title: ∆ipsA vs. WT-rep1

description:
∆ipsA vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL16988

value: deletion mutant

value: delta_ipsA harvested during exponential growth phase, CGXII glucose, date of experiment:2012-09, GEO:GSE50210

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-09, GEO:GSE50210


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:
∆ramA (100 mM lactate) vs. ∆ramA (100 mM glucose)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

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: ∆ramA (100 mM lactate)

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

tag: condition

value: delta_ramA harvested during exponential growth phase, CGXII lactate,  date of experiment:2007-04/2007-05/2007-08/2007-08

source_name: ∆ramA (100 mM glucose)

value: delta_ramA harvested during exponential growth phase, CGXII glucose,  date of experiment:2007-04/2007-05/2007-08/2007-08


title: ∆cg2842 vs. WT-rep2

description:
∆cg2842 vs. WT-rep2
Biological replicate 2 of 4
original platform:
GPL15451

value: delta_cg2842 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-07/2009-08

source_name: WT

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-07/2009-08


title: Histone ChIP-seq from psoas muscle (ENCLB261HPX)

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR533LFC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR533LFC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR456AMX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB261HPX
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

value: psoas muscle

value: tissue

tag: biosample encode accession

tag: age

value: 41 year

tag: Sex

value: female

tag: health state

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

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Shin Lin

tag: link

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

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


title: Histone ChIP-seq from heart left ventricle (ENCLB239VHH)

description:
https://www.encodeproject.org/experiments/ENCSR718MZL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR718MZL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB239VHH
size range: 200-600

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

value: heart left ventricle

value: male

value: 55 year

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

value: ENCBS471DJO at ENCODE; https://www.encodeproject.org/ENCBS471DJO/

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


description:
∆cgtSR5 (20 µM CuSO4) vs. WT (20 µM CuSO4)-rep2
Biological replicate 2 of 5
original platform:
GPL15451

source_name: ∆cgtSR5 (20 µM CuSO4)

value: deletion mutant

value: delta_cgtSR5 harvested during exponential growth phase, CGXII glucose, date of experiment:2007-11/2008-01/2008-11

source_name: WT (20 µM CuSO4)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-11/2008-01/2008-11


title: ∆cg2842 vs. WT-rep1

description:
∆cg2842 vs. WT-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: delta_cg2842 harvested during exponential growth phase, CGXII glucose, date of experiment:2009-07/2009-08

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-07/2009-08


description:
∆cg2784 (w/o MnSO4) vs. WT (w/o MnSO4)-rep1
Biological replicate 1 of 2
original platform:
GPL22561

source_name: ∆cg2784 (w/o MnSO4)

value: delta_cg2784 harvested during exponential growth phase, CGXII glucose, w/o MnSO4, date of experiment:2014-08

source_name: WT (w/o MnSO4)

value: WT harvested during exponential growth phase, CGXII glucose, w/o MnSO4, date of experiment:2014-08


title: Histone ChIP-seq from heart left ventricle (ENCLB517BOS)

description:
https://www.encodeproject.org/experiments/ENCSR718MZL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718MZL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB517BOS
size range: 200-600

value: tissue

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin


title: ∆ctaD vs. WT-rep1

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

source_name: ∆ctaD

value: delta_ctaD harvested during exponential growth phase, CGXII glucose, date of experiment:2010-01

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2010-01


description:
∆cg2784 (w/o MnSO4) vs. WT (w/o MnSO4)-rep2
Biological replicate 2 of 2
original platform:
GPL22561


title: Histone ChIP-seq from middle frontal area 46 (ENCLB039ORF)

description:
https://www.encodeproject.org/experiments/ENCSR532EYS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years)
experiment encode accession: ENCSR532EYS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR772LYM
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039ORF
size range: 200-600

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

value: middle frontal area 46

value: 83 year

value: male

value: Rush University

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

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


title: Mint-ChIP-seq from HCT116 (ENCLB311HDV)

description:
https://www.encodeproject.org/experiments/ENCSR345VKK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR345VKK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB311HDV

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

tag: line

value: cell line

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

tag: treatments

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

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

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


title: ∆ctaD vs. WT-rep2

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

value: deletion mutant

value: wild type


title: Histone ChIP-seq from psoas muscle (ENCLB320AUU)

description:
https://www.encodeproject.org/experiments/ENCSR532BDE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR532BDE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR456AMX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB320AUU
size range: 200-600

value: psoas muscle

value: tissue

value: 41 year

value: female

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

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

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


description:
∆ramA (100 mM lactate) vs. ∆ramA (100 mM glucose)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_ramA harvested during exponential growth phase, CGXII lactate,  date of experiment:2007-04/2007-05/2007-08/2007-08

value: delta_ramA harvested during exponential growth phase, CGXII glucose,  date of experiment:2007-04/2007-05/2007-08/2007-08


title: Mint-ChIP-seq from HCT116 (ENCLB111VQZ)

description:
https://www.encodeproject.org/experiments/ENCSR718JUS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR718JUS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB111VQZ

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 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: ENCBS271TPC at ENCODE; https://www.encodeproject.org/ENCBS271TPC/


title: ∆cg2750 vs. WT-rep3

description:
∆cg2750 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL28615

value: deletion mutant

value: delta_cg2750 harvested during exponential growth phase, CGXII glucose, date of experiment:2018-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2018-10


description:
∆ramA (100 mM lactate) vs. ∆ramA (100 mM glucose)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB959MIA)

description:
https://www.encodeproject.org/experiments/ENCSR720WUX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR720WUX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB959MIA

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: female

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: Histone ChIP-seq from psoas muscle (ENCLB936VHU)

description:
https://www.encodeproject.org/experiments/ENCSR532BDE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR532BDE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR456AMX
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB936VHU
size range: 200-600

value: psoas muscle

value: tissue

value: 41 year

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: Histone ChIP-seq from middle frontal area 46 (ENCLB809YVC)

description:
https://www.encodeproject.org/experiments/ENCSR340OJR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR340OJR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR405NKC
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB809YVC
size range: 200-600

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

value: middle frontal area 46

value: 90 or above year

value: Rush University

value: ENCBS873GIH at ENCODE; https://www.encodeproject.org/ENCBS873GIH/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: ∆fasR vs. WT-rep3

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

source_name: ∆fasR

value: deletion mutant

value: delta_fasR harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-12

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-12


title: ∆cpdA pEKEx2 vs. WT pEKEx2-rep1

description:
∆cpdA pEKEx2 vs. WT pEKEx2-rep1
Biological replicate 1 of 3
original platform:
GPL22794

source_name: ∆cpdA pEKEx2

value: deletion mutant + control

value: delta_cpdA pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-08, GEO:GSE81004

source_name: WT pEKEx2

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-08, GEO:GSE81004


title: Mint-ChIP-seq from HCT116 (ENCLB197GXW)

description:
https://www.encodeproject.org/experiments/ENCSR718JUS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718JUS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197GXW

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;

value: ENCBS271TPC at ENCODE; https://www.encodeproject.org/ENCBS271TPC/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB660ECD)

description:
https://www.encodeproject.org/experiments/ENCSR340OJR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR340OJR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR405NKC
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB660ECD
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS873GIH at ENCODE; https://www.encodeproject.org/ENCBS873GIH/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: Mint-ChIP-seq from HCT116 (ENCLB476JXD)

description:
https://www.encodeproject.org/experiments/ENCSR345VKK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR345VKK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB476JXD

value: cell line

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


title: ∆cg2750 vs. WT-rep1

description:
∆cg2750 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL28615

value: deletion mutant

value: delta_cg2750 harvested during exponential growth phase, CGXII glucose, date of experiment:2018-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2018-10


title: Mint-ChIP-seq from HCT116 (ENCLB199GIB)

description:
https://www.encodeproject.org/experiments/ENCSR531DRL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR531DRL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB199GIB

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden


title: ∆cg2750 vs. WT-rep2

description:
∆cg2750 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL28615


title: Mint-ChIP-seq from HCT116 (ENCLB125VDN)

description:
https://www.encodeproject.org/experiments/ENCSR531DRL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR531DRL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB125VDN

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

value: ENCBS271TPC at ENCODE; https://www.encodeproject.org/ENCBS271TPC/

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


title: ∆fasR vs. WT-rep2

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

value: delta_fasR harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-12

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-12


title: ∆fasR vs. WT-rep1

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


description:
∆phoB ∆phoD ∆phoC (w/o phosphate) vs. ∆phoB ∆phoD ∆phoC-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆phoB ∆phoD ∆phoC (w/o phosphate)

value: delta_phoBDC harvested during exponential growth phase, CGXII glucose, w/o phosphate, date of experiment:2009-06

source_name: ∆phoB ∆phoD ∆phoC

value: delta_phoBDC harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06


title: Mint-ChIP-seq from memory B cell (ENCLB921JWM)

description:
https://www.encodeproject.org/experiments/ENCSR935SBZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR935SBZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB921JWM

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

value: memory B cell

value: primary cell

value: 40 year

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from memory B cell (ENCLB305DZI)

description:
https://www.encodeproject.org/experiments/ENCSR935SBZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR935SBZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305DZI

value: male


title: Mint-ChIP-seq from HCT116 (ENCLB157UQY)

description:
https://www.encodeproject.org/experiments/ENCSR338ZOL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR338ZOL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB157UQY

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

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

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


title: Mint-ChIP-seq from HCT116 (ENCLB915GVP)

description:
https://www.encodeproject.org/experiments/ENCSR338ZOL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338ZOL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB915GVP

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


description:
∆phoB ∆phoD ∆phoC (w/o phosphate) vs. ∆phoB ∆phoD ∆phoC-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_phoBDC harvested during exponential growth phase, CGXII glucose, w/o phosphate, date of experiment:2009-06

value: delta_phoBDC harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06


title: ∆cpdA pEKEx2 vs. WT pEKEx2-rep2

description:
∆cpdA pEKEx2 vs. WT pEKEx2-rep2
Biological replicate 2 of 3
original platform:
GPL22794

value: deletion mutant + control

value: delta_cpdA pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-08, GEO:GSE81004

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-08, GEO:GSE81004


description:
∆phoB ∆phoD ∆phoC (w/o phosphate) vs. WT (w/o phosphate)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: WT (w/o phosphate)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, w/o phosphate, date of experiment:2009-06


description:
∆phoB ∆phoD ∆phoC (w/o phosphate) vs. ∆phoB ∆phoD ∆phoC-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Histone ChIP-seq from middle frontal area 46 (ENCLB025TIF)

description:
https://www.encodeproject.org/experiments/ENCSR128SVE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR128SVE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR405NKC
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB025TIF
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS873GIH at ENCODE; https://www.encodeproject.org/ENCBS873GIH/

value: Derived from ENCODE donor ENCDO730UYW; https://www.encodeproject.org/ENCDO730UYW/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB961YUY)

description:
https://www.encodeproject.org/experiments/ENCSR128SVE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR128SVE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR405NKC
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB961YUY
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: TF ChIP-seq from ovary (ENCLB291MKS)

description:
https://www.encodeproject.org/experiments/ENCSR934GQS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR934GQS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB291MKS
size range: 200-600

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

value: CTCF

value: ovary

value: 41 year

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

value: Shin Lin

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

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


title: ∆ctiP vs. WT-rep2

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

source_name: ∆ctiP

value: deletion mutant

value: delta_ctiP harvested during exponential growth phase, CGXII glucose, date of experiment:2012-11, GEO:GSE117566

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-11, GEO:GSE117566


description:
∆phoB ∆phoD ∆phoC (w/o phosphate) vs. WT (w/o phosphate)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_phoBDC harvested during exponential growth phase, CGXII glucose, w/o phosphate, date of experiment:2009-06

value: WT harvested during exponential growth phase, CGXII glucose, w/o phosphate, date of experiment:2009-06


title: Histone ChIP-seq from upper lobe of right lung (ENCLB436GZX)

description:
https://www.encodeproject.org/experiments/ENCSR337LGY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR337LGY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR750BQT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB436GZX
size range: 200-600

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

value: upper lobe of right lung

value: tissue

value: 60 year

value: male

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

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

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


title: Histone ChIP-seq from upper lobe of right lung (ENCLB792QLV)

description:
https://www.encodeproject.org/experiments/ENCSR337LGY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR337LGY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR750BQT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB792QLV
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


description:
∆phoB ∆phoD ∆phoC (w/o phosphate) vs. WT (w/o phosphate)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: ∆surf1 vs. WT-rep4

description:
∆surf1 vs. WT-rep4
Biological replicate 4 of 4
original platform:
GPL22792

value: delta_surf1 harvested during exponential growth phase, CGXII glucose, date of experiment:2017-03, GEO:GSE123974

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2017-03, GEO:GSE123974


title: Mint-ChIP-seq from activated T-cell (ENCLB100REA)

description:
https://www.encodeproject.org/experiments/ENCSR128FZE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR128FZE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR798SDW
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB100REA

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

value: primary cell

value: 21 year

value: female

value: John Stamatoyannopoulos

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

value: ENCBS649QNF at ENCODE; https://www.encodeproject.org/ENCBS649QNF/

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


title: Mint-ChIP-seq from activated T-cell (ENCLB076KWB)

description:
https://www.encodeproject.org/experiments/ENCSR128FZE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR128FZE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR798SDW
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB076KWB


title: ∆ctiP vs. WT-rep1

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

value: deletion mutant

value: delta_ctiP harvested during exponential growth phase, CGXII glucose, date of experiment:2012-11, GEO:GSE117566

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-11, GEO:GSE117566


title: Control Mint-ChIP-seq from HCT116 (ENCLB548KSV)

description:
https://www.encodeproject.org/experiments/ENCSR933ZIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933ZIE
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB548KSV

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: Erez Aiden

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

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


title: TF ChIP-seq from ovary (ENCLB896PPZ)

description:
https://www.encodeproject.org/experiments/ENCSR934GQS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR934GQS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB896PPZ
size range: 200-600

value: CTCF

value: ovary

value: tissue

value: 41 year

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

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

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


title: Control Mint-ChIP-seq from HCT116 (ENCLB431JYR)

description:
https://www.encodeproject.org/experiments/ENCSR933ZIE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR933ZIE
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB431JYR

value: cell line


title: ∆surf1 vs. WT-rep1

description:
∆surf1 vs. WT-rep1
Biological replicate 1 of 4
original platform:
GPL22792

value: deletion mutant

value: delta_surf1 harvested during exponential growth phase, CGXII glucose, date of experiment:2017-03, GEO:GSE123974

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2017-03, GEO:GSE123974


title: ∆surf1 vs. WT-rep2

description:
∆surf1 vs. WT-rep2
Biological replicate 2 of 4
original platform:
GPL22792


title: Histone ChIP-seq from lower lobe of right lung (ENCLB152BLY)

description:
https://www.encodeproject.org/experiments/ENCSR933MQW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR933MQW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR454FJM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152BLY
size range: 200-600

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

value: lower lobe of right lung

value: 60 year

value: male

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

value: ENCBS706XDW at ENCODE; https://www.encodeproject.org/ENCBS706XDW/

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


title: ∆ctiP vs. WT-rep3

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

value: delta_ctiP harvested during exponential growth phase, CGXII glucose, date of experiment:2012-11, GEO:GSE117566

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-11, GEO:GSE117566


title: Histone ChIP-seq from lower lobe of right lung (ENCLB340JRX)

description:
https://www.encodeproject.org/experiments/ENCSR933MQW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933MQW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR454FJM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340JRX
size range: 200-600

value: tissue

value: adult

value: Bradley Bernstein, Broad


title: ∆qcrA vs. ∆tatAC-rep2

description:
∆qcrA vs. ∆tatAC-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆qcrA

value: delta_qcrA harvested during exponential growth phase, CGXII glucose, date of experiment:2010-08/2010-09

source_name: ∆tatAC

value: delta_tatAC harvested during exponential growth phase, CGXII glucose, date of experiment:2010-08/2010-09


title: Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB883UNO)

description:
https://www.encodeproject.org/experiments/ENCSR530FIT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR530FIT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR663BWX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883UNO

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

value: primary cell

value: 48 year

value: John Stamatoyannopoulos

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

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

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


title: Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB585HWN)

description:
https://www.encodeproject.org/experiments/ENCSR530FIT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR530FIT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR663BWX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585HWN

value: male


title: ∆qcrA vs. ∆tatAC-rep1

description:
∆qcrA vs. ∆tatAC-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant


title: CD8 T cells, CD4 T cell depleted [S10]

city: Hershey

first: Aron

last: Lukacher

state: PA

address: 500 University Dr.

department: Microbiology & Immunology

institute: Penn State College of Medicine

description: Db LT359+CD103− CD8 T cells from the brains of Mouse Polyomvirus-infected mice at 30 dpi were sorted to purity (enriched >94% based on post-sort analysis) using a BD FACSAria II (BD Biosciences, San Diego, CA).

library_source: transcriptomic

data_processing:
The STAR Aligner v2.5 (github.com/alexdobin/STAR) with two-pass method
Raw sequence reads were trimmed for adaptor sequence/read quality was checked with FastQC
Trimmed sequence reads  were aligned to mouse genome GRCm38.96.
The gene expression  profiles were quantified using Bioconductor R package of DESeq2 version 1.26 to get the reads per kilobase of transcript per million mapped reads (RPKM)
Assembly: mm10 (GRCm38.96)
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was extracted using Trizol reagent (Ambion Life Technologies, Austin, TX).
mRNA was obtained from total RNA after depletion of rRNA using RiboGone-Mammalian Kit (Takara Bio Inc., Liaoning, China) and then purified using the AMPure PCR Purification Kit (Beckman Coulter, Indianapolis, IN). cDNA libraries were subsequently prepared using the SMARTer Stranded RNA-seq Kit (Takara Bio Inc., Liaoning, China).

tag: tissue

value: Brain

tag: cell type

value: CD8 T cell

tag: treatment

value: 250 mg of monoclonal rat anti-CD4 (GK1.5) i.p. at 6, 8, 15, 22, and 29 dpi


title: CD8 T cells, CD4 T cell depleted [S11]


description:
∆hrrA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆hrrA (2.5 µM haemin)

value: delta_hrrA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006/08,GEO:GSE26122

source_name: WT (2.5 µM haemin)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006/08,GEO:GSE26122


title: Histone ChIP-seq from lower lobe of right lung (ENCLB711CFC)

description:
https://www.encodeproject.org/experiments/ENCSR930JRJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR930JRJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR454FJM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB711CFC
size range: 200-600

value: lower lobe of right lung

value: tissue

value: 60 year

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS706XDW at ENCODE; https://www.encodeproject.org/ENCBS706XDW/

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


description:
∆hrrA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


description:
∆hrrA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆hrrA (2.5 µM FeSO4)

value: delta_hrrA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2006-07/2006/08,GEO:GSE26122

source_name: WT (2.5 µM FeSO4)

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2006-07/2006/08,GEO:GSE26122


title: Histone ChIP-seq from lower lobe of right lung (ENCLB637IXI)

description:
https://www.encodeproject.org/experiments/ENCSR930JRJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR930JRJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR454FJM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB637IXI
size range: 200-600

value: male


title: TF ChIP-seq from middle frontal area 46 (ENCLB813GBZ)

description:
https://www.encodeproject.org/experiments/ENCSR715FHW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR715FHW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813GBZ
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: 90 or above year

value: female

value: Rush University

value: ENCBS965OCN at ENCODE; https://www.encodeproject.org/ENCBS965OCN/

value: Derived from ENCODE donor ENCDO470GFA; https://www.encodeproject.org/ENCDO470GFA/


title: ∆qcrA vs. ∆tatAC-rep3

description:
∆qcrA vs. ∆tatAC-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_qcrA harvested during exponential growth phase, CGXII glucose, date of experiment:2010-08/2010-09

value: delta_tatAC harvested during exponential growth phase, CGXII glucose, date of experiment:2010-08/2010-09


title: CD8 T cells, IL21-receptor knock-out [S9]

value: Brain

value: CD8 T cell

value: 250 mg of rat IgG i.p. at 6, 8, 15, 22, and 29 dpi


title: ∆cpdA pEKEx2 vs. WT pEKEx2-rep3

description:
∆cpdA pEKEx2 vs. WT pEKEx2-rep3
Biological replicate 3 of 3
original platform:
GPL22794

source_name: ∆cpdA pEKEx2

value: deletion mutant + control

value: delta_cpdA pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-08, GEO:GSE81004

source_name: WT pEKEx2

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-08, GEO:GSE81004


description:
∆hrrSA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep2
Biological replicate 2 of 2
GAL file:
CG_GAL_PCR_Layout_16.gal

source_name: ∆hrrSA (1 µM FeSO4)

value: delta_hrrA harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2006-07/2006/08

source_name: WT (1 µM FeSO4)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2006-07/2006/08


title: CD8 T cells, IL21-receptor knock-out [S8]


title: CD8 T cells, wild-type control [S6]


title: ∆surf1 vs. WT-rep3

description:
∆surf1 vs. WT-rep3
Biological replicate 3 of 4
original platform:
GPL22792

value: delta_surf1 harvested during exponential growth phase, CGXII glucose, date of experiment:2017-03, GEO:GSE123974

source_name: WT

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2017-03, GEO:GSE123974


title: TF ChIP-seq from middle frontal area 46 (ENCLB244QTO)

description:
https://www.encodeproject.org/experiments/ENCSR715FHW/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR715FHW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB244QTO
size range: 200-600

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

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: adult

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS454HCI at ENCODE; https://www.encodeproject.org/ENCBS454HCI/


description:
∆hrrA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_hrrA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2006-07/2006/08,GEO:GSE26122

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2006-07/2006/08,GEO:GSE26122


description:
∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin) Operon-Oligo-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆hrrSA (2.5 µM haemin)

value: delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2009-10/2009-12

source_name: WT (2.5 µM haemin) Operon-Oligo

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2009-10/2009-12


description:
∆hrrA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: wild type


description:
∆hrrA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: delta_hrrA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006/08,GEO:GSE26122

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006/08,GEO:GSE26122


title: TF ChIP-seq from middle frontal area 46 (ENCLB372PTZ)

description:
https://www.encodeproject.org/experiments/ENCSR715FHW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR715FHW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB372PTZ
size range: 200-600

value: CTCF

value: Derived from ENCODE donor ENCDO470GFA; https://www.encodeproject.org/ENCDO470GFA/


title: CD8 T cells, wild-type control [S4]

description: Db LT359+CD103− CD8 T cells from the brains of Mouse Polyomvirus-infected mice at 30 dpi were sorted to purity (enriched >94% based on post-sort analysis) using a BD FACSAria II (BD Biosciences, San Diego, CA).

value: Brain

value: CD8 T cell

value: 250 mg of rat IgG i.p. at 6, 8, 15, 22, and 29 dpi


description:
∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin) Operon-Oligo-rep1
Biological replicate 1 of 2
original platform:
GPL15451


title: TF ChIP-seq from middle frontal area 46 (ENCLB647NYM)

description:
https://www.encodeproject.org/experiments/ENCSR715FHW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR715FHW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB647NYM
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: adult

value: ENCBS965OCN at ENCODE; https://www.encodeproject.org/ENCBS965OCN/


description:
∆lldR (100 mM ribose) vs. WT (100 mM ribose)-rep2
Biological replicate 2 of 2
GAL file:
CG_GAL_PCR_Layout_05.gal

source_name: ∆lldR (100 mM ribose)

value: deletion mutant

value: delta_lldR harvested during exponential growth phase, CGXII ribose, date of experiment:2006-01

source_name: WT (100 mM ribose)

value: WT harvested during exponential growth phase, CGXII ribose, date of experiment:2006-01


description:
∆hrrSA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep1
Biological replicate 1 of 2
GAL file:
CG_GAL_PCR_Layout_16.gal

value: delta_hrrSA harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2006-07/2006/08

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 1 µM FeSO4, date of experiment:2006-07/2006/08


title: CD8 T cells, wild-type control [S1]


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB743ZGT)

description:
https://www.encodeproject.org/experiments/ENCSR526IXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR526IXP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB743ZGT

source_name: Homo sapiens male adult (33 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

value: primary cell

value: 33 year

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

value: ENCBS261THR at ENCODE; https://www.encodeproject.org/ENCBS261THR/

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


title: TF ChIP-seq from MEL (ENCLB408TOM)

description:
https://www.encodeproject.org/experiments/ENCSR867SDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: MEF2A ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR867SDZ
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB408TOM

source_name: Mus musculus strain MEL MEL immortalized cell line

value: MEL

value: cell line

tag: description

value: Leukemia (K562 analog)

value: unknown

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB560UTH)

description:
https://www.encodeproject.org/experiments/ENCSR125WND/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125WND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB560UTH

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

value: primary cell

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB008GPB)

description:
https://www.encodeproject.org/experiments/ENCSR526IXP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR526IXP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB008GPB

value: 33 year

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

value: ENCBS261THR at ENCODE; https://www.encodeproject.org/ENCBS261THR/

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


title: TF ChIP-seq from MEL (ENCLB180CJJ)

description:
https://www.encodeproject.org/experiments/ENCSR867SDZ/
***************
biological replicate number: 2
technical replicate number: 1
description: MEF2A ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR867SDZ
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB180CJJ

value: MEL

value: cell line

value: Leukemia (K562 analog)

value: unknown

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/


description:
∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin) PCR product-rep1
Biological replicate 1 of 2
GAL file:
CG_GAL_PCR_Layout_16.gal

tag: genotype

value: deletion mutant

value: delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006-08

source_name: WT (2.5 µM haemin) PCR product

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006-08


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB999HWG)

description:
https://www.encodeproject.org/experiments/ENCSR125WND/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR125WND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB999HWG

value: primary cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: ∆pcrCAB vs. WT-rep1

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

source_name: ∆pcrCAB

tag: condition

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

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


title: ∆pcrCAB vs. WT-rep3

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


description:
∆chrSA ∆hrrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep1
Biological replicate 1 of 4
original platform:
GPL16988

source_name: ∆chrSA ∆hrrSA (2.5 µM FeSO4)

value: delta_chrSA delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-08/2012-11

source_name: WT (2.5 µM FeSO4)

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-08/2012-11


description:
∆chrSA ∆hrrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep2
Biological replicate 2 of 4
original platform:
GPL16988


description:
∆chrSA ∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep4
Biological replicate 4 of 4
original platform:
GPL16988

source_name: ∆chrSA ∆hrrSA (2.5 µM haemin)

value: delta_chrSA delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-08/201211

source_name: WT (2.5 µM haemin)

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-08/201211


title: Mint-ChIP-seq from HCT116 (ENCLB327JIN)

description:
https://www.encodeproject.org/experiments/ENCSR930EMO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR930EMO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR933ZIE
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327JIN

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

tag: antibody

value: cell line

value: 48 year

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


title: TF ChIP-seq from ES-E14 (ENCLB248RKY)

description:
https://www.encodeproject.org/experiments/ENCSR604XDL/
***************
biological replicate number: 2
technical replicate number: 1
description: MAFK ChIP-seq mouse ES-E14 produced by the Snyder lab
experiment encode accession: ENCSR604XDL
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR000ADJ
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB248RKY

source_name: Mus musculus strain 129/Ola ES-E14 stem cell male embryo

value: MAFK

value: mouse embryonic stem cell line E14

tag: biosample encode accession

value: embryonic

value: male

value: unknown

value: Michael Snyder, Stanford

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


description:
∆chrSA ∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep3
Biological replicate 3 of 4
original platform:
GPL16988

value: deletion mutant

value: delta_chrSA delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-08/201211

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-08/201211


description:
∆lldR (100 mM ribose) vs. WT (100 mM ribose)-rep1
Biological replicate 1 of 2
GAL file:
CG_GAL_PCR_Layout_05.gal

value: delta_lldR harvested during exponential growth phase, CGXII ribose, date of experiment:2006-01

value: WT harvested during exponential growth phase, CGXII ribose, date of experiment:2006-01


title: Mint-ChIP-seq from HCT116 (ENCLB962LRI)

description:
https://www.encodeproject.org/experiments/ENCSR930EMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR930EMO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR933ZIE
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB962LRI

value: cell line

tag: age

value: 48 year

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


description:
∆chrSA ∆hrrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep4
Biological replicate 4 of 4
original platform:
GPL16988

value: delta_chrSA delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-08/2012-11

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-08/2012-11


title: ∆pcrCAB vs. WT-rep2

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

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

source_name: WT

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


title: Histone ChIP-seq from MEL (ENCLB357RVO)

description:
https://www.encodeproject.org/experiments/ENCSR972MRN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR972MRN
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB357RVO

value: MEL

value: Leukemia (K562 analog)

value: unknown

tag: Sex

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


description:
∆chrSA ∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep1
Biological replicate 1 of 4
original platform:
GPL16988

value: deletion mutant

value: delta_chrSA delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-08/201211

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-08/201211


description:
∆chrSA ∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep2
Biological replicate 2 of 4
original platform:
GPL16988


description:
∆chrSA ∆hrrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep3
Biological replicate 3 of 4
original platform:
GPL16988

value: delta_chrSA delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-08/2012-11


title: Histone ChIP-seq from MEL (ENCLB907BII)

description:
https://www.encodeproject.org/experiments/ENCSR972MRN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR972MRN
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB907BII

value: cell line

tag: health state


description:
∆chrSA (2.5 µM haemin) vs. ∆chrSA (2.5 µM FeSO4)-rep3
Biological replicate 3 of 4
original platform:
GPL15451

source_name: ∆chrSA (2.5 µM haemin)

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-01/2012-02

source_name: ∆chrSA (2.5 µM FeSO4)

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-01/2012-02


description:
∆chrSA (2.5 µM haemin) vs. ∆chrSA (2.5 µM FeSO4)-rep4
Biological replicate 4 of 4
original platform:
GPL15451


title: Mint-ChIP-seq from natural killer cell (ENCLB437TJE)

description:
https://www.encodeproject.org/experiments/ENCSR525MZF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR525MZF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB437TJE

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

value: natural killer cell

value: primary cell

value: 41 year

value: female

tag: dev stage

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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

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


description:
∆chrSA (2.5 µM haemin) vs. ∆chrSA (2.5 µM FeSO4)-rep2
Biological replicate 2 of 4
original platform:
GPL15451

value: deletion mutant


description:
∆hrrSA (2.5 µM haemin) vs. WT (2.5 µM haemin) PCR product-rep2
Biological replicate 2 of 2
GAL file:
CG_GAL_PCR_Layout_16.gal

source_name: ∆hrrSA (2.5 µM haemin)

value: delta_hrrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006-08

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2006-07/2006-08


description:
∆chrSA (2.5 µM haemin) vs. ∆chrSA (2.5 µM FeSO4)-rep1
Biological replicate 1 of 4
original platform:
GPL15451


description:
∆chrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-02, GEO:GSE37327

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-02, GEO:GSE37327


title: TF ChIP-seq from ES-E14 (ENCLB331WVQ)

description:
https://www.encodeproject.org/experiments/ENCSR604XDL/
***************
biological replicate number: 1
technical replicate number: 1
description: MAFK ChIP-seq mouse ES-E14 produced by the Snyder lab
experiment encode accession: ENCSR604XDL
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR000ADJ
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB331WVQ

value: MAFK

value: cell line

value: mouse embryonic stem cell line E14

value: embryonic

value: male

value: unknown

tag: lab

value: Michael Snyder, Stanford

value: ENCBS043ENC at ENCODE; https://www.encodeproject.org/ENCBS043ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: TF ChIP-seq from MEL (ENCLB877LGG)

description:
https://www.encodeproject.org/experiments/ENCSR135SWH/
***************
biological replicate number: 2
technical replicate number: 1
description: NRF1 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR135SWH
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB877LGG

value: MEL

value: Leukemia (K562 analog)

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


description:
∆chrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-02, GEO:GSE37327

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-02, GEO:GSE37327


title: Mint-ChIP-seq from natural killer cell (ENCLB585LBS)

description:
https://www.encodeproject.org/experiments/ENCSR525MZF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR525MZF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585LBS

value: natural killer cell

value: primary cell

value: 41 year

value: female

value: adult

value: Bradley Bernstein, Broad

tag: source

value: John Stamatoyannopoulos

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

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

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


description:
∆chrSA (5 µM haemin) vs. WT (5 µM haemin)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆chrSA (5 µM haemin)

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 5 µM haemin, date of experiment:2011-05/2011-07

source_name: WT (5 µM haemin)

value: WT harvested during exponential growth phase, CGXII glucose, 5 µM haemin, date of experiment:2011-05/2011-07


title: Mint-ChIP-seq from natural killer cell (ENCLB482EKV)

description:
https://www.encodeproject.org/experiments/ENCSR525MZF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR525MZF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB482EKV

tag: link


title: Erythroblastic island unsorted rep2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
The 10x Genomics libraries were aligned to the mouse genome (mm10), with unique molecular index (UMI) quantified gene counts obtained using the Cell Ranger workflow using the mm10-2.1.0 reference transcriptome.  scRNA-Seq samples (n=5) was sequenced to a depth of 48 to 274 million reads, with a range of 1,330-2,182 for sorted populations and 3,443-7,715 for unsorted populations called cell barcodes from each library, and 6,192-8,159 UMI per cell on average.  CITE-Seq samples (n=2) was sequenced to a depth of 368 to 385 million reads, with a range of 8,176-8,922 called cell barcodes from each library, and 9,327-9,719 UMI per cell on average.  Cell Ranger filtered cellular barcodes were jointly analyzed for A) scRNA-Seq (CD71+, CD11b+, F4/80+, unsorted) and B) CITE-Seq data in AltAnalyze and ICGS2 (Iterative Clustering and Guide-gene selection version 2) to produce normalized gene counts (counts per ten thousand (CPTT) UMIs) and cell populations (PMID: 32207533).  ICGS2 was run on GEX-only profiles following removal of ambient background associated RNAs with SoupX (contamination fraction 15%) (PMID: 33367645).  ICGS was performed using the software default options and Euclidean clustering, with no forced resolution parameter, in addition to a PageRank down-sampling threshold of 5,000 cells.  Cell population names were revised from the original ICGS2 predictions based on the literature (marker gene driven), with an emphasis on prior well-defined hematopoietic lineage notations (13).  The software cellHarmony was used to assign cell population labels for the separate validation unsorted sample using the centroid-based cell-alignment automated workflow (PMID: 31529053).  All scRNA-Seq samples were jointly projected into a common UMAP embedding using the python library scikit-learn to train and transform the ICGS2 marker genes data using PCA (top 50 components), as described for the umap_transform function in the R uwot package.  For the CITE-Seq data, a comprehensive differential expression and gene regulatory analysis was also performed in the software cellHarmony with cell-to-cluster assignments from the joint ICGS2 analysis of the Saline and Epo samples (option --referenceType None) and an empirical Bayes moderated t-test p<0.05, FDR adjusted and fold>1.2.  Marker gene expression UMAP and bar chart visualization were performed in AltAnalyze (PMID: 20513647).
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 sparse matrices and tab-delimited text files

source_name: Bone Marrow

extract_protocol:
cell isolation protocol: Mice were euthanized by CO2 inhalation and the tibiae, femurs, and pelvic bones were harvested from mice and flushed with a 25 G needle attached to a syringe containing IMDM with 5% FBS, 1 mM CaCl2, and 1 mM MgCl2 (“EBI buffer”).  The bone marrow suspension was gently pipetted with a 1 mL pipette to break up large pieces of tissue and the filtered through a 70 µm cell strainer.  This was layered onto a BSA density gradient composed of 5ml each of EBI buffer containing 3% BSA, 1.5% BSA, and no (0%) BSA, based on modification of a protocol previously described by the Chasis laboratory (16).  After 30 min, the 0% and 1.5% layer were removed and the bone marrow clusters in the 3% BSA layer were resuspended and the cell number and volume were estimated for use in the downstream applications. For IFC of EBIs, cell clusters in the 3% BSA layer were fixed by adding paraformaldehyde to a final concentration of 4% for 30min and washed with phosphate buffered saline (PBS).  Fixed EBI preparations were blocked with anti-FcR (BD Bioscience) for 20 min at room temperature (RT), washed, and, incubated with a cocktail of fluorescently conjugated antibodies including anti-F4/80-AF647 (BM8, Biolegend), anti-CD71-BV421 (RI7217, Biolegend), and CD11b-PE (M1/70, BD Pharmingen).  Samples were incubated at RT for 30min in the dark and then washed with FACS buffer.  For nuclear staining, Hoechst 34580 (Sigma) was added with the antibodies and samples were incubated for 1hr at 37°C.  Labeled cell clusters were analyzed on an ImageStreamX (ISX-100, Amnis/Luminex) using 40x magnification and analysis was performed in IDEAS analysis software (Amnis) as previously described (11). Morphology masks were created for all channels and used for the CD71 area versus CD11b area comparison. For flow cytometry and sorting of single cells, unfractionated cells and the 3% fraction were dispersed into single cells by washing with PBS and incubating with FACS+10mM EDTA for 15 minutes on ice.  Cells were filtered and stained in FACS buffer with appropriate antibodies for 30 minutes at room temperature unless otherwise specified. To evaluate erythroblasts, cells were stained with Fixable Viability Dye efllour780 (FVD780, eBioscience), CD45-APC (30-F11, BD Pharmingen), CD44-PerCP Cy5.5 (IM7, BD Pharmingen), Ter119-FITC (TER-119, Biolegend).  To evaluate granulocyte precursors, cells were stained with a biotinylated lineage panel including CD4 (RM4-5, Biolegend), CD8 (53-6.7, Biolegend), CD19 (6D5, Biolegend), B220 (RA3-6B2, BD Pharmingen), Sca1 (D7, Biolegend), and Ter119 (TER119, Biolegend) followed by staining with streptavidin conjugated AF700 (Invitrogen), Fixable Viability Dye eflour780 (eBioscience), cKit-APC (2B8, eBioscience), CD34-PE (RAM34, BD Pharmingen), CD16/32 FcγR-FITC (2.4G2, BD Pharmingen), and Ly6G-BV421 (1A8, Biolegend).  To increase the frequency of EBI macrophages in samples sent for CITE-seq while preventing any restrictions on the analyzed population based on immunophenotype or downregulation of epitopes, negative selection for EBI macrophages was performed using Magnetic Activated Cell Sorting (MACS).
Dispersed EBIs from WT bone marrow were divided and either subjected to FACS to sort CD71+, CD11b+, and F4/80+ populations or left unsorted prior to scRNA-seq.  These four populations were then diluted to 1,000 cells/mL and loaded in each lane of a Chromium Controller Instrument (10x Genomics).  The 10x Genomics single cell 3’ v2 assay protocol was followed.
The 10x Genomics Chromium 3’ v2 assay standard protocol was followed as previously described. For CITE-Seq, single cells after dispersion of EBI clusters obtained through negative selection to include and enrich for EBI macrophages were labeled with Total-Seq A Antibody Derived Tags (ADTs) according to manufacturer’s protocol (https://www.biolegend.com/en-us/protocols/totalseq-a-antibodies-and-cell-hashing-with-10x-single-cell-3-reagent-kit-v3-3-1-protocol).
Sequencing was performed on the Illumina HiSeq-4000 platform or Illumina NovaSeq.

treatment_protocol: Male or female wild-type (WT) C57BL/6J mice aged 3-6mo were used for all experiments unless otherwise specified.  Gfi1-/- and Gfi1+/- littermates were used at 8-9 weeks of age due to decreased survival of Gfi1-/- mice.  For Epo-induced stress erythropoiesis, WT mice were administered 1200 U/kg Epo diluted in saline, subcutaneously, once daily for 10 days.

value: Adult

value: erythroblastic islands

value: unsorted


description:
∆chrSA (5 µM haemin) vs. WT (5 µM haemin)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: wild type


title: Erythroblastic island unsorted rep1


title: Mint-ChIP-seq from HCT116 (ENCLB583BFT)

description:
https://www.encodeproject.org/experiments/ENCSR929ULO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR929ULO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR861TAI
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB583BFT

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

tag: line

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: ENCBS456IZA at ENCODE; https://www.encodeproject.org/ENCBS456IZA/

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


title: Mint-ChIP-seq from natural killer cell (ENCLB438FRJ)

description:
https://www.encodeproject.org/experiments/ENCSR525MZF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR525MZF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430XVL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB438FRJ

value: natural killer cell

value: primary cell

value: 41 year

value: female

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

tag: treatments

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

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


description:
∆chrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-02, GEO:GSE37327

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-02, GEO:GSE37327


title: Histone ChIP-seq from middle frontal area 46 (ENCLB284ELW)

description:
https://www.encodeproject.org/experiments/ENCSR532EYS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years)
experiment encode accession: ENCSR532EYS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR772LYM
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB284ELW
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 83 year

value: male

value: Rush University

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

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


description:
∆chrSA (5 µM haemin) vs. WT (5 µM haemin)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 5 µM haemin, date of experiment:2011-05/2011-07

value: WT harvested during exponential growth phase, CGXII glucose, 5 µM haemin, date of experiment:2011-05/2011-07


title: Erythroblastic island CD71+

value: Adult

tag: tissue

value: erythroblastic islands


title: Mint-ChIP-seq from HCT116 (ENCLB536EUS)

description:
https://www.encodeproject.org/experiments/ENCSR929ULO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR929ULO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR861TAI
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB536EUS

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

value: ENCBS456IZA at ENCODE; https://www.encodeproject.org/ENCBS456IZA/

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


description:
∆chrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-02, GEO:GSE37327

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-02, GEO:GSE37327


description:
∆clgR (10 µM CdS) vs. WT (10 µM CdS)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆clgR (10 µM CdS)

value: delta_clgR harvested during exponential growth phase, CGXII glucose, 10 µM cadmium, date of experiment:2009-11

source_name: WT (10 µM CdS)

value: WT harvested during exponential growth phase, CGXII glucose, 10 µM cadmium, date of experiment:2009-11


description:
∆clgR (10 µM CdS) vs. WT (10 µM CdS)-rep1
Biological replicate 1 of 2
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB262ZBC)

description:
https://www.encodeproject.org/experiments/ENCSR335LKT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR335LKT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB262ZBC

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

value: male

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


title: Erythroblastic island saline (ADT)

description:
CITE-Seq_clusters
ADT counts are available in theGSM5876275_Saline-BM.h5 file.

value: Adult

value: erythroblastic islands

value: saline


description:
∆chrSA (2.5 µM FeSO4) vs. WT (2.5 µM FeSO4)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-02, GEO:GSE37327

source_name: WT (2.5 µM FeSO4)

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM FeSO4, date of experiment:2012-02, GEO:GSE37327


title: TF ChIP-seq from MEL (ENCLB260TRK)

description:
https://www.encodeproject.org/experiments/ENCSR135SWH/
***************
biological replicate number: 1
technical replicate number: 1
description: NRF1 ChIP-seq mouse MEL produced by the Snyder lab
experiment encode accession: ENCSR135SWH
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR000ADN
encode release date: 2014-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB260TRK

source_name: Mus musculus strain MEL MEL immortalized cell line

value: MEL

value: cell line

value: Leukemia (K562 analog)

value: unknown

value: not collected

value: Bing Ren, UCSD

value: ENCBS049ENC at ENCODE; https://www.encodeproject.org/ENCBS049ENC/

value: Derived from ENCODE donor ENCDO073AAA; https://www.encodeproject.org/ENCDO073AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2111; http://web.expasy.org/cellosaurus/CVCL_2111

value: ENCODE dbxrefs MEL; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MEL


title: ∆clgR vs. WT Operon-Oligo-rep3

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

source_name: ∆clgR

value: deletion mutant

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

source_name: WT Operon-Oligo

value: wild type

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


title: ∆clgR vs. WT Operon-Oligo-rep2

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


description:
∆chrSA (2.5 µM haemin) vs. WT (2.5 µM haemin)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_chrSA harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-02, GEO:GSE37327

source_name: WT (2.5 µM haemin)

value: WT harvested during exponential growth phase, CGXII glucose, 2.5 µM haemin, date of experiment:2012-02, GEO:GSE37327


title: Histone ChIP-seq from middle frontal area 46 (ENCLB371DNM)

description:
https://www.encodeproject.org/experiments/ENCSR125KVG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR125KVG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB371DNM
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: adult

value: Bradley Bernstein, Broad

value: Rush University

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

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


title: Mint-ChIP-seq from HCT116 (ENCLB834VWE)

description:
https://www.encodeproject.org/experiments/ENCSR335LKT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR335LKT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB834VWE

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

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


title: ∆ctaD vs. WT-rep3

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

source_name: ∆ctaD

value: deletion mutant

value: delta_ctaD harvested during exponential growth phase, CGXII glucose, date of experiment:2010-01

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2010-01


title: ∆cg2151 vs. WT-rep3

description:
∆cg2151 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_cg2151 harvested during exponential growth phase, CGXII glucose, date of experiment:2011-11

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-11


title: ∆cg2151 vs. WT-rep2

description:
∆cg2151 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: ∆clgR vs. WT Operon-Oligo-rep1

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

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

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


title: Erythroblastic island F4/80+

value: Adult

value: erythroblastic islands


description:
∆recA (0.6 µM mitomycin C) vs. WT (0.6 µM mitomycin C)-rep3
Biological replicate 3 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 (ENCLB234ZHD)

description:
https://www.encodeproject.org/experiments/ENCSR122NDV/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB234ZHD

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

value: 50 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB738ZZI)

description:
https://www.encodeproject.org/experiments/ENCSR125KVG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125KVG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB738ZZI
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

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

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


title: Erythroblastic island erythropoietin stimulated (ADT)

description:
CITE-Seq_clusters
ADT counts are available in the GSM5876273_Epo-BM.h5 file.

source_name: Bone Marrow

value: Adult

value: erythroblastic islands

value: erythropoietin stimulated


title: Erythroblastic island saline

value: saline


title: Erythroblastic island CD11b+


description:
∆recA (0.6 µM mitomycin C) vs. WT (0.6 µM mitomycin C)-rep2
Biological replicate 2 of 3
original platform:
GPL22561

value: deletion mutant

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

value: wild type

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: matHG E11.5

city: Columbus

first: Madhumita

last: Basu

state: Ohio

address: 700 Children's Drive

department: Center for Cardiovascular Research

institute: Nationwide Children's Hospital

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

source_name: Mouse embryonic heart from diabetic 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

value: whole heart

tag: strain

value: wildtype

tag: disease status

value: Diabteic

tag: timepoint


title: ∆cg2151 vs. WT-rep1

description:
∆cg2151 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451

tag: genotype

value: delta_cg2151 harvested during exponential growth phase, CGXII glucose, date of experiment:2011-11

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-11


title: ∆recA vs. WT-rep3

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

source_name: ∆recA

tag: condition

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

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


title: Erythroblastic island erythropoietin stimulated


title: matHG E9.5

value: Diabetic


title: ∆recA vs. WT-rep1

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


title: Histone ChIP-seq from right lobe of liver (ENCLB459WXV)

description:
https://www.encodeproject.org/experiments/ENCSR119XNK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR119XNK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR683VJG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB459WXV
size range: 200-600

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

tag: antibody

value: right lobe of liver

value: tissue

value: 16 year

value: female

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

value: child

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS374JJR at ENCODE; https://www.encodeproject.org/ENCBS374JJR/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: Histone ChIP-seq from right lobe of liver (ENCLB137WNR)

description:
https://www.encodeproject.org/experiments/ENCSR119XNK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR119XNK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR683VJG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB137WNR
size range: 200-600

tag: biosample encode accession