCLB604RHH)

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/ENCSR870XPB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR870XPB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB604RHH

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

tag: antibody

tag: biosample encode accession

tag: age

tag: Sex

tag: dev stage

tag: lab

tag: source

tag: treatments

tag: link

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


title: WT pMV1-lysG (CGXII, 4% myo-inositol) vs. WT pMV1 (CGXII, 4% myo-inositol)-rep1

description: Biological replicate 1 of 2

source_name: wild type + overexpression

value: WT pMV1-lysG harvested during exponential growth phase,CGXII 4% myo-inositol, 100 µM IPTG, date of experiment:2003-02

source_name: wild type + control

value: WT pMV1 harvested during exponential growth phase,CGXII 4% myo-inositol, 100 µM IPTG, date of experiment:2003-02


title: ∆acnR (4% glucose, 40 mM glutamate, 500 µM FeSO4) vs. ∆acnR (4% glucose, 40 mM glutamate)-rep2

description: Biological replicate 2 of 5

value: WT harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-02


title: Histone ChIP-seq from placenta (ENCLB255AMR)

description:
https://www.encodeproject.org/experiments/ENCSR681RQP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR681RQP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR889ZOH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB255AMR
size range: 200-600

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: unknown

value: embryonic

value: ENCBS506MMH at ENCODE; https://www.encodeproject.org/ENCBS506MMH/

value: Derived from ENCODE donor ENCDO353NXC; https://www.encodeproject.org/ENCDO353NXC/


title: WT pMV1-lysG (BHI) vs. WT pMV1 (BHI)-rep1

description: Biological replicate 1 of 2

value: WT pMV1-lysG harvested during exponential growth phase, BHI, 100 µM, date of experiment:2001-08/2001-09

value: WT pMV1 harvested during exponential growth phase, BHI, 100 µM, date of experiment:2001-08/2001-09


title: WT pMV1-lysG (BHI) vs. WT pMV1 (BHI)-rep2

description: Biological replicate 2 of 2


title: ∆acnR (4% glucose, 20 mM glutamate) vs. WT (4% glucose, 20 mM glutamate)-rep1

description: Biological replicate 1 of 13

value: delta_acnR harvested during exponential growth phase, CGXII glucose, 20 mM glutamate, date of experiment:2002-11

value: WT harvested during exponential growth phase, CGXII glucose, 20 mM glutamate, date of experiment:2002-11


title: TF ChIP-seq from placenta (ENCLB809QWR)

description:
https://www.encodeproject.org/experiments/ENCSR291YNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291YNH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR889ZOH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB809QWR
size range: 200-600

value: CTCF

value: female

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos


title: Control ChIP-seq from CD4-positive, alpha-beta T cell (ENCLB982KCH)

description:
https://www.encodeproject.org/experiments/ENCSR679HAK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR679HAK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB982KCH
size range: 200-600

source_name: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

value: 20 year

value: male

value: adult

value: Charles Lee

value: ENCBS636BLJ at ENCODE; https://www.encodeproject.org/ENCBS636BLJ/

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


title: Mint-ChIP-seq from natural killer cell (ENCLB154ILA)

description:
https://www.encodeproject.org/experiments/ENCSR870XPB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR870XPB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB154ILA

value: natural killer cell

value: 41 year

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: TF ChIP-seq from placenta (ENCLB565WMV)

description:
https://www.encodeproject.org/experiments/ENCSR291YNH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR291YNH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR889ZOH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB565WMV
size range: 200-600

value: CTCF

value: placenta

value: tissue

value: unknown

value: embryonic

value: ENCBS506MMH at ENCODE; https://www.encodeproject.org/ENCBS506MMH/

value: Derived from ENCODE donor ENCDO353NXC; https://www.encodeproject.org/ENCDO353NXC/


title: ∆lysG (CGXII, 4% myo-inositol) vs. WT (CGXII, 4% myo-inositol)-rep2

description: Biological replicate 2 of 2

value: delta_lysG harvested exponential growth phase, CGXII 4% myo-inositol, date of experiment:2003-02

value: WT harvested exponential growth phase, CGXII 4% myo-inositol, date of experiment:2003-02


title: Mint-ChIP-seq from natural killer cell (ENCLB246FHN)

description:
https://www.encodeproject.org/experiments/ENCSR870XPB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR870XPB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB246FHN

value: primary cell

value: female

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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


title: Mint-ChIP-seq from MCF 10A (ENCLB658MSL)

description:
https://www.encodeproject.org/experiments/ENCSR291QUA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR291QUA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB658MSL

source_name: Homo sapiens MCF 10A cell line

tag: line

value: MCF 10A

value: cell line

value: 36 year

tag: health state

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: ∆acnR (4% glucose, 20 mM glutamate) vs. WT (4% glucose, 20 mM glutamate)-rep2

description: Biological replicate 2 of 13

value: delta_acnR harvested during exponential growth phase, CGXII glucose, 20 mM glutamate, date of experiment:2002-11

value: WT harvested during exponential growth phase, CGXII glucose, 20 mM glutamate, date of experiment:2002-11


title: Control ChIP-seq from CD4-positive, alpha-beta T cell (ENCLB883KQS)

description:
https://www.encodeproject.org/experiments/ENCSR679HAK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR679HAK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883KQS
size range: 200-600

value: CD4-positive, alpha-beta T cell

value: 20 year

value: male

value: Charles Lee

value: ENCBS636BLJ at ENCODE; https://www.encodeproject.org/ENCBS636BLJ/

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


title: ∆lysG (CGXII, 4% myo-inositol) vs. WT (CGXII, 4% myo-inositol)-rep1

description: Biological replicate 1 of 2

value: delta_lysG harvested exponential growth phase, CGXII 4% myo-inositol, date of experiment:2003-02

value: WT harvested exponential growth phase, CGXII 4% myo-inositol, date of experiment:2003-02


title: ∆acnR (4% glucose, 40 mM glutamate, 500 µM FeSO4) vs. ∆acnR (4% glucose, 40 mM glutamate)-rep4

description: Biological replicate 4 of 5

value: delta_acn harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-01

value: WT harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-04


title: Mint-ChIP-seq from Calu3 (ENCLB388TPN)

description:
https://www.encodeproject.org/experiments/ENCSR288ZHE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR288ZHE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB388TPN

source_name: Homo sapiens Calu3 cell line

value: cell line

value: 25 year

value: Lung adenocarcinoma

value: adult

value: Bradley Bernstein, Broad

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 MCF 10A (ENCLB564KZV)

description:
https://www.encodeproject.org/experiments/ENCSR291QUA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR291QUA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB564KZV

value: MCF 10A

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: ∆lysG (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep2

description: Biological replicate 2 of 3

value: delta_lysG harvested exponential growth phase, CGXII glucose, date of experiment:2002-07/2002-01/2002-12

value: WT harvested exponential growth phase, CGXII glucose, date of experiment:2002-07/2002-01/2002-12


title: ∆ramB (CGXII, 1% acetate) vs. WT (CGXII, 1% acetate)-rep6

description: Biological replicate 6 of 6

value: delta_ramB harvested during exponential growth phase, CGXII 1% acetate, date of experiment:2003-02

value: WT harvested during exponential growth phase, CGXII 1% acetate, date of experiment:2003-02


title: Mint-ChIP-seq from Calu3 (ENCLB950MTJ)

description:
https://www.encodeproject.org/experiments/ENCSR288ZHE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR288ZHE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR372VUZ
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB950MTJ

value: cell line

value: 25 year

value: male


title: ∆ramB (CGXII, 1% acetate) vs. WT (CGXII, 1% acetate)-rep5

description: Biological replicate 5 of 6


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB673HIC)

description:
https://www.encodeproject.org/experiments/ENCSR677ZIJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR677ZIJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR528KGH
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB673HIC

source_name: Homo sapiens male adult (42 years) regulatory T primary cell

value: primary cell

value: adult

value: 42 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS164RWQ at ENCODE; https://www.encodeproject.org/ENCBS164RWQ/

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


title: ∆lysG (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep1

description: Biological replicate 1 of 3


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB292PSZ)

description:
https://www.encodeproject.org/experiments/ENCSR677ZIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR677ZIJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR528KGH
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB292PSZ


title: Mint-ChIP-seq from HCT116 (ENCLB518USK)

description:
https://www.encodeproject.org/experiments/ENCSR287XHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287XHR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB518USK

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens MED14 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: 48 year

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: ENCBS067KQC at ENCODE; https://www.encodeproject.org/ENCBS067KQC/

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


title: ∆lysG (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep3

description: Biological replicate 3 of 3

value: delta_lysG harvested exponential growth phase, CGXII glucose, date of experiment:2002-07/2002-01/2002-12

value: WT harvested exponential growth phase, CGXII glucose, date of experiment:2002-07/2002-01/2002-12


title: Mint-ChIP-seq from HCT116 (ENCLB575JBR)

description:
https://www.encodeproject.org/experiments/ENCSR287XHR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR287XHR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB575JBR

value: cell line


title: Mint-ChIP-seq from HCT116 (ENCLB701ANT)

description:
https://www.encodeproject.org/experiments/ENCSR671XCL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR671XCL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR099TYF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB701ANT

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

value: male

value: ENCBS033MSP at ENCODE; https://www.encodeproject.org/ENCBS033MSP/


title: ∆mtrA vs. WT Operon-Oligo-rep2

description:
∆mtrA vs. WT Operon-Oligo-rep2
Biological replicate 2 of 4
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: ∆mtrA

tag: genotype

value: deletion mutant

value: delta_mtrA harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04/2008-04

source_name: WT Operon-Oligo

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04/2008-04


title: ∆mtrA vs. WT Operon-Oligo-rep3

description:
∆mtrA vs. WT Operon-Oligo-rep3
Biological replicate 3 of 4
original platform:
GPL15451


title: ∆mtrA vs. WT Operon-Oligo-rep4

description:
∆mtrA vs. WT Operon-Oligo-rep4
Biological replicate 4 of 4
original platform:
GPL15451


title: ∆mtrA vs. WT Operon-Oligo-rep1

description:
∆mtrA vs. WT Operon-Oligo-rep1
Biological replicate 1 of 4
original platform:
GPL15451


title: ∆whiB vs. WT-rep4

description:
∆whiB vs. WT-rep4
Biological replicate 4 of 4
original platform:
GPL22792

source_name: ∆whiB

value: delta_whiB harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03

source_name: WT

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03


title: ∆mtrA vs. WT PCR-Product-rep1

description:
∆mtrA vs. WT PCR-Product-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_09.gal

value: delta_mtrA harvested during exponential growth phase, CGXII glucose, date of experiment:2004-09

source_name: WT PCR-Product

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2004-09


title: Histone ChIP-seq from right lobe of liver (ENCLB196WGG)

description:
https://www.encodeproject.org/experiments/ENCSR281JVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR281JVN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB196WGG
size range: 200-600

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

value: 41 year

value: female

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS971GGI at ENCODE; https://www.encodeproject.org/ENCBS971GGI/

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


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB092EPO)

description:
https://www.encodeproject.org/experiments/ENCSR669MWS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR669MWS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR390KLC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB092EPO

source_name: Homo sapiens male adult (40 years) stimulated activated naive 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 naive 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: ENCBS304VHM at ENCODE; https://www.encodeproject.org/ENCBS304VHM/

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


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB048EAS)

description:
https://www.encodeproject.org/experiments/ENCSR669MWS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR669MWS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR390KLC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB048EAS


title: ∆whiB vs. WT-rep3

description:
∆whiB vs. WT-rep3
Biological replicate 3 of 4
original platform:
GPL22792

value: deletion mutant

value: delta_whiB harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03


title: Mint-ChIP-seq from HCT116 (ENCLB187LHO)

description:
https://www.encodeproject.org/experiments/ENCSR671XCL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR671XCL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR099TYF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB187LHO

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

value: ENCBS033MSP at ENCODE; https://www.encodeproject.org/ENCBS033MSP/

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


title: Mint-ChIP-seq from HCT116 (ENCLB453YDU)

description:
https://www.encodeproject.org/experiments/ENCSR494YVB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494YVB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB453YDU

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: male

value: Bradley Bernstein, Broad

value: ENCBS456GWO at ENCODE; https://www.encodeproject.org/ENCBS456GWO/


title: Mint-ChIP-seq from HCT116 (ENCLB023HUK)

description:
https://www.encodeproject.org/experiments/ENCSR494YVB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR494YVB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB023HUK


title: Silenced lcpA vs. WT-rep1

description:
Silenced lcpA vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22561

source_name: Silenced lcpA

value: silencing

value: Silenced lcpA harvested during exponential growth phase, CGXII glucose, date of experiment:2014-09

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-09


title: ∆whiB vs. WT-rep1

description:
∆whiB vs. WT-rep1
Biological replicate 1 of 4
original platform:
GPL22792

value: deletion mutant

value: delta_whiB harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03


title: Silenced lcpA vs. WT-rep2

description:
Silenced lcpA vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22561

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-10


title: Histone ChIP-seq from right lobe of liver (ENCLB506UOF)

description:
https://www.encodeproject.org/experiments/ENCSR281JVN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR281JVN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB506UOF
size range: 200-600

value: right lobe of liver

value: tissue

value: 41 year

value: female

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

value: Shin Lin

value: ENCBS971GGI at ENCODE; https://www.encodeproject.org/ENCBS971GGI/

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


description:
WT pAN6-cg0764 (w/o IPTG) vs. WT pAN6 (w/o IPTG)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: WT pAN6-cg0764 (w/o IPTG)

value: wild type + overexpression

value: WT pAN6-cg0764 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-03/2007-04

source_name: WT pAN6 (w/o IPTG)

value: WT pAN6 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-03/2007-04


title: Histone ChIP-seq from heart left ventricle (ENCLB518MRP)

description:
https://www.encodeproject.org/experiments/ENCSR490KKS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR490KKS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB518MRP
size range: 200-600

source_name: Homo sapiens male adult (69 years) heart left ventricle tissue

value: heart left ventricle

value: 69 year

value: male

value: ischemic (EF 25% LVEDD 5.7; RV mildly dilated, moderate dysfunction)

value: adult

value: Bradley Bernstein, Broad

value: ENCBS987PRB at ENCODE; https://www.encodeproject.org/ENCBS987PRB/

value: Derived from ENCODE donor ENCDO477WED; https://www.encodeproject.org/ENCDO477WED/


title: Silenced lcpA vs. WT-rep3

description:
Silenced lcpA vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22561

value: silencing

value: Silenced lcpA harvested during exponential growth phase, CGXII glucose, date of experiment:2014-09

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-11


description:
WT pAN6-cg0764 (w/o IPTG) vs. WT pAN6 (w/o IPTG)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Histone ChIP-seq from heart left ventricle (ENCLB610PRO)

description:
https://www.encodeproject.org/experiments/ENCSR490KKS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR490KKS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR632MPN
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB610PRO
size range: 200-600

value: tissue

value: Shin Lin


title: ∆whiB vs. WT-rep2

description:
∆whiB vs. WT-rep2
Biological replicate 2 of 4
original platform:
GPL22792

value: deletion mutant

value: delta_whiB harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-03


title: Mint-ChIP-seq from HCT116 (ENCLB295GQS)

description:
https://www.encodeproject.org/experiments/ENCSR280DQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR280DQH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR933ZIE
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB295GQS

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: colorectal carcinoma

value: Erez Aiden

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

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


title: ∆cg0764 (BHI) vs. WT (BHI)-rep3

description:
∆cg0764 (BHI) vs. WT (BHI)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cg0764 (BHI)

value: delta_cg0764 harvested during exponential growth phase, BHI, date of experiment:2007-03/2007-04

source_name: WT (BHI)

value: WT harvested during exponential growth phase, BHI, date of experiment:2007-03/2007-04


title: Histone ChIP-seq from heart left ventricle (ENCLB041HLA)

description:
https://www.encodeproject.org/experiments/ENCSR488RAV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on heart left ventricle tissue male adult (66 years).
experiment encode accession: ENCSR488RAV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR061EXX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB041HLA
size range: 200-600

source_name: Homo sapiens male adult (66 years) heart left ventricle tissue

value: heart left ventricle

value: male

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: adult

value: 66 year

value: Bradley Bernstein, Broad

value: ENCBS966SZA at ENCODE; https://www.encodeproject.org/ENCBS966SZA/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: Mint-ChIP-seq from memory B cell (ENCLB706JRZ)

description:
https://www.encodeproject.org/experiments/ENCSR668WVS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR668WVS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB706JRZ

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/


title: Mint-ChIP-seq from memory B cell (ENCLB542XUW)

description:
https://www.encodeproject.org/experiments/ENCSR668WVS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR668WVS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB542XUW


description:
WT pAN6-cg0764 (w/o IPTG) vs. WT pAN6 (w/o IPTG)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: wild type + overexpression

value: WT pAN6-cg0764 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-03/2007-04

value: wild type

value: WT pAN6 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-03/2007-04


title: ∆cg0764 (BHI) vs. WT (BHI)-rep2

description:
∆cg0764 (BHI) vs. WT (BHI)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cg0764 harvested during exponential growth phase, BHI, date of experiment:2007-03/2007-04

value: WT harvested during exponential growth phase, BHI, date of experiment:2007-03/2007-04


description:
∆cg0764 (CGXII, 70 mM glucose) vs. WT (CGXII, 70 mM glucose)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cg0764 (CGXII, 70 mM glucose)

value: delta_cg0764 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-02

source_name: WT (CGXII, 70 mM glucose)

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-02


description:
∆cg0764 (CGXII, 70 mM glucose) vs. WT (CGXII, 70 mM glucose)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from activated T-helper 17 cell (ENCLB631AEQ)

description:
https://www.encodeproject.org/experiments/ENCSR488FJP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR488FJP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR122NDV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB631AEQ

source_name: Homo sapiens male adult (50 years) activated T-helper 17 primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-helper 17 cell

value: 50 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS307XMP at ENCODE; https://www.encodeproject.org/ENCBS307XMP/

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


title: Mint-ChIP-seq from HCT116 (ENCLB408SYQ)

description:
https://www.encodeproject.org/experiments/ENCSR667XWM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR667XWM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR848XKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB408SYQ

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

value: cell line

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

value: ENCBS599GGB at ENCODE; https://www.encodeproject.org/ENCBS599GGB/

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


title: Mint-ChIP-seq from HCT116 (ENCLB480DDQ)

description:
https://www.encodeproject.org/experiments/ENCSR280DQH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR280DQH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR933ZIE
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB480DDQ

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


title: Mint-ChIP-seq from activated T-helper 17 cell (ENCLB176GMV)

description:
https://www.encodeproject.org/experiments/ENCSR488FJP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR488FJP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR122NDV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB176GMV

value: primary cell

value: John Stamatoyannopoulos


title: Mint-ChIP-seq from HCT116 (ENCLB587BYO)

description:
https://www.encodeproject.org/experiments/ENCSR487CTA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR487CTA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB587BYO

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

value: ENCBS844UBK at ENCODE; https://www.encodeproject.org/ENCBS844UBK/


title: Mint-ChIP-seq from HCT116 (ENCLB418NRQ)

description:
https://www.encodeproject.org/experiments/ENCSR667XWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR667XWM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR848XKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB418NRQ


title: Histone ChIP-seq from placenta (ENCLB041KIE)

description:
https://www.encodeproject.org/experiments/ENCSR667HPT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR667HPT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR889ZOH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB041KIE
size range: 200-600

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: unknown

value: female

value: embryonic

value: ENCBS506MMH at ENCODE; https://www.encodeproject.org/ENCBS506MMH/

value: Derived from ENCODE donor ENCDO353NXC; https://www.encodeproject.org/ENCDO353NXC/


title: ∆mntR vs. WT-rep2

description:
∆mntR vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22792

source_name: ∆mntR

value: deletion mutant

value: delta_mntR harvested during exponential growth phase, CGXII glucose, date of experiment:2013-10

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-10


title: Mint-ChIP-seq from HCT116 (ENCLB271PWT)

description:
https://www.encodeproject.org/experiments/ENCSR487CTA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR487CTA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB271PWT

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden


title: ∆mntR vs. WT-rep3

description:
∆mntR vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22792


description:
∆cg0764 (CGXII, 70 mM glucose) vs. WT (CGXII, 70 mM glucose)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_cg0764 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-02

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-02


title: Histone ChIP-seq from heart left ventricle (ENCLB633BHC)

description:
https://www.encodeproject.org/experiments/ENCSR488RAV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on heart left ventricle tissue male adult (66 years).
experiment encode accession: ENCSR488RAV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR061EXX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB633BHC
size range: 200-600

value: heart left ventricle

value: tissue

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: Shin Lin

value: ENCBS966SZA at ENCODE; https://www.encodeproject.org/ENCBS966SZA/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: ∆mntR vs. WT-rep1

description:
∆mntR vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22792

value: deletion mutant

value: delta_mntR harvested during exponential growth phase, CGXII glucose, date of experiment:2013-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-10


title: ∆cg0764 (BHI) vs. WT (BHI)-rep1

description:
∆cg0764 (BHI) vs. WT (BHI)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_cg0764 harvested during exponential growth phase, BHI, date of experiment:2007-03/2007-04

value: WT harvested during exponential growth phase, BHI, date of experiment:2007-03/2007-04


description:
∆esrSR pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆esrSR pEKEx2-AmyE

value: deletion mutant + overexpression

value: delta_esrSR pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2010-10/2011-07

source_name: WT pEKEx2-AmyE

value: wild type + control

value: WT pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2010-10/2011-07


description:
∆esrSR pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB560JGI)

description:
https://www.encodeproject.org/experiments/ENCSR663SHP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (35 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR663SHP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB560JGI

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: adult

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: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB689OFB)

description:
https://www.encodeproject.org/experiments/ENCSR485YGX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR485YGX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR737MLQ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB689OFB

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

value: IgD-negative memory B cell

tag: description

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/


title: Histone ChIP-seq from placenta (ENCLB918YPQ)

description:
https://www.encodeproject.org/experiments/ENCSR667HPT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR667HPT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR889ZOH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB918YPQ
size range: 200-600

value: placenta

value: tissue

value: female

value: embryonic

value: John Stamatoyannopoulos

value: ENCBS506MMH at ENCODE; https://www.encodeproject.org/ENCBS506MMH/

value: Derived from ENCODE donor ENCDO353NXC; https://www.encodeproject.org/ENCDO353NXC/


title: ∆esrSR pEKEx3-esrR vs. WT pEKEx3-rep3

description:
∆esrSR pEKEx3-esrR vs. WT pEKEx3-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆esrSR pEKEx3-esrR

value: deletion mutant + overexpression

value: delta_esrSR pEKEx3-esrR harvested during exponential growth phase 60 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-07, GEO:GSE97961

source_name: WT pEKEx3

value: deletion mutant + control

value: delta_esrSR pEKEx3 harvested during exponential growth phase 60 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-07, GEO:GSE97961


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB669ANG)

description:
https://www.encodeproject.org/experiments/ENCSR663SHP/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on CD4-positive naive resting alpha-beta T cell male adult (35 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR663SHP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669ANG

value: primary cell

value: male

value: adult

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: ∆esrSR pEKEx3-esrR vs. WT pEKEx3-rep1

description:
∆esrSR pEKEx3-esrR vs. WT pEKEx3-rep1
Biological replicate 1 of 3
original platform:
GPL15451


description:
∆esrSR pEKEx2-AmyE (1 mM IPTG) vs. ∆esrSR pEKEx2-AmyE (w/o IPTG)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

source_name: ∆esrSR pEKEx2-AmyE (1 mM IPTG)

value: delta_esrSR pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2010-10

source_name: ∆esrSR pEKEx2-AmyE (w/o IPTG)

value: delta_esrSR pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth, CGXII glucose, w/o IPTG, date of experiment:2010-10


description:
∆esrSR pEKEx2-AmyE (1 mM IPTG) vs. ∆esrSR pEKEx2-AmyE (w/o IPTG)-rep3
Biological replicate 3 of 3
original platform:
GPL15451


description:
∆esrSR pEKEx2-AmyE (1 mM IPTG) vs. ∆esrSR pEKEx2-AmyE (w/o IPTG)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: ∆esrSR pEKEx3-esrR vs. WT pEKEx3-rep2

description:
∆esrSR pEKEx3-esrR vs. WT pEKEx3-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Histone ChIP-seq from middle frontal area 46 (ENCLB856YXE)

description:
https://www.encodeproject.org/experiments/ENCSR278JAH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR278JAH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB856YXE
size range: 200-600

source_name: Homo sapiens female adult (79 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 79 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS246FGU at ENCODE; https://www.encodeproject.org/ENCBS246FGU/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB998VMH)

description:
https://www.encodeproject.org/experiments/ENCSR278JAH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR278JAH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB998VMH
size range: 200-600

value: adult


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB512AEN)

description:
https://www.encodeproject.org/experiments/ENCSR482VIB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR482VIB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB512AEN

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: David Hafler

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

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


title: ∆esrl vs. WT-rep3

description:
∆esrl vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆esrl

value: deletion mutant

value: delta_esrl harvested during exponential growth phase, CGXII glucose, date of experiment:2011-09, GEO:GSE97961

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-09, GEO:GSE97961


title: ∆esrSR vs. WT-rep1

description:
∆esrSR vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451

source_name: ∆esrSR

value: delta_esrSR harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03


title: Histone ChIP-seq from middle frontal area 46 (ENCLB146MYI)

description:
https://www.encodeproject.org/experiments/ENCSR278JAH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR278JAH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB146MYI
size range: 200-600

value: middle frontal area 46

value: tissue

value: 79 year

value: female

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS836MZE at ENCODE; https://www.encodeproject.org/ENCBS836MZE/


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB208ZWQ)

description:
https://www.encodeproject.org/experiments/ENCSR485YGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR485YGX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR737MLQ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB208ZWQ

value: IgD-negative memory B cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

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

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


title: Mint-ChIP-seq from HCT116 (ENCLB351SQO)

description:
https://www.encodeproject.org/experiments/ENCSR276REC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR276REC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR704TRV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB351SQO

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

value: ENCBS982XND at ENCODE; https://www.encodeproject.org/ENCBS982XND/

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


title: Mint-ChIP-seq from HCT116 (ENCLB187IWT)

description:
https://www.encodeproject.org/experiments/ENCSR276REC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR276REC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR704TRV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB187IWT

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB457LEJ)

description:
https://www.encodeproject.org/experiments/ENCSR482VIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR482VIB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB457LEJ

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

value: multiple sclerosis

value: David Hafler

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

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


description:
∆csoR (50 µM CuSO4) vs. WT (50 µM CuSO4)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆csoR (50 µM CuSO4)

value: deletion mutant

value: delta_csoR harvested during exponential growth phase, CGXII glucose 50 µM CuSO4, date of experiment:2011-04

source_name: WT (50 µM CuSO4)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose 50 µM CuSO4, date of experiment:2011-04


title: Histone ChIP-seq from middle frontal area 46 (ENCLB686QGU)

description:
https://www.encodeproject.org/experiments/ENCSR278JAH/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR278JAH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB686QGU
size range: 200-600

value: middle frontal area 46

value: tissue

value: 79 year

value: female

value: Rush University

value: ENCBS836MZE at ENCODE; https://www.encodeproject.org/ENCBS836MZE/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: ∆esrSR vs. WT-rep2

description:
∆esrSR vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: delta_esrSR harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB751TZF)

description:
https://www.encodeproject.org/experiments/ENCSR482TGI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR482TGI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR456XXL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB751TZF
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS269FKR at ENCODE; https://www.encodeproject.org/ENCBS269FKR/

value: Derived from ENCODE donor ENCDO553CCA; https://www.encodeproject.org/ENCDO553CCA/


description:
∆csoR (50 µM CuSO4) vs. WT (50 µM CuSO4)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_csoR harvested during exponential growth phase, CGXII glucose 50 µM CuSO4, date of experiment:2011-04

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose 50 µM CuSO4, date of experiment:2011-04


description:
∆csoR (20 µM CuSO4) vs. WT (20 µM CuSO4)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆csoR (20 µM CuSO4)

value: delta_csoR harvested during exponential growth phase, CGXII glucose 20 µM CuSO4, date of experiment:2011-03

source_name: WT (20 µM CuSO4)

value: WT harvested during exponential growth phase, CGXII glucose 20 µM CuSO4, date of experiment:2011-03


title: ∆esrSR vs. WT-rep3

description:
∆esrSR vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: WT


title: Mint-ChIP-seq from natural killer cell (ENCLB608AHQ)

description:
https://www.encodeproject.org/experiments/ENCSR477FRO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR477FRO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB608AHQ

source_name: Homo sapiens male adult (33 years) natural killer primary cell

value: natural killer cell

value: 33 year

value: male

value: adult

value: Charles Lee

value: ENCBS358EEP at ENCODE; https://www.encodeproject.org/ENCBS358EEP/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB592SMY)

description:
https://www.encodeproject.org/experiments/ENCSR482TGI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR482TGI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR456XXL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592SMY
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler


title: ∆csoR vs. WT-rep4

description:
∆csoR vs. WT-rep4
Biological replicate 4 of 4
original platform:
GPL15451

source_name: ∆csoR

value: deletion mutant

value: delta_csoR harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03


title: Mint-ChIP-seq from natural killer cell (ENCLB906YWV)

description:
https://www.encodeproject.org/experiments/ENCSR477FRO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR477FRO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB906YWV

value: natural killer cell

value: Bradley Bernstein, Broad


description:
∆csoR (20 µM CuSO4) vs. WT (20 µM CuSO4)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_csoR harvested during exponential growth phase, CGXII glucose 20 µM CuSO4, date of experiment:2011-03

value: WT harvested during exponential growth phase, CGXII glucose 20 µM CuSO4, date of experiment:2011-03


description:
∆csoR (20 µM CuSO4) vs. WT (20 µM CuSO4)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Control Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB403GEH)

description:
https://www.encodeproject.org/experiments/ENCSR663BWX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR663BWX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB403GEH

source_name: Homo sapiens male adult (48 years) activated naive CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: 48 year

value: male

value: adult

value: John Stamatoyannopoulos

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS319ZAQ at ENCODE; https://www.encodeproject.org/ENCBS319ZAQ/

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


description:
∆csoR (50 µM CuSO4) vs. WT (50 µM CuSO4)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_csoR harvested during exponential growth phase, CGXII glucose 50 µM CuSO4, date of experiment:2011-04

value: WT harvested during exponential growth phase, CGXII glucose 50 µM CuSO4, date of experiment:2011-04


title: ∆esrl vs. WT-rep2

description:
∆esrl vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_esrl harvested during exponential growth phase, CGXII glucose, date of experiment:2011-09, GEO:GSE97961

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-09, GEO:GSE97961


title: Control Mint-ChIP-seq from Caco-2 (ENCLB132TZD)

description:
https://www.encodeproject.org/experiments/ENCSR662AMW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR662AMW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB132TZD

source_name: Homo sapiens Caco-2 cell line

value: cell line

value: 72 year

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: ∆esrl vs. WT-rep1

description:
∆esrl vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: wild type


title: Control ChIP-seq from CD14-positive monocyte (ENCLB968BEV)

description:
https://www.encodeproject.org/experiments/ENCSR660UYR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR660UYR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB968BEV
size range: 200-600

source_name: Homo sapiens male adult (30 years) CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

value: 30 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS640YHQ at ENCODE; https://www.encodeproject.org/ENCBS640YHQ/

value: Derived from ENCODE donor ENCDO544CHQ; https://www.encodeproject.org/ENCDO544CHQ/


title: Control Mint-ChIP-seq from Caco-2 (ENCLB659OXP)

description:
https://www.encodeproject.org/experiments/ENCSR662AMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR662AMW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB659OXP


title: Histone ChIP-seq from right lobe of liver (ENCLB010VME)

description:
https://www.encodeproject.org/experiments/ENCSR660PFN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR660PFN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010VME
size range: 200-600

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

value: 41 year

value: female

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

value: Shin Lin

value: ENCBS971GGI at ENCODE; https://www.encodeproject.org/ENCBS971GGI/

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


title: ∆csoR vs. WT-rep3

description:
∆csoR vs. WT-rep3
Biological replicate 3 of 4
original platform:
GPL15451

value: deletion mutant

value: delta_csoR harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-03


title: Control ChIP-seq from CD14-positive monocyte (ENCLB122VVF)

description:
https://www.encodeproject.org/experiments/ENCSR660UYR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR660UYR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB122VVF
size range: 200-600

value: CD14-positive monocyte

value: primary cell

value: 30 year

value: male

value: adult


description:
∆ramB ∆sdhCAB (400 mM glycerine) vs. WT (400 mM glycerine)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆ramB ∆sdhCAB (400 mM glycerine)

value: delta_ramB delta_sdhCAB harvested during exponential growth phase, CGXII 400 mM glycine, date of experiment:2007-05

source_name: WT (400 mM glycerine)

value: WT harvested during exponential growth phase, CGXII 400 mM glycine, date of experiment:2007-05


title: ∆csoR vs. WT-rep2

description:
∆csoR vs. WT-rep2
Biological replicate 2 of 4
original platform:
GPL15451


title: ∆csoR vs. WT-rep1

description:
∆csoR vs. WT-rep1
Biological replicate 1 of 4
original platform:
GPL15451


title: Histone ChIP-seq from right lobe of liver (ENCLB171HFS)

description:
https://www.encodeproject.org/experiments/ENCSR660PFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR660PFN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB171HFS
size range: 200-600

value: right lobe of liver

value: tissue

value: 41 year

value: Bradley Bernstein, Broad


description:
∆ramB ∆sdhCAB (400 mM glycerine) vs. WT (400 mM glycerine)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


description:
∆ramB ∆sdhCAB (400 mM glycerine) vs. WT (400 mM glycerine)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from naive B cell (ENCLB767ISP)

description:
https://www.encodeproject.org/experiments/ENCSR660EVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR660EVU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR056PPJ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB767ISP

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

value: naive B cell

value: 40 year

value: John Stamatoyannopoulos

value: ENCBS857XIR at ENCODE; https://www.encodeproject.org/ENCBS857XIR/

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


title: Control Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB779PAH)

description:
https://www.encodeproject.org/experiments/ENCSR663BWX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR663BWX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779PAH

value: 48 year

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS319ZAQ at ENCODE; https://www.encodeproject.org/ENCBS319ZAQ/

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


title: Mint-ChIP-seq from naive B cell (ENCLB145XSY)

description:
https://www.encodeproject.org/experiments/ENCSR660EVU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR660EVU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR056PPJ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB145XSY

value: primary cell

value: male


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB666JJP)

description:
https://www.encodeproject.org/experiments/ENCSR272VRX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR272VRX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB666JJP

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: adult

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:
∆cyaB (100 mM glucose, 100 mM acetate) vs. WT (100 mM glucose, 100 mM acetate)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

source_name: ∆cyaB (100 mM glucose, 100 mM acetate)

value: deletion mutant

value: delta_cyaB harvested during exponential growth phase, CGXII 100 mM glucose, 100 mM acetate, date of experiment:2009-02, GEO:GSE140408

source_name: WT (100 mM glucose, 100 mM acetate)

value: wild type

value: WT harvested during exponential growth phase, CGXII 100 mM glucose, 100 mM acetate, date of experiment:2009-02, GEO:GSE140408


description:
∆cyaB (100 mM glucose, 100 mM acetate) vs. WT (100 mM glucose, 100 mM acetate)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: TF ChIP-seq from middle frontal area 46 (ENCLB843CTQ)

description:
https://www.encodeproject.org/experiments/ENCSR275JVX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR275JVX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR018KWK
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB843CTQ
size range: 200-600

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

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS641FUL at ENCODE; https://www.encodeproject.org/ENCBS641FUL/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: Mint-ChIP-seq from WTC11 (ENCLB923OJK)

description:
https://www.encodeproject.org/experiments/ENCSR473GYW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR473GYW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB923OJK

source_name: Homo sapiens WTC11 cell line

value: cell line

value: male

value: adult

value: 30 year

tag: passage number

value: Yin Shen

value: ENCBS869UGY at ENCODE; https://www.encodeproject.org/ENCBS869UGY/

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


title: ∆phdR vs. WT-rep2

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

source_name: ∆phdR

value: deletion mutant

value: delta_phdR harvested during exponential growth phase, CGXII glucose, date of experiment:2014-07, GEO:GSE69413

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-07, GEO:GSE69414


description:
∆cyaB (4% glucose) vs. WT (4% glucose)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cyaB (4% glucose)

value: delta_cyaB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-02

source_name: WT (4% glucose)

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-02


title: Mint-ChIP-seq from WTC11 (ENCLB880FRC)

description:
https://www.encodeproject.org/experiments/ENCSR473GYW/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR473GYW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB880FRC

value: Bradley Bernstein, Broad

value: ENCBS532TBS at ENCODE; https://www.encodeproject.org/ENCBS532TBS/


title: Mint-ChIP-seq from WTC11 (ENCLB206WNM)

description:
https://www.encodeproject.org/experiments/ENCSR473GYW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR473GYW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB206WNM


description:
∆cyaB (4% glucose) vs. WT (4% glucose)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB490THP)

description:
https://www.encodeproject.org/experiments/ENCSR272QSF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR272QSF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB490THP

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

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

value: ENCBS844UBK at ENCODE; https://www.encodeproject.org/ENCBS844UBK/

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


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB163WEM)

description:
https://www.encodeproject.org/experiments/ENCSR272VRX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272VRX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR490HRA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB163WEM

value: primary cell

value: male

value: adult

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:
∆cyaB (4% glucose) vs. WT (4% glucose)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cyaB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-02

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-02


title: ∆cg0210 vs. WT-rep2

description:
∆cg0210 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL28615

value: delta_cg0210 harvested during exponential growth phase, CGXII 2% myo-inositol, date of experiment:2019-06

source_name: WT

value: WT harvested during exponential growth phase, CGXII 2% myo-inositol, date of experiment:2019-06


title: TF ChIP-seq from middle frontal area 46 (ENCLB825PNC)

description:
https://www.encodeproject.org/experiments/ENCSR275JVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR275JVX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR018KWK
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB825PNC
size range: 200-600

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS641FUL at ENCODE; https://www.encodeproject.org/ENCBS641FUL/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: ∆iolR vs. WT-rep2

description:
∆iolR vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆iolR

value: delta_iolR harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05, GEO:GSE44812

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05, GEO:GSE44812


title: WT pAN6-cg0210 vs. WT-rep2

description:
WT pAN6-cg0210 vs. WT-rep2
Biological replicate 2 of 2
original platform:
GPL28615

source_name: WT pAN6-cg0210

value: wild type + overexpression

value: WT pAN6-cg0210 harvested during exponential growth phase, CGXII 2% myo-inositol, 100 µM IPTG, date of experiment:2019-07

value: wild type + control

value: WT pAN6 harvested during exponential growth phase, CGXII 2% myo-inositol, 100 µM IPTG, date of experiment:2019-07


title: ∆phdR vs. WT-rep1

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

value: deletion mutant

value: delta_phdR harvested during exponential growth phase, CGXII glucose, date of experiment:2014-07, GEO:GSE69413

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-07, GEO:GSE69413


title: 375_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep9

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep9
Biological replicate 9 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal

source_name: ∆panBC ∆il

value: deletion mutant + overexpression

value: delta_panBC delta_ilvA pJC1-ilvBNCD harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, 100 µM IPTG, date of experiment:2002-01/2002-03

source_name: A pJC1-il

value: deletion mutant + control

value: delta_panBC delta_ilvA pJC1 harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, date of experiment:2002-01/2002-03


title: ∆iolR vs. WT-rep1

description:
∆iolR vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: 374_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep8

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep8
Biological replicate 8 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal


title: WT pAN6-cg0210 vs. WT-rep1

description:
WT pAN6-cg0210 vs. WT-rep1
Biological replicate 1 of 2
original platform:
GPL28615


description:
∆cyaB (100 mM glucose, 100 mM acetate) vs. WT (100 mM glucose, 100 mM acetate)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_cyaB harvested during exponential growth phase, CGXII 100 mM glucose, 100 mM acetate, date of experiment:2009-02, GEO:GSE140408

value: WT harvested during exponential growth phase, CGXII 100 mM glucose, 100 mM acetate, date of experiment:2009-02, GEO:GSE140408


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB346GBZ)

description:
https://www.encodeproject.org/experiments/ENCSR864RGX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR864RGX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897UBR
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB346GBZ

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

value: primary cell

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS715FVA at ENCODE; https://www.encodeproject.org/ENCBS715FVA/

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


title: ∆cg0210 vs. WT-rep1

description:
∆cg0210 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL28615

value: deletion mutant

value: delta_cg0210 harvested during exponential growth phase, CGXII 2% myo-inositol, date of experiment:2019-06

value: wild type

value: WT harvested during exponential growth phase, CGXII 2% myo-inositol, date of experiment:2019-06


title: Mint-ChIP-seq from HCT116 (ENCLB059FCE)

description:
https://www.encodeproject.org/experiments/ENCSR272QSF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272QSF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB059FCE

value: cell line

value: 48 year

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS844UBK at ENCODE; https://www.encodeproject.org/ENCBS844UBK/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB070CBS)

description:
https://www.encodeproject.org/experiments/ENCSR659MOZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR659MOZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR018KWK
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB070CBS
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: male

value: adult

value: Rush University

value: ENCBS641FUL at ENCODE; https://www.encodeproject.org/ENCBS641FUL/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: ∆cg0210 vs. WT-rep3

description:
∆cg0210 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL28615

value: deletion mutant

value: delta_cg0210 harvested during exponential growth phase, CGXII 2% myo-inositol, date of experiment:2019-06

value: wild type


title: Mint-ChIP-seq from natural killer cell (ENCLB812EZT)

description:
https://www.encodeproject.org/experiments/ENCSR270TNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR270TNP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR294RLP
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB812EZT

source_name: Homo sapiens female adult (41 years) natural killer primary cell

value: natural killer cell

value: primary cell

value: 41 year

value: female

value: John Stamatoyannopoulos

value: ENCBS543UGM at ENCODE; https://www.encodeproject.org/ENCBS543UGM/

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


title: 372_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep6

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep6
Biological replicate 6 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal

value: deletion mutant + overexpression

value: delta_panBC delta_ilvA pJC1-ilvBNCD harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, 100 µM IPTG, date of experiment:2002-01/2002-03

value: deletion mutant + control

value: delta_panBC delta_ilvA pJC1 harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, date of experiment:2002-01/2002-03


title: Mint-ChIP-seq from WTC11 (ENCLB180HDK)

description:
https://www.encodeproject.org/experiments/ENCSR473GYW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on WTC11
experiment encode accession: ENCSR473GYW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR686JHP
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB180HDK

value: cell line

value: male

value: adult

value: 30 year

value: Bradley Bernstein, Broad

value: Yin Shen

value: ENCBS869UGY at ENCODE; https://www.encodeproject.org/ENCBS869UGY/

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


title: ∆iolR vs. WT-rep3

description:
∆iolR vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_iolR harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05, GEO:GSE44812

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-05, GEO:GSE44812


title: Histone ChIP-seq from ovary (ENCLB032FFI)

description:
https://www.encodeproject.org/experiments/ENCSR276MDP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR276MDP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB032FFI
size range: 200-600

source_name: Homo sapiens female adult (41 years) ovary tissue

value: ovary

value: tissue

value: 41 year

value: female

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

value: Shin Lin

value: ENCBS327NVM at ENCODE; https://www.encodeproject.org/ENCBS327NVM/

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


title: 370_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep4

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep4
Biological replicate 4 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal

value: deletion mutant + overexpression

value: delta_panBC delta_ilvA pJC1-ilvBNCD harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, 100 µM IPTG, date of experiment:2002-01/2002-03

value: deletion mutant + control

value: delta_panBC delta_ilvA pJC1 harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, date of experiment:2002-01/2002-03


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB642RQZ)

description:
https://www.encodeproject.org/experiments/ENCSR864RGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR864RGX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897UBR
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642RQZ

value: primary cell

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS715FVA at ENCODE; https://www.encodeproject.org/ENCBS715FVA/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB872OOF)

description:
https://www.encodeproject.org/experiments/ENCSR659MOZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR659MOZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR018KWK
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872OOF
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS641FUL at ENCODE; https://www.encodeproject.org/ENCBS641FUL/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: 373_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep7

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep7
Biological replicate 7 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal

value: deletion mutant + overexpression

value: delta_panBC delta_ilvA pJC1-ilvBNCD harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, 100 µM IPTG, date of experiment:2002-01/2002-03

value: deletion mutant + control

value: delta_panBC delta_ilvA pJC1 harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, date of experiment:2002-01/2002-03


title: Mint-ChIP-seq from natural killer cell (ENCLB324ALB)

description:
https://www.encodeproject.org/experiments/ENCSR270TNP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR270TNP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR294RLP
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB324ALB

value: natural killer cell

value: primary cell

value: 41 year

value: female

value: adult

value: John Stamatoyannopoulos

value: ENCBS543UGM at ENCODE; https://www.encodeproject.org/ENCBS543UGM/

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


title: 367_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep1

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep1
Biological replicate 1 of 9
GAL file:
CG_GAL_PCR_Layout_08.gal


title: 368_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep2

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep2
Biological replicate 2 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal


title: Histone ChIP-seq from right lobe of liver (ENCLB068UGK)

description:
https://www.encodeproject.org/experiments/ENCSR864OOO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR864OOO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB068UGK
size range: 200-600

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

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

value: Shin Lin

value: ENCBS971GGI at ENCODE; https://www.encodeproject.org/ENCBS971GGI/

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


title: Mint-ChIP-seq from HCT116 (ENCLB199BKE)

description:
https://www.encodeproject.org/experiments/ENCSR265SCJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR265SCJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB199BKE

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS844UBK at ENCODE; https://www.encodeproject.org/ENCBS844UBK/

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


title: 371_∆panBC ∆ilvA pJC1-ilvBNCDvs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep5

description:
∆panBC ∆ilvA pJC1-ilvBNCD (0.9 mM isoleucine, 0.5 µM pantothenate) vs. ∆panBC ∆ilvA pJC1 (0.9 mM isoleucine, 0.5 µM pantothenate)-rep5
Biological replicate 5 of 9
GAL file:
CG_GAL_PCR_Layout_06.gal

value: deletion mutant + overexpression

value: delta_panBC delta_ilvA pJC1-ilvBNCD harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, 100 µM IPTG, date of experiment:2002-01/2002-03

value: deletion mutant + control

value: delta_panBC delta_ilvA pJC1 harvested during exponential growth phase, CGXII 0.9 mM isoleucine, 0.5 µM pantothenate, date of experiment:2002-01/2002-03


title: Histone ChIP-seq from right lobe of liver (ENCLB524MPF)

description:
https://www.encodeproject.org/experiments/ENCSR864OOO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR864OOO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB524MPF
size range: 200-600

value: right lobe of liver

value: tissue

value: 41 year

value: female

value: adult