title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB019EKF)

description:
https://www.encodeproject.org/experiments/ENCSR714MWV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR714MWV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897UBR
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB019EKF

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

tag: age

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: ∆recA vs. WT-rep2

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

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.
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.

molecule: total RNA

organism: Corynebacterium glutamicum

source_name: ∆recA

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: genotype

value: deletion mutant

tag: condition

value: delta_recA harvested during exponential growth phase, CGXII glucose, date of experiment:2013-11/2014-02

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-11/2014-02


title: CNTRL E11.5

type: SRA

city: Columbus

first: Madhumita

last: Basu

state: Ohio

address: 700 Children's Drive

department: Center for Cardiovascular Research

country: USA

institute: Nationwide Children's Hospital

library_source: transcriptomic

data_processing:
We used the 10X Genomics' Cell Ranger pipeline to demultiplex and convert Illumina bcl output into fastq files.
We mapped the fastq reads to the mouse genome mm10 (version mm10-3.0.0) from downloaded from 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build) using count function in Cell Ranger pipeline version (3.1.0) to generate gene expression matrix
This data was processed using Natian running Seurat (version 3.0) to perform normalization and identification of genes with the highest variability, prinicpal componenet analysis, dimensionality reduction. Subsequently, individual Seurat files were merged using Natian (Singlecelltranscriptomics.org) running Seurat (version 3.0)
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger pipeline outputs (1 market matrix (.mtx), barcode (.tsv) and features (.tsv) file for each sample) compressed to tar.gz file

organism: Mus musculus

source_name: Mouse embryonic heart from nondiabetic dam

growth_protocol: Not applicable

extract_protocol:
Embryos (E9.5 and E11.5) were removed from yolk sac, whole hearts microdissected in diethylpyrocarbonate-treated PBS, dissociated into single cell suspension using Collagenase II (Worthington) and TryPLE. >85-90% viable cells were used to prepare single GEMs using 10XGenomics Chromium Controller. The quality of cDNA were assessed using High Sensitivity  D5000 ScreenTape® on Agilent 2200 TapeStation. After adjusting all four samples (CNTRL vs. matHG-exposed E9.5 and E11.5) to similar concentrations, each single-cell cDNA sample was used for library preparation using Chromium Single Cell 3′ Library & Gel Bead Kit v2 and Chromium i7 Multiplex Kit (10X Genomics,PN-120237, PN-120262) and quantified using High Sensitivity D1000 ScreenTape®. Single-cell libraries were sequenced on the Illumina Hiseq4000 platform with 2 X 150 bp read length using standard Illumina protocol.
Chromium Single Cell 3′ Library & Gel Bead Kit v2 and Chromium i7 Multiplex Kit (10X Genomics,PN-120237, PN-120262)
Single-cell RNA-seq libraries were sequenced on the Illumina Hiseq4000 platform (2x150 bp read length)

treatment_protocol: Not applicable

tag: tissue

value: whole heart

tag: strain

value: wildtype

tag: disease status

value: Nondiabetic or control

tag: timepoint


title: ∆fruR (LB) vs. WT (LB)-rep2

description:
∆fruR (LB) vs. WT (LB)-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_00.gal

source_name: ∆fruR (LB)

value: delta_fruR harvested during exponential growth phase, LB, date of experiment:2004-11/2005-01

source_name: WT (LB)

value: WT harvested during exponential growth phase, LB, date of experiment:2004-11/2005-01


title: CNTRL E9.5


description:
∆dtxR (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep3
Biological replicate 3 of 3
GAL file:
CG_GAL_PCR_Layout_05.gal

source_name: ∆dtxR (1 µM FeSO4)

value: delta_dtxR harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2005-08/2005-10

source_name: WT (1 µM FeSO4)

value: WT harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2005-08/2005-10


description:
∆dtxR (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_00.gal


title: ∆fruR (LB) vs. WT (LB)-rep1

description:
∆fruR (LB) vs. WT (LB)-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_00.gal


description:
∆recA (0.6 µM mitomycin C) vs. WT (0.6 µM mitomycin C)-rep1
Biological replicate 1 of 3
original platform:
GPL22561

source_name: ∆recA (0.6 µM mitomycin C)

value: delta_recA harvested during exponential growth phase 30 min after addition of 0.6 µM mitomycin C, CGXII glucose, date of experiment:2014-02

source_name: WT (0.6 µM mitomycin C)

value: WT harvested during exponential growth phase 30 min after addition of 0.6 µM mitomycin C, CGXII glucose, date of experiment:2014-02


title: Control Mint-ChIP-seq from activated T-helper 17 cell (ENCLB784MZQ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR122NDV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR122NDV
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB784MZQ

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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: primary cell

tag: biosample encode accession

value: 50 year

tag: Sex

value: male

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: John Stamatoyannopoulos

tag: treatments

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;

tag: link

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 CD14-positive monocyte (ENCLB201VQO)

description:
https://www.encodeproject.org/experiments/ENCSR690NZN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD14-positive monocyte.
experiment encode accession: ENCSR690NZN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR086KHK
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB201VQO
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens CD14-positive monocyte primary cell

tag: antibody

value: CD14-positive monocyte

tag: description

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

value: not collected

tag: health state

value: healthy

value: unknown

value: David Hafler

value: ENCBS666ANY at ENCODE; https://www.encodeproject.org/ENCBS666ANY/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB565RNG)

description:
https://www.encodeproject.org/experiments/ENCSR929JEV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR929JEV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB565RNG
fragmentation methods: none

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

value: primary cell

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

tag: age

value: ENCBS677DRS at ENCODE; https://www.encodeproject.org/ENCBS677DRS/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB912YDH)

description:
https://www.encodeproject.org/experiments/ENCSR929JEV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR929JEV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB912YDH
fragmentation methods: none

value: Bradley Bernstein, Broad


description:
∆dtxR (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_05.gal

tag: genotype

value: deletion mutant

value: delta_dtxR harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2005-08/2005-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2005-08/2005-10


title: ∆fruR (LB) vs. WT (LB)-rep3

description:
∆fruR (LB) vs. WT (LB)-rep3
Biological replicate 3 of 3
GAL file:
CG_GAL_PCR_Layout_00.gal

tag: condition

value: delta_fruR harvested during exponential growth phase, LB, date of experiment:2004-11/2005-01

value: WT harvested during exponential growth phase, LB, date of experiment:2004-11/2005-01


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB377NSU)

description:
https://www.encodeproject.org/experiments/ENCSR690NZN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD14-positive monocyte.
experiment encode accession: ENCSR690NZN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR086KHK
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB377NSU
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: CD14-positive monocyte

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

value: not collected


description:
∆dtxR (100 µM FeSO4) vs. WT (100 µM FeSO4)-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_00.gal

source_name: ∆dtxR (100 µM FeSO4)

value: delta_dtxR harvested during exponential growth phase, CGXII glucose, 100 µM FeSO4, date of experiment:2005-08/2005-10

source_name: WT (100 µM FeSO4)

value: WT harvested during exponential growth phase, CGXII glucose, 100 µM FeSO4, date of experiment:2005-08/2005-10


title: Mint-ChIP-seq from H9 (ENCLB091LSF)

description:
https://www.encodeproject.org/experiments/ENCSR294RPI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR294RPI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2022-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB091LSF
fragmentation methods: none

source_name: Homo sapiens H9 cell line

tag: line

value: cell line

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

tag: passage number

value: ENCBS965ZIX at ENCODE; https://www.encodeproject.org/ENCBS965ZIX/

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


description:
∆dtxR (100 µM FeSO4) vs. WT (100 µM FeSO4)-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_05.gal

value: deletion mutant

value: wild type


title: Mint-ChIP-seq from H9 (ENCLB111RMS)

description:
https://www.encodeproject.org/experiments/ENCSR294RPI/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR294RPI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2022-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB111RMS
fragmentation methods: none

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB945TMS)

description:
https://www.encodeproject.org/experiments/ENCSR332BVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR332BVN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR390KLC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB945TMS

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: adult

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: 665_∆aceE ∆pyc 100 mM HCO3- vs. ∆aceE ∆pyc_7hours -rep2

description:
∆aceE ∆pyc (4% glucose, 1.5% acetate, 100 mM HCO3-, 7 hours) vs. ∆aceE ∆pyc  (4% glucose, 1.5% acetate, 7 hours)-rep2
Biological replicate 2 of 2
original platform:
GPL22561

value: delta_aceE delta_pyc harvested after 7 hours, CGXII glucose, 1.5% acetate, 100 mM HCO3-, date of experiment:2016-12

value: delta_aceE delta_pyc harvested after 7 hours, CGXII glucose, 1.5% acetate, date of experiment:2016-12


title: 666_∆aceE ∆pyc 100 mM HCO3- vs. ∆aceE ∆pyc_13hours-rep1

description:
∆aceE ∆pyc (4% glucose, 1.5% acetate, 100 mM HCO3-, 13 hours) vs. ∆aceE ∆pyc  (4% glucose, 1.5% acetate, 13 hours)-rep1
Biological replicate 1 of 2
original platform:
GPL22561

value: delta_aceE delta_pyc harvested after 13 hours, CGXII glucose, 1.5% acetate, 100 mM HCO3-, date of experiment:2016-12

value: delta_aceE delta_pyc harvested after 13 hours, CGXII glucose, 1.5% acetate, date of experiment:2016-12


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB935QFT)

description:
https://www.encodeproject.org/experiments/ENCSR332BVN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR332BVN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR390KLC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB935QFT


description:
∆aceE ∆pyc (4% glucose, 1.5% acetate) vs. ∆aceE  (4% glucose, 1.5% acetate)-rep3
Biological replicate 3 of 3
original platform:
GPL28615

source_name: ∆aceE ∆pyc (4% glucose, 1.5% acetate)

value: delta_aceE delta_pyc harvested during exponential growth phase, CGXII glucose, 1.5% acetate, date of experiment:2018-10, GEO:GSE134218

source_name: ∆aceE  (4% glucose, 1.5% acetate)

value: delta_aceE harvested during exponential growth phase, CGXII glucose, 1.5% acetate, date of experiment:2018-10, GEO:GSE134218


title: Mint-ChIP-seq from H9 (ENCLB580FKE)

description:
https://www.encodeproject.org/experiments/ENCSR294RPI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR294RPI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2022-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB580FKE
fragmentation methods: none

value: cell line

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS965ZIX at ENCODE; https://www.encodeproject.org/ENCBS965ZIX/

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


title: Mint-ChIP-seq from naive B cell (ENCLB404TDZ)

description:
https://www.encodeproject.org/experiments/ENCSR712YZE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR712YZE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR575ZCX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB404TDZ

source_name: Homo sapiens female adult (39 years) naive B primary cell

value: naive B cell

value: primary cell

value: 39 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS531INH at ENCODE; https://www.encodeproject.org/ENCBS531INH/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: 664_∆aceE ∆pyc 100 mM HCO3- vs. ∆aceE ∆pyc_7hours-rep1

description:
∆aceE ∆pyc (4% glucose, 1.5% acetate, 100 mM HCO3-, 7 hours) vs. ∆aceE ∆pyc  (4% glucose, 1.5% acetate, 7 hours)-rep1
Biological replicate 1 of 2
original platform:
GPL22561

value: deletion mutant

value: delta_aceE delta_pyc harvested after 7 hours, CGXII glucose, 1.5% acetate, 100 mM HCO3-, date of experiment:2016-12

value: delta_aceE delta_pyc harvested after 7 hours, CGXII glucose, 1.5% acetate, date of experiment:2016-12


title: Mint-ChIP-seq from H9 (ENCLB194POH)

description:
https://www.encodeproject.org/experiments/ENCSR294RPI/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K4me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR294RPI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2022-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB194POH
fragmentation methods: none

value: cell line

value: female

value: healthy


description:
∆aceE ∆pyc (4% glucose, 1.5% acetate) vs. ∆aceE  (4% glucose, 1.5% acetate)-rep1
Biological replicate 1 of 3
original platform:
GPL28615

value: delta_aceE delta_pyc harvested during exponential growth phase, CGXII glucose, 1.5% acetate, date of experiment:2018-10, GEO:GSE134218

value: delta_aceE harvested during exponential growth phase, CGXII glucose, 1.5% acetate, date of experiment:2018-10, GEO:GSE134218


description:
∆aceE ∆pyc (4% glucose, 1.5% acetate) vs. ∆aceE  (4% glucose, 1.5% acetate)-rep2
Biological replicate 2 of 3
original platform:
GPL28615


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB406CCY)

description:
https://www.encodeproject.org/experiments/ENCSR495RPG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR495RPG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406CCY
fragmentation methods: none

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell

value: CD8-positive, alpha-beta memory T cell

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

value: not collected

value: unknown

value: David Hafler

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: 659_∆aceE ∆ureD-E188* vs. ∆aceE_production phase-rep2

description:
∆aceE ∆ureD-E188* (4% glucose, 1.5% acetate, production phase) vs. ∆aceE (4% glucose, 1.5% acetate, production phase)-rep2
Biological replicate 2 of 3
original platform:
GPL22561

value: deletion mutant + mutation

value: delta_aceE delta_iolA-E188* harvested during production phase, CGXII glucose,1.5% acetate, date of experiment:2015-11

value: delta_aceE harvested during production phase, CGXII glucose,1.5% acetate, date of experiment:2015-11


title: 667_∆aceE ∆pyc 100 mM HCO3- vs. ∆aceE ∆pyc_13hours-rep2

description:
∆aceE ∆pyc (4% glucose, 1.5% acetate, 100 mM HCO3-, 13 hours) vs. ∆aceE ∆pyc  (4% glucose, 1.5% acetate, 13 hours)-rep2
Biological replicate 2 of 2
original platform:
GPL22561

value: deletion mutant

value: delta_aceE delta_pyc harvested after 13 hours, CGXII glucose, 1.5% acetate, 100 mM HCO3-, date of experiment:2016-12

value: delta_aceE delta_pyc harvested after 13 hours, CGXII glucose, 1.5% acetate, date of experiment:2016-12


title: 660_∆aceE ∆ureD-E188* vs. ∆aceE_production phase-rep3

description:
∆aceE ∆ureD-E188* (4% glucose, 1.5% acetate, production phase) vs. ∆aceE (4% glucose, 1.5% acetate, production phase)-rep3
Biological replicate 3 of 3
original platform:
GPL22561


title: TF ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB560LOW)

description:
https://www.encodeproject.org/experiments/ENCSR116AKQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR116AKQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR701JGD
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB560LOW
size range: 200-600

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CTCF

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 21 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS529SCX at ENCODE; https://www.encodeproject.org/ENCBS529SCX/

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB600KBU)

description:
https://www.encodeproject.org/experiments/ENCSR495RPG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR495RPG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR749PSE
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB600KBU
fragmentation methods: none

value: CD8-positive, alpha-beta memory T cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS020LPJ at ENCODE; https://www.encodeproject.org/ENCBS020LPJ/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: 657_∆aceE ∆ureD-E188* vs. ∆aceE_growth phase-rep3

description:
∆aceE ∆ureD-E188* (4% glucose, 1.5% acetate, growth phase) vs. ∆aceE (4% glucose, 1.5% acetate, growth phase)-rep3
Biological replicate 3 of 3
original platform:
GPL22561

value: deletion mutant + mutation

value: delta_aceE delta_iolA-E188* harvested during exponential growth phase, CGXII glucose,1.5% acetate, date of experiment:2015-11

value: deletion mutant

value: delta_aceE harvested during exponential growth phase, CGXII glucose,1.5% acetate, date of experiment:2015-11


title: 656_∆aceE ∆ureD-E188* vs. ∆aceE_growth phase-rep2

description:
∆aceE ∆ureD-E188* (4% glucose, 1.5% acetate, growth phase) vs. ∆aceE (4% glucose, 1.5% acetate, growth phase)-rep2
Biological replicate 2 of 3
original platform:
GPL22561


title: TF ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB852KWC)

description:
https://www.encodeproject.org/experiments/ENCSR116AKQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR116AKQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR701JGD
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB852KWC
size range: 200-600

value: CTCF

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 21 year

value: male

value: adult


title: 658_∆aceE ∆ureD-E188* vs. ∆aceE_production phase-rep1

description:
∆aceE ∆ureD-E188* (4% glucose, 1.5% acetate, production phase) vs. ∆aceE (4% glucose, 1.5% acetate, production phase)-rep1
Biological replicate 1 of 3
original platform:
GPL22561

value: delta_aceE delta_iolA-E188* harvested during production phase, CGXII glucose,1.5% acetate, date of experiment:2015-11

value: delta_aceE harvested during production phase, CGXII glucose,1.5% acetate, date of experiment:2015-11


title: TF ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB869CCK)

description:
https://www.encodeproject.org/experiments/ENCSR116AKQ/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR116AKQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR701JGD
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB869CCK
size range: 200-600

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS529SCX at ENCODE; https://www.encodeproject.org/ENCBS529SCX/

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB734VCY)

description:
https://www.encodeproject.org/experiments/ENCSR928YUX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR928YUX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB734VCY
fragmentation methods: none

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

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS862LJK at ENCODE; https://www.encodeproject.org/ENCBS862LJK/

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


title: Mint-ChIP-seq from naive B cell (ENCLB544TYU)

description:
https://www.encodeproject.org/experiments/ENCSR712YZE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR712YZE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR575ZCX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB544TYU

value: naive B cell

value: primary cell

value: 39 year

value: female

value: John Stamatoyannopoulos

value: ENCBS531INH at ENCODE; https://www.encodeproject.org/ENCBS531INH/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


description:
∆dtxR (100 µM FeSO4) vs. WT (100 µM FeSO4)-rep3
Biological replicate 3 of 3
GAL file:
CG_GAL_PCR_Layout_05.gal

value: deletion mutant

value: delta_dtxR harvested during exponential growth phase, CGXII glucose, 100 µM FeSO4, date of experiment:2005-08/2005-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 100 µM FeSO4, date of experiment:2005-08/2005-10


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB708UDG)

description:
https://www.encodeproject.org/experiments/ENCSR928YUX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR928YUX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB708UDG
fragmentation methods: none

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

value: not collected

value: Bradley Bernstein, Broad


description:
∆aceE Evo5 (4% glucose, 1.5% acetate, 28 hours) vs. ∆aceE Evo3  (4% glucose, 1.5% acetate, 28 hours)-rep2
Biological replicate 2 of 3
original platform:
GPL22792

source_name: ∆aceE E

value: deletion mutant + evolution

value: delta_aceE Evo5 harvested after cultivation for 28 hours, CGXII glucose,1.5% acetate, date of experiment:2014-05

source_name: o5 (4% glucose, 1.5% acetate, 28 hours)

value: delta_aceE Evo3 harvested after cultivation for 28 hours, CGXII glucose,1.5% acetate, date of experiment:2014-05


description:
∆aceE Evo5 (4% glucose, 1.5% acetate, 28 hours) vs. ∆aceE Evo3  (4% glucose, 1.5% acetate, 28 hours)-rep3
Biological replicate 3 of 3
original platform:
GPL22792


description:
∆aceE Evo4 (4% glucose, 1.5% acetate, 28 hours) vs. ∆aceE Evo3  (4% glucose, 1.5% acetate, 28 hours)-rep2
Biological replicate 2 of 3
original platform:
GPL22792

value: delta_aceE Evo4 harvested after cultivation for 28 hours, CGXII glucose,1.5% acetate, date of experiment:2014-05

source_name: o4 (4% glucose, 1.5% acetate, 28 hours)


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB455KJJ)

description:
https://www.encodeproject.org/experiments/ENCSR710SZV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR710SZV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB455KJJ

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

value: primary cell

value: 48 year

value: male

value: adult

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

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB895FAH)

description:
https://www.encodeproject.org/experiments/ENCSR277XYX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR277XYX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128CIX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895FAH
fragmentation methods: none

source_name: Homo sapiens naive thymus-derived CD4-positive, alpha-beta T primary cell with multiple sclerosis

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

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS040CMJ at ENCODE; https://www.encodeproject.org/ENCBS040CMJ/

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


description:
∆aceE Evo4 (4% glucose, 1.5% acetate, 28 hours) vs. ∆aceE Evo3  (4% glucose, 1.5% acetate, 28 hours)-rep1
Biological replicate 1 of 3
original platform:
GPL22792


description:
∆aceE Evo4 (4% glucose, 1.5% acetate, 28 hours) vs. ∆aceE Evo3  (4% glucose, 1.5% acetate, 28 hours)-rep3
Biological replicate 3 of 3
original platform:
GPL22792


title: 655_∆aceE ∆ureD-E188* vs. ∆aceE_growth phase-rep1

description:
∆aceE ∆ureD-E188* (4% glucose, 1.5% acetate, growth phase) vs. ∆aceE (4% glucose, 1.5% acetate, growth phase)-rep1
Biological replicate 1 of 3
original platform:
GPL22561

value: deletion mutant + mutation

value: delta_aceE delta_iolA-E188* harvested during exponential growth phase, CGXII glucose,1.5% acetate, date of experiment:2015-11

value: deletion mutant

value: delta_aceE harvested during exponential growth phase, CGXII glucose,1.5% acetate, date of experiment:2015-11


description:
∆aceE Evo5 (4% glucose, 1.5% acetate, 28 hours) vs. ∆aceE Evo3  (4% glucose, 1.5% acetate, 28 hours)-rep1
Biological replicate 1 of 3
original platform:
GPL22792

value: deletion mutant + evolution

value: delta_aceE Evo5 harvested after cultivation for 28 hours, CGXII glucose,1.5% acetate, date of experiment:2014-05

value: delta_aceE Evo3 harvested after cultivation for 28 hours, CGXII glucose,1.5% acetate, date of experiment:2014-05


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB469ILM)

description:
https://www.encodeproject.org/experiments/ENCSR277XYX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR277XYX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128CIX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469ILM
fragmentation methods: none

value: primary cell

value: not collected

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from nephron (ENCLB371MMA)

description:
https://www.encodeproject.org/experiments/ENCSR866NTZ/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR866NTZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB371MMA
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/

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


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB128TGC)

description:
https://www.encodeproject.org/experiments/ENCSR714MWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR714MWV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897UBR
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB128TGC

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: 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: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB625UOY)

description:
https://www.encodeproject.org/experiments/ENCSR710SZV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR710SZV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB625UOY

value: primary cell

value: 48 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB126TUF)

description:
https://www.encodeproject.org/experiments/ENCSR284IKS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR284IKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128KDZ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB126TUF

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell with multiple sclerosis

value: CD8-positive, alpha-beta memory T cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS757PLC at ENCODE; https://www.encodeproject.org/ENCBS757PLC/

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


title: ∆cg2040 vs. WT-rep1

description:
∆cg2040 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cg2040 harvested during exponential growth phase, CGXII glucose,date of experiment:2010-10/2010-11

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose,date of experiment:2010-10/2010-11


title: Mint-ChIP-seq from nephron (ENCLB236LTW)

description:
https://www.encodeproject.org/experiments/ENCSR866NTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR866NTZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB236LTW
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid, 35 days post differentiation

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS391CFV at ENCODE; https://www.encodeproject.org/ENCBS391CFV/

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


title: ∆cg2040 vs. WT-rep2

description:
∆cg2040 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from nephron (ENCLB208WTB)

description:
https://www.encodeproject.org/experiments/ENCSR866NTZ/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR866NTZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB208WTB
fragmentation methods: none

value: Bradley Bernstein, Broad


description:
∆gntR1 (100 mM gluconate) vs. WT (100 mM gluconate)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆gntR1 (100 mM gluconate)

value: delta_gntR1 harvested during exponential growth phase, CGXII gluconate,date of experiment:2007-04

source_name: WT (100 mM gluconate)

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


title: Mint-ChIP-seq from HCT116 (ENCLB992IAA)

description:
https://www.encodeproject.org/experiments/ENCSR331KOJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR331KOJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR071RJS
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB992IAA

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

value: ENCBS816ZRZ at ENCODE; https://www.encodeproject.org/ENCBS816ZRZ/

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


description:
∆gntR1 (100 mM gluconate) vs. WT (100 mM gluconate)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant

value: wild type


description:
∆gntR1 (100 mM glucose) vs. WT (100 mM glucose)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆gntR1 (100 mM glucose)

value: delta_gntR1 harvested during exponential growth phase, CGXII glucose,date of experiment:2007-04

source_name: WT (100 mM glucose)

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


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

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

value: deletion mutant + overexpression

value: delta_sigB pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2012-03

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

value: deletion mutant + control

value: delta_sigB pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, w/o IPTG, date of experiment:2012-03


title: ∆cg2040 vs. WT-rep3

description:
∆cg2040 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_cg2040 harvested during exponential growth phase, CGXII glucose,date of experiment:2010-10/2010-11

value: WT harvested during exponential growth phase, CGXII glucose,date of experiment:2010-10/2010-11


title: Mint-ChIP-seq from nephron (ENCLB094GUW)

description:
https://www.encodeproject.org/experiments/ENCSR866NTZ/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR866NTZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB094GUW
fragmentation methods: none

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS391CFV at ENCODE; https://www.encodeproject.org/ENCBS391CFV/

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


title: Mint-ChIP-seq from HCT116 (ENCLB291KBI)

description:
https://www.encodeproject.org/experiments/ENCSR331KOJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR331KOJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR071RJS
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB291KBI

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

value: ENCBS816ZRZ at ENCODE; https://www.encodeproject.org/ENCBS816ZRZ/

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


title: Mint-ChIP-seq from nephron (ENCLB417JQL)

description:
https://www.encodeproject.org/experiments/ENCSR866NTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR866NTZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB417JQL
fragmentation methods: none

value: nephron

value: organoid

value: ENCBS165DBC at ENCODE; https://www.encodeproject.org/ENCBS165DBC/


description:
∆sigB pEKEx2-AmyE (1 mM IPTG) vs. ∆sigB pEKEx2-AmyE (w/o IPTG)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_sigB pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2012-03

value: deletion mutant + control

value: delta_sigB pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, w/o IPTG, date of experiment:2012-03


description:
∆sigB pEKEx2-AmyE (1 mM IPTG) vs. WT pEKEx2-AmyE (1 mM IPTG)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: WT pEKEx2-AmyE (1 mM IPTG)

value: wild type + overexpression

value: WT pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2012-03


title: Mint-ChIP-seq from HCT116 (ENCLB059ISC)

description:
https://www.encodeproject.org/experiments/ENCSR523IAZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR523IAZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR898CSY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB059ISC

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 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: Bradley Bernstein, Broad

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

value: ENCBS929EFP at ENCODE; https://www.encodeproject.org/ENCBS929EFP/


title: Mint-ChIP-seq from HCT116 (ENCLB452MMH)

description:
https://www.encodeproject.org/experiments/ENCSR709PFC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR709PFC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR853IEG
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB452MMH

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

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: ENCBS828BDT at ENCODE; https://www.encodeproject.org/ENCBS828BDT/


description:
∆sigB pEKEx2-AmyE (1 mM IPTG) vs. WT pEKEx2-AmyE (1 mM IPTG)-rep1
Biological replicate 1 of 2
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB108MON)

description:
https://www.encodeproject.org/experiments/ENCSR709PFC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR709PFC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR853IEG
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB108MON

value: Erez Aiden

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


description:
∆gntR12 (50 mM glucose, 50 mM gluconate) vs. WT (50 mM glucose, 50 mM gluconate)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_gntR12 harvested during exponential growth phase, CGXII 50 mM glucose, 50 mM gluconate date of experiment:2007-03

source_name: WT (50 mM glucose, 50 mM gluconate)

value: wild type

value: WT harvested during exponential growth phase, CGXII 50 mM glucose, 50 mM gluconate date of experiment:2007-03


title: Mint-ChIP-seq from HCT116 (ENCLB428OFK)

description:
https://www.encodeproject.org/experiments/ENCSR523IAZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR523IAZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR898CSY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB428OFK


description:
∆gntR12 (50 mM glucose, 50 mM gluconate) vs. WT (50 mM glucose, 50 mM gluconate)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB667AKK)

description:
https://www.encodeproject.org/experiments/ENCSR709KME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR709KME
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR390KLC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB667AKK

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: 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/


description:
∆gntR1 (100 mM glucose) vs. WT (100 mM glucose)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: delta_gntR1 harvested during exponential growth phase, CGXII glucose,date of experiment:2007-04

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


title: Mint-ChIP-seq from naive B cell (ENCLB459BOY)

description:
https://www.encodeproject.org/experiments/ENCSR272YVX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR272YVX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR707UVZ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB459BOY
fragmentation methods: none

source_name: Homo sapiens naive B primary cell with multiple sclerosis

value: naive B 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: David Hafler

value: ENCBS049BNE at ENCODE; https://www.encodeproject.org/ENCBS049BNE/

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


description:
∆gntR12 (50 mM glucose, 50 mM gluconate) vs. WT (50 mM glucose, 50 mM gluconate)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_gntR12 harvested during exponential growth phase, CGXII 50 mM glucose, 50 mM gluconate date of experiment:2007-03

value: wild type

value: WT harvested during exponential growth phase, CGXII 50 mM glucose, 50 mM gluconate date of experiment:2007-03


description:
∆gntR12 (100 mM gluconate) vs. WT (100 mM gluconate)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆gntR12 (100 mM gluconate)

value: delta_gntR12 harvested during exponential growth phase, CGXII gluconate, date of experiment:2007-03

value: WT harvested during exponential growth phase, CGXII gluconate, date of experiment:2007-03


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB807VWK)

description:
https://www.encodeproject.org/experiments/ENCSR649FUX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on IgD-negative memory B cell with multiple sclerosis.
experiment encode accession: ENCSR649FUX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR808EUQ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB807VWK

source_name: Homo sapiens IgD-negative memory B primary cell with multiple sclerosis

value: IgD-negative memory B cell

value: primary cell

value: ENCBS720RJK at ENCODE; https://www.encodeproject.org/ENCBS720RJK/


description:
∆gntR12 (100 mM gluconate) vs. WT (100 mM gluconate)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB003OTG)

description:
https://www.encodeproject.org/experiments/ENCSR709KME/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR709KME
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR390KLC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB003OTG

value: stimulated activated naive B cell

value: 40 year

value: male

value: adult

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 nephron (ENCLB964HYD)

description:
https://www.encodeproject.org/experiments/ENCSR866NTZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR866NTZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519LKT
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB964HYD
fragmentation methods: none

value: nephron

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS391CFV at ENCODE; https://www.encodeproject.org/ENCBS391CFV/

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


title: Histone ChIP-seq from right lobe of liver (ENCLB295SSM)

description:
https://www.encodeproject.org/experiments/ENCSR927CRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR927CRV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB295SSM
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: 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:
∆gntR12 (100 mM gluconate) vs. WT (100 mM gluconate)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_gntR12 harvested during exponential growth phase, CGXII gluconate, date of experiment:2007-03

value: wild type

value: WT harvested during exponential growth phase, CGXII gluconate, date of experiment:2007-03


description:
∆gntR2 (100 mM gluconate) vs. WT (100 mM gluconate)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆gntR2 (100 mM gluconate)

value: delta_gntR2 harvested during exponential growth phase, CGXII gluconate, date of experiment:2007-04

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


title: Histone ChIP-seq from right lobe of liver (ENCLB806MFJ)

description:
https://www.encodeproject.org/experiments/ENCSR927CRV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR927CRV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR309LQG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB806MFJ
size range: 200-600

value: female

value: adult

value: Bradley Bernstein, Broad


description:
∆gntR12 (4% glucose) vs. WT (4% glucose)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆gntR12 (4% glucose)

value: delta_gntR12 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-03

source_name: WT (4% glucose)

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB860HRZ)

description:
https://www.encodeproject.org/experiments/ENCSR245YME/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte.
experiment encode accession: ENCSR245YME
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR086KHK
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB860HRZ
fragmentation methods: none

source_name: Homo sapiens CD14-positive monocyte primary cell

value: CD14-positive monocyte

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS666ANY at ENCODE; https://www.encodeproject.org/ENCBS666ANY/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


description:
∆gntR2 (4% glucose) vs. WT (4% glucose) Operon-Oligo-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆gntR2 (4% glucose)

value: deletion mutant

value: delta_gntR2 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04

source_name: WT (4% glucose) Operon-Oligo

value: wild type

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


description:
∆gntR12 (4% glucose) vs. WT (4% glucose)-rep3
Biological replicate 3 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB628QMG)

description:
https://www.encodeproject.org/experiments/ENCSR331GZV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR331GZV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB628QMG

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB463ZRU)

description:
https://www.encodeproject.org/experiments/ENCSR245YME/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte.
experiment encode accession: ENCSR245YME
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR086KHK
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB463ZRU
fragmentation methods: none

value: CD14-positive monocyte

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from naive B cell (ENCLB029UZL)

description:
https://www.encodeproject.org/experiments/ENCSR272YVX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR272YVX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR707UVZ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB029UZL
fragmentation methods: none

value: naive B cell

value: multiple sclerosis

value: David Hafler

value: ENCBS049BNE at ENCODE; https://www.encodeproject.org/ENCBS049BNE/

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


description:
∆gntR2 (100 mM gluconate) vs. WT (100 mM gluconate)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant

value: delta_gntR2 harvested during exponential growth phase, CGXII gluconate, date of experiment:2007-04

source_name: WT (100 mM gluconate)

value: wild type

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


description:
∆gntR12 (4% glucose) vs. WT (4% glucose)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_gntR12 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-03

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


description:
∆gntR2 (4% glucose) vs. WT (4% glucose) Operon-Oligo-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: delta_gntR2 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04

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


title: Mint-ChIP-seq from HCT116 (ENCLB148CJA)

description:
https://www.encodeproject.org/experiments/ENCSR331DKH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR331DKH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB148CJA

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: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB753IIW)

description:
https://www.encodeproject.org/experiments/ENCSR182QBE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR182QBE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753IIW

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS929PLQ at ENCODE; https://www.encodeproject.org/ENCBS929PLQ/

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


title: Mint-ChIP-seq from HCT116 (ENCLB013FCN)

description:
https://www.encodeproject.org/experiments/ENCSR331GZV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR331GZV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR873HRN
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB013FCN

value: cell line

value: 48 year

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

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


title: Mint-ChIP-seq from naive B cell (ENCLB830COR)

description:
https://www.encodeproject.org/experiments/ENCSR617GMR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on naive B cell with multiple sclerosis.
experiment encode accession: ENCSR617GMR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR707UVZ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830COR

value: naive B cell

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

value: ENCBS049BNE at ENCODE; https://www.encodeproject.org/ENCBS049BNE/


title: Mint-ChIP-seq from naive B cell (ENCLB436YUC)

description:
https://www.encodeproject.org/experiments/ENCSR617GMR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on naive B cell with multiple sclerosis.
experiment encode accession: ENCSR617GMR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR707UVZ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB436YUC


title: WT pEKEx2-alpC vs. WT pEKEx2-rep1

description:
WT pEKEx2-alpC vs. WT pEKEx2-rep1
Biological replicate 1 of 4
original platform:
GPL15451

source_name: WT pEKEx2-alpC

value: wild type + overexpression

value: WT pEKEx2-alpC harvested during exponential growth phase,CGXII glucose, 0.5 mM IPTG, date of experiment:2011-07

source_name: WT pEKEx2

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase,CGXII glucose, 0.5 mM IPTG, date of experiment:2011-07


title: ∆CGP3 vs. WT-rep3

description:
∆CGP3 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_CGP3 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-01

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-01


title: ∆CGP3 vs. WT-rep2

description:
∆CGP3 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: WT pEKEx2-alpC vs. WT pEKEx2-rep3

description:
WT pEKEx2-alpC vs. WT pEKEx2-rep3
Biological replicate 3 of 4
original platform:
GPL15451


title: WT pEKEx2-alpC vs. WT pEKEx2-rep4

description:
WT pEKEx2-alpC vs. WT pEKEx2-rep4
Biological replicate 4 of 4
original platform:
GPL15451


title: ∆CGP3 vs. WT-rep1

description:
∆CGP3 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB923QWX)

description:
https://www.encodeproject.org/experiments/ENCSR331DKH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR331DKH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB923QWX

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB705WZE)

description:
https://www.encodeproject.org/experiments/ENCSR649FUX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on IgD-negative memory B cell with multiple sclerosis.
experiment encode accession: ENCSR649FUX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR808EUQ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705WZE

value: IgD-negative memory B cell

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

value: ENCBS720RJK at ENCODE; https://www.encodeproject.org/ENCBS720RJK/

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


title: Histone ChIP-seq from psoas muscle (ENCLB213RAG)

description:
https://www.encodeproject.org/experiments/ENCSR518TWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR518TWC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR456AMX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB213RAG
size range: 200-600

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

value: psoas muscle

value: tissue

value: 41 year

value: female

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

value: Shin Lin

value: ENCBS168AIQ at ENCODE; https://www.encodeproject.org/ENCBS168AIQ/

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB039AAS)

description:
https://www.encodeproject.org/experiments/ENCSR182QBE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR182QBE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039AAS

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: Bradley Bernstein, Broad

value: ENCBS929PLQ at ENCODE; https://www.encodeproject.org/ENCBS929PLQ/


title: Mint-ChIP-seq from HCT116 (ENCLB098SRK)

description:
https://www.encodeproject.org/experiments/ENCSR924JRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR924JRE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR846UXS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB098SRK

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

value: ENCBS720OOT at ENCODE; https://www.encodeproject.org/ENCBS720OOT/

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


title: WT pEKEx2-acn vs. WT pEKEx2-rep6

description:
WT pEKEx2-acn vs. WT pEKEx2-rep6
Biological replicate 6 of 6
GAL file:
CG_GAL_PCR_Layout_15.gal

source_name: WT pEKEx2-acn

value: wild type + overexpression

value: WT pEKEx2-acn harvested during exponential growth phase,CGXII glucose, 1 mM IPTG, date of experiment:2003-10

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase,CGXII glucose, 1 mM IPTG, date of experiment:2003-10


title: WT pEKEx2-acn vs. WT pEKEx2-rep5

description:
WT pEKEx2-acn vs. WT pEKEx2-rep5
Biological replicate 5 of 6
GAL file:
CG_GAL_PCR_Layout_15.gal


title: ∆alpC vs. WT-rep2

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

source_name: ∆alpC

value: deletion mutant

value: delta_alpC harvested during exponential growth phase, CGXII glucose, date of experiment:2010-07/2010-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2010-07/2010-10


title: ∆alpC vs. WT-rep1

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


title: ∆alpC vs. WT-rep3

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


title: WT pEKEx2-alpC vs. WT pEKEx2-rep2

description:
WT pEKEx2-alpC vs. WT pEKEx2-rep2
Biological replicate 2 of 4
original platform:
GPL15451

value: WT pEKEx2-alpC harvested during exponential growth phase,CGXII glucose, 0.5 mM IPTG, date of experiment:2011-07

value: WT pEKEx2 harvested during exponential growth phase,CGXII glucose, 0.5 mM IPTG, date of experiment:2011-07


title: Mint-ChIP-seq from HCT116 (ENCLB832WWO)

description:
https://www.encodeproject.org/experiments/ENCSR924JRE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR924JRE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR846UXS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB832WWO

value: cell line

value: 48 year

value: male

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from nephron (ENCLB688XQP)

description:
https://www.encodeproject.org/experiments/ENCSR153QIM/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR153QIM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB688XQP
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid originated from H9, preserved by cryopreservation

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS202RGJ at ENCODE; https://www.encodeproject.org/ENCBS202RGJ/

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


title: Mint-ChIP-seq from nephron (ENCLB659EHQ)

description:
https://www.encodeproject.org/experiments/ENCSR153QIM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR153QIM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB659EHQ
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) nephron organoid originated from H9, 21 days post differentiation

value: derived from H9 nephron progenitor cells (NPCs) harvested at day 21

value: ENCBS378CGA at ENCODE; https://www.encodeproject.org/ENCBS378CGA/


title: WT pEKEx2-acn vs. WT pEKEx2-rep2

description:
WT pEKEx2-acn vs. WT pEKEx2-rep2
Biological replicate 2 of 6
GAL file:
CG_GAL_PCR_Layout_15.gal

value: wild type + overexpression

value: WT pEKEx2-acn harvested during exponential growth phase,CGXII glucose, 1 mM IPTG, date of experiment:2003-10

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase,CGXII glucose, 1 mM IPTG, date of experiment:2003-10


title: Mint-ChIP-seq from nephron (ENCLB474TOG)

description:
https://www.encodeproject.org/experiments/ENCSR153QIM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR153QIM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB474TOG
fragmentation methods: none

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from psoas muscle (ENCLB425EBT)

description:
https://www.encodeproject.org/experiments/ENCSR518TWC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR518TWC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR456AMX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB425EBT
size range: 200-600

value: psoas muscle

value: tissue

value: 41 year

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

value: adult

value: Shin Lin

value: ENCBS168AIQ at ENCODE; https://www.encodeproject.org/ENCBS168AIQ/

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


title: WT pEKEx2-acn vs. WT pEKEx2-rep3

description:
WT pEKEx2-acn vs. WT pEKEx2-rep3
Biological replicate 3 of 6
GAL file:
CG_GAL_PCR_Layout_15.gal


title: WT pEKEx2-acn vs. WT pEKEx2-rep4

description:
WT pEKEx2-acn vs. WT pEKEx2-rep4
Biological replicate 4 of 6
GAL file:
CG_GAL_PCR_Layout_15.gal


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB350UYC)

description:
https://www.encodeproject.org/experiments/ENCSR111BQQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR111BQQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB350UYC

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

value: primary cell

value: 38 year

value: male

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from nephron (ENCLB999DNE)

description:
https://www.encodeproject.org/experiments/ENCSR153QIM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR153QIM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB999DNE
fragmentation methods: none

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS202RGJ at ENCODE; https://www.encodeproject.org/ENCBS202RGJ/

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


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB067LQM)

description:
https://www.encodeproject.org/experiments/ENCSR357TLJ/
***************
biological replicate number: 2
technical replicate number: 4
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR357TLJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB067LQM
fragmentation methods: none

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

value: nephron progenitor cell

value: in vitro differentiated cells

value: H9 NPC (Day 8):Nephron progenitor cells derived from H9 ES cells

value: Bradley Bernstein, Broad

value: ENCBS491YOI at ENCODE; https://www.encodeproject.org/ENCBS491YOI/


description:
∆acn (4% glucose, 100 mM glutamat, 35 µM FeSO4) vs. WT (4% glucose, 100 mM glutamat, 35 µM FeSO4)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_acn harvested during exponential growth phase, CGXII glucose, 100 mM glutamat, 35 µM FeSO4, date of experiment:2008-09

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 100 mM glutamat, 35 µM FeSO4, date of experiment:2008-09


description:
∆acn (4% glucose, 100 mM glutamat, 35 µM FeSO4) vs. WT (4% glucose, 100 mM glutamat, 35 µM FeSO4)-rep3
Biological replicate 3 of 3
original platform:
GPL15451


description:
∆acn (4% glucose, 100 mM glutamat, 35 µM FeSO4) vs. WT (4% glucose, 100 mM glutamat, 35 µM FeSO4)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: WT pEKEx2-acn vs. WT pEKEx2-rep1

description:
WT pEKEx2-acn vs. WT pEKEx2-rep1
Biological replicate 1 of 6
GAL file:
CG_GAL_PCR_Layout_15.gal

value: wild type + overexpression

value: WT pEKEx2-acn harvested during exponential growth phase,CGXII glucose, 1 mM IPTG, date of experiment:2003-10

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase,CGXII glucose, 1 mM IPTG, date of experiment:2003-10


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB068FLT)

description:
https://www.encodeproject.org/experiments/ENCSR357TLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR357TLJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB068FLT
fragmentation methods: none

value: female

value: healthy

value: embryonic

value: 5 day

value: ENCBS835ZTQ at ENCODE; https://www.encodeproject.org/ENCBS835ZTQ/


description:
∆pup pVEx1-10XHIS-TEV pup Ala mutant (BHI) vs. ∆pup pVEx1-10XHIS-TEV pup (BHI)-rep4
Biological replicate 4 of 4
original platform:
GPL16988

value: deletion mutant + overexpression

value: delta_pup pVEx1-10XHIS-TEV pup Ala mutant harvested during exponential growth phase, BHI, date of experiment:2012-10/2012-11

source_name: ∆pup pVEx1-10XHIS-TEV pup (BHI)

value: deletion mutant + control

value: delta_pup pVEx1 harvested during exponential growth phase, BHI, date of experiment:2012-10/2012-11


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB764KTL)

description:
https://www.encodeproject.org/experiments/ENCSR109NVM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR109NVM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB764KTL

source_name: Homo sapiens female adult (39 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: 39 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

value: ENCBS218KXX at ENCODE; https://www.encodeproject.org/ENCBS218KXX/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB460XKB)

description:
https://www.encodeproject.org/experiments/ENCSR357TLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR357TLJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460XKB
fragmentation methods: none

value: nephron progenitor cell

value: in vitro differentiated cells

value: H9 NPC (Day 8):Nephron progenitor cells derived from H9 ES cells

value: female

value: healthy

value: Joseph Bonventre

value: ENCBS491YOI at ENCODE; https://www.encodeproject.org/ENCBS491YOI/

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


description:
∆pup pVEx1-10XHIS-TEV pup Ala mutant (BHI) vs. ∆pup pVEx1-10XHIS-TEV pup (BHI)-rep3
Biological replicate 3 of 4
original platform:
GPL16988

value: deletion mutant + overexpression

value: delta_pup pVEx1-10XHIS-TEV pup Ala mutant harvested during exponential growth phase, BHI, date of experiment:2012-10/2012-11

value: deletion mutant + control

value: delta_pup pVEx1 harvested during exponential growth phase, BHI, date of experiment:2012-10/2012-11


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB267GRU)

description:
https://www.encodeproject.org/experiments/ENCSR109NVM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR109NVM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB267GRU

value: stimulated activated naive B cell

value: primary cell

value: 39 year

value: adult

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from HCT116 (ENCLB217ITJ)

description:
https://www.encodeproject.org/experiments/ENCSR329LNO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR329LNO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB217ITJ

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: Erez Aiden

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

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

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


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB527QAA)

description:
https://www.encodeproject.org/experiments/ENCSR357TLJ/
***************
biological replicate number: 2
technical replicate number: 3
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR357TLJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB527QAA
fragmentation methods: none

value: nephron progenitor cell

value: in vitro differentiated cells

value: H9 NPC (Day 8):Nephron progenitor cells derived from H9 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS491YOI at ENCODE; https://www.encodeproject.org/ENCBS491YOI/

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


description:
∆pup pVEx1-10XHIS-TEV pup Ala mutant (BHI) vs. ∆pup pVEx1-10XHIS-TEV pup (BHI)-rep1
Biological replicate 1 of 4
original platform:
GPL16988

value: deletion mutant + overexpression

value: delta_pup pVEx1-10XHIS-TEV pup Ala mutant harvested during exponential growth phase, BHI, date of experiment:2012-10/2012-11

value: deletion mutant + control

value: delta_pup pVEx1 harvested during exponential growth phase, BHI, date of experiment:2012-10/2012-11


title: Mint-ChIP-seq from HCT116 (ENCLB192BLH)

description:
https://www.encodeproject.org/experiments/ENCSR329LNO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR329LNO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB192BLH

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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


description:
∆pup pVEx1-10XHIS-TEV pup Ala mutant (BHI) vs. ∆pup pVEx1-10XHIS-TEV pup (BHI)-rep2
Biological replicate 2 of 4
original platform:
GPL16988


description:
∆pup (CGXII, 4% glucose, 1 µM FeSO4) vs. WT (CGXII, 4% glucose, 1 µM FeSO4)-rep2
Biological replicate 2 of 3
original platform:
GPL22792

source_name: ∆pup (CGXII, 4% glucose, 1 µM FeSO4)

value: deletion mutant

value: delta_pup harvested during exponential growth phase, CGXII glucose 1 µM FeSO4, date of experiment:2012-05/2012-06, GEO:GSE48038

source_name: WT (CGXII, 4% glucose, 1 µM FeSO4)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose 1 µM FeSO4, date of experiment:2012-05/2012-06, GEO:GSE48038


description:
∆pup (CGXII, 4% glucose, 1 µM FeSO4) vs. WT (CGXII, 4% glucose, 1 µM FeSO4)-rep1
Biological replicate 1 of 3
original platform:
GPL22792


description:
∆pup (CGXII, 4% glucose, 1 µM FeSO4) vs. WT (CGXII, 4% glucose, 1 µM FeSO4)-rep3
Biological replicate 3 of 3
original platform:
GPL22792


title: Mint-ChIP-seq from nephron progenitor cell (ENCLB394WTO)

description:
https://www.encodeproject.org/experiments/ENCSR357TLJ/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR357TLJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB394WTO
fragmentation methods: none

value: nephron progenitor cell

value: in vitro differentiated cells

value: H9 NPC (Day 8):Nephron progenitor cells derived from H9 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS491YOI at ENCODE; https://www.encodeproject.org/ENCBS491YOI/

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


description:
∆pup (CGXII, 4% glucose) vs. WT CGXII (CGXII, 4% glucose)-rep3
Biological replicate 3 of 3
original platform:
GPL16988

source_name: ∆pup (CGXII, 4% glucose)

value: delta_pup harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06, GEO:GSE48038

source_name: WT CGXII (CGXII, 4% glucose)

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-05/2012-06, GEO:GSE48038


description:
∆pup (CGXII, 4% glucose) vs. WT CGXII (CGXII, 4% glucose)-rep2
Biological replicate 2 of 3
original platform:
GPL16988


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB095LFO)

description:
https://www.encodeproject.org/experiments/ENCSR111BQQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR111BQQ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB095LFO

value: primary cell

value: 38 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


description:
∆pup (CGXII, 4% glucose) vs. WT CGXII (CGXII, 4% glucose)-rep1
Biological replicate 1 of 3
original platform:
GPL16988

value: deletion mutant

value: wild type


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB904BYQ)

description:
https://www.encodeproject.org/experiments/ENCSR328LCV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328LCV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB904BYQ

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

value: 48 year

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

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB176ONB)

description:
https://www.encodeproject.org/experiments/ENCSR141UTI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR141UTI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB176ONB
fragmentation methods: none

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

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: healthy

value: embryonic

value: 5 day

value: Kevin Eggan and Ralda Nehme

value: ENCBS167WAM at ENCODE; https://www.encodeproject.org/ENCBS167WAM/


title: ∆pup (BHI) vs. WT (BHI)-rep3

description:
∆pup (BHI) vs. WT (BHI)-rep3
Biological replicate 3 of 3
original platform:
GPL17304

source_name: ∆pup (BHI)

value: delta_pup harvested during exponential growth phase, BHI, date of experiment:2012-05/2012-06, GEO:GSE48038

source_name: WT (BHI)

value: WT harvested during exponential growth phase, BHI, date of experiment:2012-05/2012-06, GEO:GSE48038


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB406AYA)

description:
https://www.encodeproject.org/experiments/ENCSR328LCV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR328LCV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406AYA

value: primary cell

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos


title: Control ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB323MCT)

description:
https://www.encodeproject.org/experiments/ENCSR515GMO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR515GMO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB323MCT
size range: 200-600

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

value: 20 year

value: Charles Lee

value: ENCBS326GDW at ENCODE; https://www.encodeproject.org/ENCBS326GDW/

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB411OEH)

description:
https://www.encodeproject.org/experiments/ENCSR141UTI/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR141UTI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB411OEH
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: neural progenitor cell

value: in vitro differentiated cells

value: rapid NPCs, NGN2 +patterning; these are a form of neural progenitor cell -- see more here:https://docs.google.com/document/d/1VDqqe1h1WrG4kDADTFBROGCJrrNvYw5IHCNyMTYUASw/edit#heading=h.gjdgxs

value: female

value: ENCBS959UMI at ENCODE; https://www.encodeproject.org/ENCBS959UMI/

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