title: Mint-ChIP-seq from nephron progenitor cell (ENCLB665RKU)

description:
https://www.encodeproject.org/experiments/ENCSR357TLJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron progenitor cell
experiment encode accession: ENCSR357TLJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR425YBK
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB665RKU
fragmentation methods: none

value: nephron progenitor cell

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

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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


title: Mint-ChIP-seq from neural progenitor cell (ENCLB259SPJ)

status: Public on Jul 22 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR141UTI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR141UTI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB259SPJ
fragmentation methods: none

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

value: neural progenitor cell

value: in vitro differentiated cells

tag: description

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

tag: biosample encode accession

tag: Sex

value: female

tag: health state

tag: dev stage

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kevin Eggan and Ralda Nehme

tag: link

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

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


title: ∆pup (BHI) vs. WT (BHI)-rep1

type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

description:
∆pup (BHI) vs. WT (BHI)-rep1
Biological replicate 1 of 3
original platform:
GPL17304

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: ∆pup (BHI)

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

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

tag: genotype

value: deletion mutant

tag: condition

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

source_name: WT (BHI)

value: wild type

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


description:
∆ndh ∆mdh spontaneous mutant (2% acetate) vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22792

value: delta_ndh delta_mdh (spontaneous mutation) harvested during exponential growth phase, CGXII acetate, date of experiment:2013-04

source_name: WT

value: WT harvested during exponential growth phase, CGXII acetate, date of experiment:2013-04


title: ∆pup (BHI) vs. WT (BHI)-rep2

description:
∆pup (BHI) vs. WT (BHI)-rep2
Biological replicate 2 of 3
original platform:
GPL17304


title: Control ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB550TTV)

description:
https://www.encodeproject.org/experiments/ENCSR515GMO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR515GMO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB550TTV
size range: 200-600

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

value: primary cell

value: 20 year

value: male

value: adult

value: Charles Lee

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

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


title: ∆ndh (4% lactate) vs. WT-rep2

description:
∆ndh (4% lactate) vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22792

source_name: ∆ndh (4% lactate)

value: delta_ndh harvested during exponential growth phase, CGXII lactate, date of experiment:2013-04

value: WT harvested during exponential growth phase, CGXII lactate, date of experiment:2013-04


description:
∆ndh ∆mdh spontaneous mutant (2% acetate) vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22792


title: ∆ndh (4% lactate) vs. WT-rep3

description:
∆ndh (4% lactate) vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22792


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB002YHF)

description:
https://www.encodeproject.org/experiments/ENCSR350UKV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR350UKV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR456XXL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB002YHF
fragmentation methods: none

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

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: Histone ChIP-seq from right lobe of liver (ENCLB602MKD)

description:
https://www.encodeproject.org/experiments/ENCSR511ICH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR511ICH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR886ATT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB602MKD
size range: 200-600

source_name: Homo sapiens female adult (47 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

value: 47 year

value: female

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

value: Shin Lin

value: ENCBS025MJZ at ENCODE; https://www.encodeproject.org/ENCBS025MJZ/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: Histone ChIP-seq from right lobe of liver (ENCLB644RWQ)

description:
https://www.encodeproject.org/experiments/ENCSR511ICH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR511ICH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR886ATT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB644RWQ
size range: 200-600

value: adult


title: ∆ndh (4% lactate) vs. WT-rep1

description:
∆ndh (4% lactate) vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22792

value: deletion mutant

value: delta_ndh harvested during exponential growth phase, CGXII lactate, date of experiment:2013-04

value: wild type

value: WT harvested during exponential growth phase, CGXII lactate, date of experiment:2013-04


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB630CML)

description:
https://www.encodeproject.org/experiments/ENCSR109HWF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR109HWF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB630CML

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

tag: treatments

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: ∆ndh (2% acetate) vs. WT-rep2

description:
∆ndh (2% acetate) vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22792

source_name: ∆ndh (2% acetate)

value: delta_ndh harvested during exponential growth phase, CGXII acetate, date of experiment:2013-04

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-06


title: ∆ndh (2% acetate) vs. WT-rep1

description:
∆ndh (2% acetate) vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22792

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-05


title: ∆ndh (4% glucose) vs. WT-rep2

description:
∆ndh (4% glucose) vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22792

source_name: ∆ndh (4% glucose)

value: delta_ndh harvested during exponential growth phase, CGXII glucose, date of experiment:2013-04

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-04


title: ∆ndh (4% glucose) vs. WT-rep1

description:
∆ndh (4% glucose) vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22792

value: deletion mutant


title: ∆ndh (4% glucose) vs. WT-rep3

description:
∆ndh (4% glucose) vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22792


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB633NGD)

description:
https://www.encodeproject.org/experiments/ENCSR538URI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR538URI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR808EUQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB633NGD

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

value: IgD-negative memory B cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB976UGD)

description:
https://www.encodeproject.org/experiments/ENCSR109HWF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR109HWF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB976UGD

value: primary cell

value: 33 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB525RJT)

description:
https://www.encodeproject.org/experiments/ENCSR538URI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human IgD-negative memory B cell
experiment encode accession: ENCSR538URI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR808EUQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB525RJT


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB022NWP)

description:
https://www.encodeproject.org/experiments/ENCSR510LOM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR510LOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR934ZBY
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB022NWP
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

value: CD4-positive, alpha-beta memory T cell

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

value: healthy

value: ENCBS668VBU at ENCODE; https://www.encodeproject.org/ENCBS668VBU/

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


title: ∆ndh (2% acetate) vs. WT-rep3

description:
∆ndh (2% acetate) vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22792

value: deletion mutant

value: delta_ndh harvested during exponential growth phase, CGXII acetate, date of experiment:2013-04

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2013-07


description:
∆ndh ∆mdh spontaneous mutant (2% acetate) vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22792

value: delta_ndh delta_mdh (spontaneous mutation) harvested during exponential growth phase, CGXII acetate, date of experiment:2013-04

value: WT harvested during exponential growth phase, CGXII acetate, date of experiment:2013-04


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB178JPQ)

description:
https://www.encodeproject.org/experiments/ENCSR350UKV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on CD4-positive, CD25-positive, alpha-beta regulatory T cell.
experiment encode accession: ENCSR350UKV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR456XXL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB178JPQ

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: Mint-ChIP-seq from HFFc6 (ENCLB256TAJ)

description:
https://www.encodeproject.org/experiments/ENCSR129TUY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR129TUY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB256TAJ
fragmentation methods: none

source_name: Homo sapiens HFFc6 cell line, preserved by cryopreservation

tag: line

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

tag: passage number

value: ENCBS794NUP at ENCODE; https://www.encodeproject.org/ENCBS794NUP/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


description:
WT pVWEx1-cg1633 (w/o MgSO4) vs. WT pVWEx1 (w/o MgSO4)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: WT pVWEx1-cg1633 (w/o MgSO4)

value: wild type + overexpression

value: WT pVWEx1-cg1633 harvested during exponential growth phase,CGXII glucose, w/o MgSO4, 1 mM IPTG, date of experiment:2007-09/2007-10

source_name: WT pVWEx1 (w/o MgSO4)

value: wild type + control

value: WT pVWEx1 harvested during exponential growth phase,CGXII glucose, w/o MgSO4, 1 mM IPTG, date of experiment:2007-09/2007-10


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB314TKF)

description:
https://www.encodeproject.org/experiments/ENCSR284IKS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR284IKS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR128KDZ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB314TKF
fragmentation methods: none

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

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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


title: Mint-ChIP-seq from HFFc6 (ENCLB206FSE)

description:
https://www.encodeproject.org/experiments/ENCSR129TUY/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR129TUY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB206FSE
fragmentation methods: none

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass


title: Mint-ChIP-seq from HFFc6 (ENCLB152XTI)

description:
https://www.encodeproject.org/experiments/ENCSR129TUY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR129TUY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152XTI
fragmentation methods: none

value: Job Dekker

value: ENCBS217PYK at ENCODE; https://www.encodeproject.org/ENCBS217PYK/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: Mint-ChIP-seq from natural killer cell (ENCLB504JMR)

description:
https://www.encodeproject.org/experiments/ENCSR326YSR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR326YSR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR294RLP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504JMR

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

value: natural killer cell

value: primary cell

value: 41 year

value: female

value: adult

value: John Stamatoyannopoulos

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

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


description:
∆cg1633 (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep2
Biological replicate 2 of 2
original platform:
GPL22561

source_name: ∆cg1633 (CGXII, 4% glucose)

value: deletion mutant

value: delta_cg1633 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-02

source_name: WT (CGXII, 4% glucose)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2015-02


description:
∆cg1633 (LB, 50 mM citrate) vs. WT (LB)-rep1
Biological replicate 1 of 2
GAL file:
CG_GAL_PCR_Layout_04.gal

source_name: ∆cg1633 (LB, 50 mM citrate)

value: delta_cg1633 harvested during exponential growth phase, LB 50 mM citrate, date of experiment:2004-11

source_name: WT (LB)

value: WT harvested during exponential growth phase, LB 50 mM citrate, date of experiment:2004-11


description:
WT pVWEx1-cg1633 (w/o MgSO4) vs. WT pVWEx1 (w/o MgSO4)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: wild type + overexpression

value: WT pVWEx1-cg1633 harvested during exponential growth phase,CGXII glucose, w/o MgSO4, 1 mM IPTG, date of experiment:2007-09/2007-10

value: wild type + control

value: WT pVWEx1 harvested during exponential growth phase,CGXII glucose, w/o MgSO4, 1 mM IPTG, date of experiment:2007-09/2007-10


title: Mint-ChIP-seq from natural killer cell (ENCLB831EWM)

description:
https://www.encodeproject.org/experiments/ENCSR326YSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR326YSR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR294RLP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB831EWM

value: natural killer cell

value: primary cell

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from HFFc6 (ENCLB105QQE)

description:
https://www.encodeproject.org/experiments/ENCSR129TUY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human HFFc6
experiment encode accession: ENCSR129TUY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR114FEG
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB105QQE
fragmentation methods: none

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: ENCBS217PYK at ENCODE; https://www.encodeproject.org/ENCBS217PYK/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


description:
WT pAN6-ftsR (50 µM IPTG) vs. WT pAN6 (50 µM IPTG)-rep1
Biological replicate 1 of 2
original platform:
GPL22561

source_name: WT pAN6-ftsR (50 µM IPTG)

value: wild type + overexpression

value: WT pAN6-ftsR harvested during exponential growth phase,CGXII glucose, 50 µM IPTG, date of experiment:2015-03

source_name: WT pAN6 (50 µM IPTG)

value: WT pAN6 harvested during exponential growth phase,CGXII glucose, 50 µM IPTG, date of experiment:2015-03


title: Mint-ChIP-seq from HCT116 (ENCLB476INN)

description:
https://www.encodeproject.org/experiments/ENCSR108CCH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR108CCH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR848XKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB476INN

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SMARCA5

value: 48 year

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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


description:
∆cg1633 (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep1
Biological replicate 1 of 2
original platform:
GPL22561

value: deletion mutant

value: delta_cg1633 harvested during exponential growth phase, CGXII glucose, date of experiment:2015-02

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2015-02


description:
WT pAN6-ftsR (10 µM IPTG) vs. WT pAN6 (10 µM IPTG)-rep2
Biological replicate 2 of 2
original platform:
GPL22561

source_name: WT pAN6-ftsR (10 µM IPTG)

value: WT pAN6-ftsR harvested during exponential growth phase,CGXII glucose, 10 µM IPTG, date of experiment:2015-03

source_name: WT pAN6 (10 µM IPTG)

value: wild type + control

value: WT pAN6 harvested during exponential growth phase,CGXII glucose, 10 µM IPTG, date of experiment:2015-03


title: Mint-ChIP-seq from HCT116 (ENCLB902EBZ)

description:
https://www.encodeproject.org/experiments/ENCSR108CCH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR108CCH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR848XKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB902EBZ

value: cell line

value: male

value: Bradley Bernstein, Broad


description:
WT pAN6-ftsR (10 µM IPTG) vs. WT pAN6 (10 µM IPTG)-rep1
Biological replicate 1 of 2
original platform:
GPL22561

value: wild type + overexpression


description:
MB001::PgntK-PftsZ ∆ftsR vs. MB001::PgntK-ftsZ-rep4
Biological replicate 4 of 4
original platform:
GPL22561

source_name: MB001::PgntK-PftsZ ∆ftsR

value: deletion mutant + promoter exchange

value: MB001::PgntK-PftsZ delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05

value: parent strain + promoter exchange

value: MB001::PgntK-PftsZ harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05


title: Mint-ChIP-seq from natural killer cell (ENCLB476YWC)

description:
https://www.encodeproject.org/experiments/ENCSR326JGI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR326JGI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR387IEL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB476YWC

source_name: Homo sapiens male adult (47 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 7...

value: natural killer cell

value: primary cell

value: 47 year

value: adult

value: John Stamatoyannopoulos

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

value: ENCBS177IBD at ENCODE; https://www.encodeproject.org/ENCBS177IBD/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB684CMP)

description:
https://www.encodeproject.org/experiments/ENCSR521SFR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR521SFR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR019FIH
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB684CMP
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NovaSeq 6000

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

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

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS229YZM at ENCODE; https://www.encodeproject.org/ENCBS229YZM/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


description:
MB001::PgntK-PftsZ ∆ftsR vs. MB001::PgntK-ftsZ-rep3
Biological replicate 3 of 4
original platform:
GPL22561

value: deletion mutant + promoter exchange

value: MB001::PgntK-PftsZ delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05

value: parent strain + promoter exchange

value: MB001::PgntK-PftsZ harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05


title: Mint-ChIP-seq from neural progenitor cell (ENCLB774XOK)

description:
https://www.encodeproject.org/experiments/ENCSR141UTI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived neural progenitor cell
experiment encode accession: ENCSR141UTI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR010GRX
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB774XOK
fragmentation methods: none

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

value: neural progenitor cell

value: in vitro differentiated cells

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

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Kevin Eggan and Ralda Nehme

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

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


title: Mint-ChIP-seq from brain (ENCLB875WXC)

description:
https://www.encodeproject.org/experiments/ENCSR708ZJU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR708ZJU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB875WXC
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) brain organoid, 90 days post differentiation

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS291HMT at ENCODE; https://www.encodeproject.org/ENCBS291HMT/

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


description:
∆cg1633 (LB, 50 mM citrate) vs. WT (LB)-rep2
Biological replicate 2 of 2
GAL file:
CG_GAL_PCR_Layout_04.gal

value: deletion mutant

value: delta_cg1633 harvested during exponential growth phase, LB 50 mM citrate, date of experiment:2004-11

value: wild type

value: WT harvested during exponential growth phase, LB 50 mM citrate, date of experiment:2004-11


title: Mint-ChIP-seq from brain (ENCLB455CCA)

description:
https://www.encodeproject.org/experiments/ENCSR708ZJU/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR708ZJU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB455CCA
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS377FQM at ENCODE; https://www.encodeproject.org/ENCBS377FQM/


title: Mint-ChIP-seq from HCT116 (ENCLB909JIO)

description:
https://www.encodeproject.org/experiments/ENCSR510LJL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR510LJL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR704TRV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB909JIO

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

value: cell line

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

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

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


description:
MB001::PgntK-PftsZ ∆ftsR vs. MB001::PgntK-ftsZ-rep2
Biological replicate 2 of 4
original platform:
GPL22561

value: deletion mutant + promoter exchange

value: MB001::PgntK-PftsZ delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05

value: parent strain + promoter exchange

value: MB001::PgntK-PftsZ harvested during exponential growth phase, CGXII glucose, date of experiment:2016-05


title: MB001 ∆ftsR vs. MB001-rep8

description:
MB001 ∆ftsR vs. MB001-rep8
Biological replicate 8 of 8
original platform:
GPL22561

source_name: MB001 ∆ftsR

value: MB001 delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02

value: parent strain

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02


description:
MB001::PgntK-PftsZ ∆ftsR vs. MB001::PgntK-ftsZ-rep1
Biological replicate 1 of 4
original platform:
GPL22561


title: Mint-ChIP-seq from brain (ENCLB526OBO)

description:
https://www.encodeproject.org/experiments/ENCSR708ZJU/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR708ZJU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB526OBO
fragmentation methods: none

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS524OMS at ENCODE; https://www.encodeproject.org/ENCBS524OMS/

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


description:
WT pAN6-ftsR (50 µM IPTG) vs. WT pAN6 (50 µM IPTG)-rep2
Biological replicate 2 of 2
original platform:
GPL22561

value: wild type + overexpression

value: WT pAN6-ftsR harvested during exponential growth phase,CGXII glucose, 50 µM IPTG, date of experiment:2015-03

value: wild type + control

value: WT pAN6 harvested during exponential growth phase,CGXII glucose, 50 µM IPTG, date of experiment:2015-03


title: MB001 ∆ftsR vs. MB001-rep6

description:
MB001 ∆ftsR vs. MB001-rep6
Biological replicate 6 of 8
original platform:
GPL22561

value: deletion mutant


title: MB001 ∆ftsR vs. MB001-rep5

description:
MB001 ∆ftsR vs. MB001-rep5
Biological replicate 5 of 8
original platform:
GPL22561

value: MB001 delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02


title: Mint-ChIP-seq from brain (ENCLB786TTG)

description:
https://www.encodeproject.org/experiments/ENCSR708ZJU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR708ZJU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB786TTG
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS291HMT at ENCODE; https://www.encodeproject.org/ENCBS291HMT/


title: MB001 ∆ftsR vs. MB001-rep3

description:
MB001 ∆ftsR vs. MB001-rep3
Biological replicate 3 of 8
original platform:
GPL22561

value: parent strain

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02


title: Histone ChIP-seq from heart left ventricle (ENCLB827WXP)

description:
https://www.encodeproject.org/experiments/ENCSR105VFR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on heart left ventricle tissue male adult (55 years).
experiment encode accession: ENCSR105VFR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB827WXP
size range: 200-600

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

value: heart left ventricle

value: tissue

value: 55 year

value: Shin Lin

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/


title: MB001 ∆ftsR vs. MB001-rep2

description:
MB001 ∆ftsR vs. MB001-rep2
Biological replicate 2 of 8
original platform:
GPL22561


title: Histone ChIP-seq from heart left ventricle (ENCLB202RXN)

description:
https://www.encodeproject.org/experiments/ENCSR105VFR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on heart left ventricle tissue male adult (55 years).
experiment encode accession: ENCSR105VFR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR979YKY
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB202RXN
size range: 200-600

value: male

value: adult


title: Mint-ChIP-seq from natural killer cell (ENCLB813QWF)

description:
https://www.encodeproject.org/experiments/ENCSR326JGI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR326JGI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR387IEL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813QWF

value: natural killer cell

value: primary cell

value: 47 year

value: John Stamatoyannopoulos

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

value: ENCBS177IBD at ENCODE; https://www.encodeproject.org/ENCBS177IBD/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: MB001 ∆ftsR vs. MB001-rep4

description:
MB001 ∆ftsR vs. MB001-rep4
Biological replicate 4 of 8
original platform:
GPL22561

value: deletion mutant

value: MB001 delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02

value: parent strain

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02


title: TF ChIP-seq from Calu3 (ENCLB483NAC)

description:
https://www.encodeproject.org/experiments/ENCSR921ERP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR921ERP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR871UJG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483NAC
size range: 200-600

source_name: Homo sapiens Calu3 cell line

value: CTCF

value: cell line

value: 25 year

value: Lung adenocarcinoma

value: Bradley Bernstein, Broad

value: Mats Ljungman

value: ENCBS990GIS at ENCODE; https://www.encodeproject.org/ENCBS990GIS/

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


title: Mint-ChIP-seq from HCT116 (ENCLB742QCZ)

description:
https://www.encodeproject.org/experiments/ENCSR510LJL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR510LJL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR704TRV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB742QCZ

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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


title: TF ChIP-seq from Calu3 (ENCLB214ERW)

description:
https://www.encodeproject.org/experiments/ENCSR921ERP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR921ERP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR871UJG
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB214ERW
size range: 200-600


title: Mint-ChIP-seq from brain (ENCLB123CRL)

description:
https://www.encodeproject.org/experiments/ENCSR708ZJU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR708ZJU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB123CRL
fragmentation methods: none

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: 53 year

value: Paola Arlotta

value: ENCBS377FQM at ENCODE; https://www.encodeproject.org/ENCBS377FQM/

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


title: MB001 ∆ftsR vs. MB001-rep7

description:
MB001 ∆ftsR vs. MB001-rep7
Biological replicate 7 of 8
original platform:
GPL22561

value: deletion mutant

value: MB001 delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02

value: parent strain

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02


title: Mint-ChIP-seq from HCT116 (ENCLB856JJN)

description:
https://www.encodeproject.org/experiments/ENCSR324ZNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR324ZNP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR071RJS
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB856JJN

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

value: cell line

value: 48 year

value: male

value: Bradley Bernstein, Broad

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


title: Mint-ChIP-seq from nephron (ENCLB726PPQ)

description:
https://www.encodeproject.org/experiments/ENCSR103RLW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR103RLW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726PPQ
fragmentation methods: none

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

value: nephron

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB750VAK)

description:
https://www.encodeproject.org/experiments/ENCSR509YOX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR509YOX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR570TYL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB750VAK
fragmentation methods: none

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

value: CD4-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: unknown

value: David Hafler

value: ENCBS300QBR at ENCODE; https://www.encodeproject.org/ENCBS300QBR/

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


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4))  vs. ∆odhI (70 mM gluc, 151 mM (NH4)2SO4), w/o urea)-rep3

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4))  vs. ∆odhI (70 mM glucose, 151 mM (NH4)2SO4), w/o urea)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-01/2007-02

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, date of experiment:2007-01/2007-02


title: Mint-ChIP-seq from HCT116 (ENCLB947IRT)

description:
https://www.encodeproject.org/experiments/ENCSR324ZNP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR324ZNP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR071RJS
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB947IRT

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


title: ∆ftsR vs. WT-rep1

description:
∆ftsR vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL22561

source_name: ∆ftsR

value: delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2014-04, GEO:GSE107921

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-04, GEO:GSE107921


title: Mint-ChIP-seq from nephron (ENCLB426LQY)

description:
https://www.encodeproject.org/experiments/ENCSR103RLW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR103RLW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB426LQY
fragmentation methods: none

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

value: nephron

value: organoid

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

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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

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


title: TF ChIP-seq from heart right ventricle (ENCLB572QDN)

description:
https://www.encodeproject.org/experiments/ENCSR105KGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105KGD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR597PTH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572QDN
size range: 200-600

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

value: CTCF

value: heart right ventricle

value: tissue

value: 55 year

value: male

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

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

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB705JCD)

description:
https://www.encodeproject.org/experiments/ENCSR509YOX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR509YOX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR570TYL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705JCD
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS300QBR at ENCODE; https://www.encodeproject.org/ENCBS300QBR/

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


title: Mint-ChIP-seq from brain (ENCLB645YWL)

description:
https://www.encodeproject.org/experiments/ENCSR708ZJU/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived brain organoid
experiment encode accession: ENCSR708ZJU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR141MUD
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB645YWL
fragmentation methods: none

value: brain

value: organoid

value: brain organoids created by Arlotta lab using new protocol to create more reliable organoids.

value: 53 year

value: Paola Arlotta

value: ENCBS524OMS at ENCODE; https://www.encodeproject.org/ENCBS524OMS/

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


description:
∆odhI (70 mM glutamine, w/o urea and (NH4)2SO4))  vs. ∆odhI (151 mM (NH4)2SO4), w/o urea)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

value: deletion mutant

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2006-09

source_name: ∆odhI (151 mM (NH4)2SO4), w/o urea)

value: wild type

value: WT harvested exponential growth phase, CGXII 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2006-09


title: TF ChIP-seq from heart right ventricle (ENCLB666MOZ)

description:
https://www.encodeproject.org/experiments/ENCSR105KGD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR105KGD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR597PTH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB666MOZ
size range: 200-600

value: CTCF

value: heart right ventricle

value: tissue

value: 55 year

value: male

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

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

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


title: Mint-ChIP-seq from nephron (ENCLB287NKW)

description:
https://www.encodeproject.org/experiments/ENCSR103RLW/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR103RLW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB287NKW
fragmentation methods: none

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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

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


title: ∆ftsR vs. WT-rep3

description:
∆ftsR vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL22561

value: deletion mutant

value: delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2014-04, GEO:GSE107921

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-04, GEO:GSE107921


description:
∆odhI (70 mM glutamine, w/o urea and (NH4)2SO4))  vs. ∆odhI (151 mM (NH4)2SO4), w/o urea)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2006-09

value: WT harvested exponential growth phase, CGXII 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2006-09


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4)  vs. WT (70 mM gluc, gln, w/o urea, (NH4)2SO4) -rep2

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4) PCR-product-rep2
Biological replicate 2 of 2
GAL file:
CG_GAL_PCR_Layout_05.gal

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2006-09

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2006-09


title: ∆odhI vs WT (70 mM gluc, gln,100 µM FeSO4, w/o urea, (NH4)2SO4)-rep2

description:
∆odhI (70 mM glucose, 70 mM glutamine,100 µM FeSO4, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine,100 µM FeSO4, w/o urea and (NH4)2SO4) PCR-product-rep2
Biological replicate 2 of 2
original platform:
GPL15451

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2006-10

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2006-10


title: Mint-ChIP-seq from nephron (ENCLB170EGU)

description:
https://www.encodeproject.org/experiments/ENCSR103RLW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived nephron organoid
experiment encode accession: ENCSR103RLW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR397RWM
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB170EGU
fragmentation methods: none

value: nephron

value: organoid

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

value: female

value: Bradley Bernstein, Broad

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


title: MB001 ∆ftsR vs. MB001-rep1

description:
MB001 ∆ftsR vs. MB001-rep1
Biological replicate 1 of 8
original platform:
GPL22561

value: MB001 delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02

value: parent strain

value: MB001 harvested during exponential growth phase, CGXII glucose, date of experiment:2016-10/2017-02


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4))  vs. ∆odhI (70 mM gluc, 151 mM (NH4)2SO4), w/o urea)-rep2

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4))  vs. ∆odhI (70 mM glucose, 151 mM (NH4)2SO4), w/o urea)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-01/2007-02

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, date of experiment:2007-01/2007-02


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4)  vs. WT (70 mM gluc, gln, w/o urea, (NH4)2SO4) -rep1

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4) PCR-product-rep1
Biological replicate 1 of 2
GAL file:
CG_GAL_PCR_Layout_05.gal

value: wild type


title: ∆odhI vs WT (70 mM gluc, gln, 100 µM FeSO4, w/o urea, (NH4)2SO4)-rep3

description:
∆odhI (70 mM glucose, 70 mM glutamine, 100 µM FeSO4, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, 100 µM FeSO4, w/o urea and (NH4)2SO4) Operon-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2007-01/2007-02

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2007-01/2007-02


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB405QRN)

description:
https://www.encodeproject.org/experiments/ENCSR920JVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR920JVT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB405QRN

source_name: Homo sapiens female adult (39 years) stimulated activated naive B primary cell treated with 1ug/mL anti-CD40 for 72 hours, 100 ng/mL Interleukin-4 for 72 hours, 10ug/mL anti-IgM for 72 hours

value: stimulated activated naive B cell

value: primary cell

value: 39 year

value: adult

value: 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: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4))  vs. ∆odhI (70 mM gluc, 151 mM (NH4)2SO4), w/o urea)-rep1

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4))  vs. ∆odhI (70 mM glucose, 151 mM (NH4)2SO4), w/o urea)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB262AFE)

description:
https://www.encodeproject.org/experiments/ENCSR905UNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR905UNZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB262AFE
fragmentation methods: none

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

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: ∆odhI vs WT (70 mM gluc, gln, 100 µM FeSO4, w/o urea, (NH4)2SO4)-rep2

description:
∆odhI (70 mM glucose, 70 mM glutamine, 100 µM FeSO4, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, 100 µM FeSO4, w/o urea and (NH4)2SO4) Operon-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2007-01/2007-02

value: wild type

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2007-01/2007-02


title: ∆ftsR vs. WT-rep2

description:
∆ftsR vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL22561

value: delta_ftsR harvested during exponential growth phase, CGXII glucose, date of experiment:2014-04, GEO:GSE107921

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2014-04, GEO:GSE107921


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4)  vs. WT (70 mM gluc, gln, w/o urea, (NH4)2SO4)-rep3

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4) Operon-oligo-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-02

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-02


title: ∆odhI vs WT (70 mM gluc, gln, 100 µM FeSO4, w/o urea, (NH4)2SO4)-rep1

description:
∆odhI (70 mM glucose, 70 mM glutamine, 100 µM FeSO4, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, 100 µM FeSO4, w/o urea and (NH4)2SO4) Operon-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB436VAR)

description:
https://www.encodeproject.org/experiments/ENCSR920JVT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR920JVT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB436VAR

value: stimulated activated naive B cell

value: primary cell

value: 39 year

value: female

value: adult

value: John Stamatoyannopoulos

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

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

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


title: TF ChIP-seq from activated B cell (ENCLB899IBW)

description:
https://www.encodeproject.org/experiments/ENCSR105HEC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR105HEC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR003FJP
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB899IBW
size range: 200-600

source_name: Homo sapiens male adult (22 years) activated B primary cell

value: CTCF

value: activated B cell

value: 22 year

value: male

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS458DQO at ENCODE; https://www.encodeproject.org/ENCBS458DQO/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB178IYW)

description:
https://www.encodeproject.org/experiments/ENCSR905UNZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR905UNZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR958CUX
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB178IYW
fragmentation methods: none

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: Mint-ChIP-seq from immature natural killer cell (ENCLB213HCY)

description:
https://www.encodeproject.org/experiments/ENCSR102BZX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human immature natural killer cell.
experiment encode accession: ENCSR102BZX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR050UUC
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB213HCY
fragmentation methods: none
instrument models: Illumina HiSeq 2500,Illumina NovaSeq 6000

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

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

value: healthy

value: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

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


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4)  vs. WT (70 mM gluc, gln, w/o urea, (NH4)2SO4)-rep2

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4) Operon-oligo-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-02

value: wild type

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-02


description:
∆atpBEFHAGDC (OD ca. 20) vs. WT (OD ca. 20)-rep4
Biological replicate 4 of 4
original platform:
GPL15451

source_name: ∆atpBEFHAGDC (OD ca. 20)

value: delta_atpBEFHAGCD harvested OD 20, CGXII glucose, date of experiment:2008-05

source_name: WT (OD ca. 20)

value: WT harvested OD 20, CGXII glucose, date of experiment:2008-05


title: TF ChIP-seq from activated B cell (ENCLB037BUC)

description:
https://www.encodeproject.org/experiments/ENCSR105HEC/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR105HEC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR003FJP
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB037BUC
size range: 200-600

value: CTCF

value: activated B cell

value: 22 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS458DQO at ENCODE; https://www.encodeproject.org/ENCBS458DQO/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: ∆odhI  vs WT (70 mM gluc, gln,100 µM FeSO4, w/o urea, (NH4)2SO4)-rep1

description:
∆odhI (70 mM glucose, 70 mM glutamine,100 µM FeSO4, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine,100 µM FeSO4, w/o urea and (NH4)2SO4) PCR-product-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2006-10

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, 100 µM FeSO4, date of experiment:2006-10


title: TF ChIP-seq from activated B cell (ENCLB803LHL)

description:
https://www.encodeproject.org/experiments/ENCSR105HEC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105HEC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR003FJP
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB803LHL
size range: 200-600

value: primary cell


description:
∆atpBEFHAGDC (OD ca. 20) vs. WT (OD ca. 20)-rep3
Biological replicate 3 of 4
original platform:
GPL15451

value: deletion mutant


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB446AAS)

description:
https://www.encodeproject.org/experiments/ENCSR065UTP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR065UTP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB446AAS
fragmentation methods: none

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

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/

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


description:
∆atpBEFHAGDC (OD ca. 20) vs. WT (OD ca. 20)-rep2
Biological replicate 2 of 4
original platform:
GPL15451

value: delta_atpBEFHAGCD harvested OD 20, CGXII glucose, date of experiment:2008-05

value: wild type

value: WT harvested OD 20, CGXII glucose, date of experiment:2008-05


title: Mint-ChIP-seq from HCT116 (ENCLB356CLU)

description:
https://www.encodeproject.org/experiments/ENCSR324QIZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR324QIZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR704TRV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB356CLU

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


description:
∆atpBEFHAGDC (OD ca. 20) vs. WT (OD ca. 20)-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: deletion mutant


title: ∆atpBEFHAGDC vs. WT-rep3

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

source_name: ∆atpBEFHAGDC

value: delta_atpBEFHAGCD harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-10

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-10


title: ∆atpBEFHAGDC vs. WT-rep1

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


title: Mint-ChIP-seq from HCT116 (ENCLB349DTF)

description:
https://www.encodeproject.org/experiments/ENCSR324QIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR324QIZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR704TRV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB349DTF


title: ∆atpBEFHAGDC vs. WT-rep2

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB705MNC)

description:
https://www.encodeproject.org/experiments/ENCSR041YWB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR041YWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR887UYJ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB705MNC
fragmentation methods: none

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: CD4+ memory cells from healthy donor

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS963BXF at ENCODE; https://www.encodeproject.org/ENCBS963BXF/

value: Derived from ENCODE donor ENCDO258PRN; https://www.encodeproject.org/ENCDO258PRN/


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB697ZEU)

description:
https://www.encodeproject.org/experiments/ENCSR041YWB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR041YWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR887UYJ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB697ZEU
fragmentation methods: none


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB465KFX)

description:
https://www.encodeproject.org/experiments/ENCSR707ZDY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR707ZDY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR995LKY
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB465KFX

source_name: Homo sapiens male adult (36 years) effector memory CD8-positive, alpha-beta T primary cell

value: 36 year

value: male

value: adult

value: John Stamatoyannopoulos

value: ENCBS527GUI at ENCODE; https://www.encodeproject.org/ENCBS527GUI/

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


title: Mint-ChIP-seq from brain (ENCLB968RVY)

description:
https://www.encodeproject.org/experiments/ENCSR041JSH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR041JSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB968RVY
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) brain organoid, 30 days post differentiation

value: brain

value: organoid

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS219JHY at ENCODE; https://www.encodeproject.org/ENCBS219JHY/

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


title: ∆atpBEF vs. WT-rep3

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

source_name: ∆atpBEF

value: deletion mutant

value: delta_atpBEF harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-10


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB856PLV)

description:
https://www.encodeproject.org/experiments/ENCSR707ZDY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR707ZDY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR995LKY
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB856PLV

value: primary cell

value: 36 year

value: male

value: adult


title: dis3l2_ctr_2_4_rM

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

library_source: transcriptomic

data_processing:
For PAIso-seq: Subreads were converted into circular consensus sequences (CCS) by number of passes ≥10. CCS-LIMA barcode detection process was run to mark the reads for the presence of barcodes. The IsoSeq Refine step was run to find full-length non-chimeric (FLNC) reads classified by (a) the presence of 5’ and 3’ primer sequences on ends, (b) the correct orientation of the 5’ and 3’ barcode sequences, (c) the presence of poly(A), (d) the chimeric sequences with barcode in the middle were removed. Fastq read and poly(A) length were processed (Liu et al. 2019). For mapping analysis, the sam files were processed using id_features_pandas.py file using Mus_musculus.GRCm38.102.gtf as the reference (details in mapping.ipynb). The 3’ unmapped region was extracted using get_sam_tails.py using all the sam files as the input. The length of the unmapped region of each transcript was recorded as cigar_S_len (details in get_sam_unmapped_tails.ipynb). The summarized information for all transcripts of all libraries is in the PAIsoSeq_Wu_2022.csv file. For all PAIso-seq analysis and figure preparation, codes are available at https://github.com/Di-aswater/public-dis3l2-analysis.
For RNA-seq: When processing sequencing data, original FASTQ files were mapped to mm10 using STAR (2.7.8a) (Dobin et al. 2013). BAM files were counted using HTSeq (0.11.4) (Anders et al. 2015). Differential analysis was performed using DESeq2 (Love et al. 2014). All the RNA-seq analysis codes are available at https://github.com/Di-aswater/public-dis3l2-analysis.
Assembly: mm10
Supplementary files format and content: All count.txt files contain the raw reads of each gene.
Supplementary files format and content: All report.csv files contain the information of each CCS read, including length, polyA, etc.
Supplementary files format and content: The PAIsoSeq_Wu_2022.csv matrix contains summarized information of all PAIso-seq results. Columns include CCS_ID, genotype, mouse ID, oocyte ID, gene ID, gene name, fastq sequence, polyA sequence, polyA length, tail sequence, tail length, uracil number and percent and transcript type

organism: Mus musculus

source_name: GV oocytes

extract_protocol:
For PAIso-seq, single oocytes were lysed in 11 microliters of newly prepared lysis buffer. The lysis buffer contained 0.5 microliter of SUPERase• In™ RNase Inhibitor (20 U/microliter) (ThermoFisher AM2696) and 10 microliters of 0.2% Triton X-100 in PBS. For regular single oocyte RNA-seq, in poly(A)-based RNA, the single oocyte was lysed in 2.5 microliters of RLT+; in ribominus RNA-seq, the single oocyte was lysed in the lysis buffer from the Ovation Solo kit.
For PAIso-seq: Oocyte lysate was heated at 80 °C for 5 min. 1 microliter of 1:10^5 diluted ERCC was added to each oocyte lysate. Each oocyte was barcoded at the end extension step with differently indexed dU-containing DNA templates. In each 12 microliter oocyte lysate, 1 microliter end extension oligo (50 micromolar) was added and reaction was incubated at 80 °C for 5 min, 37 °C for 10 min to anneal the end extension oligo to the poly(A) of RNA. After annealing, 1 microliter DTT (100 micromolar, SuperScript™ II Reverse Transcriptase kit, Thermo Fisher 18064014), 4 microliter of Superscript II first-strand buffer (5X), 1 microliter dNTP mix (Thermo Fisher 18427013), 0.5 microliter SUPERase• In™ RNase Inhibitor (20 U/microliter) (ThermoFisher AM2696), 1 microliter Klenow Fragment (3'→5' exo-) (NEB M0212S), 0.5 microliter nuclease-free water was added to each reaction. Oocyte lysates were incubated at 37 °C for 1 h and 80 °C for 10 min. 1 microliter USER enzyme (NEB M5505S) was added to each reaction and incubated at 37 °C for 30 min to digest the end-extension oligos. RNA from each reaction was purified using NucleoSpin RNA XS Micro kit (Takara 740902.50). Each sample was eluted using 15 microliter nuclease-free water.   7 microliter of the above purified end-extended RNA was used for reverse transcription and template switching. In each reaction, there was 7 microliter RNA, 0.4 microliter RT primer and 1 microliter dNTP. Reaction was incubated at 72 °C for 3 min and put on ice immediately. 1 microliter SuperScript II reverse transcriptase (200 U/microliter) (Thermo Fisher 18064014), 0.5 microliter RNase Inhibitor (ThermoFisher AM2696), 4 microliter Superscript II first-strand buffer (5X), 1 microliter DTT, 4 microliter Betaine (5M) (Sigma Aldrich B0300-1VL), 0.12 microliter MgCl2 (1M), 0.2 microliter template switch oligo, 0.78 microliter nuclease free water was added to each reaction. Reactions were incubated at 42 °C for 90 min, 10 cycles of 50 °C for 2 min followed by 42 °C for 2 min and 70 °C for 15 min. Reactions were then amplified by PCR for 26 cycles. In each PCR reaction, there were 20 microliter reverse transcription product, 25 microliter KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems KK2601), 5 microliter PCR primer. PCR reaction was purified using AMPure XP beads (Beckman Coulter A63881). cDNA samples were then processed at National Information Solutions Cooperative (NISC) for PacBio sequencing library preparation and PacBio sequencing. Samples were run on 2 SMRTCells and sequenced on the Sequel II (25 h collection time).
For poly(A) based RNA seq: Poly(A) RNA was enriched by oligo-dT beads and reverse transcribed. cDNA was amplified and purified for library construction using the Nextera XT kit. For ribominus RNA-seq, the library was constructed following the Ovation Solo Kit protocol

tag: tissue

value: GV oocytes

value: ctr


title: dis3l2_ctr_2_2_rM


title: dis3l2_ctr_2_3_rM


title: ∆odhI (70 mM gluc, gln, w/o urea, (NH4)2SO4)  vs. WT (70 mM gluc, gln, w/o urea, (NH4)2SO4)-rep1

description:
∆odhI (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4)  vs. WT (70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4) Operon-oligo-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: delta_odhI harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-02

value: WT harvested exponential growth phase, CGXII 70 mM glucose, 70 mM glutamine, w/o urea and (NH4)2SO4, date of experiment:2007-02


title: dis3l2_ctr_2_1_rM


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB345LTA)

description:
https://www.encodeproject.org/experiments/ENCSR065UTP/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR065UTP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB345LTA
fragmentation methods: none

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS370LJB at ENCODE; https://www.encodeproject.org/ENCBS370LJB/

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


title: ∆atpBEF vs. WT-rep1

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

value: deletion mutant

value: delta_atpBEF harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-10

source_name: WT

value: wild type


title: ∆atpBEF vs. WT-rep2

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

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-09/2007-10


title: Control ChIP-seq from middle frontal area 46 (ENCLB670ZBI)

description:
https://www.encodeproject.org/experiments/ENCSR105CRB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on middle frontal area 46 tissue male adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR105CRB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670ZBI
size range: 200-600

source_name: Homo sapiens male adult (90 or above years) with mild cognitive impairment; middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: male

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS049LCH at ENCODE; https://www.encodeproject.org/ENCBS049LCH/

value: Derived from ENCODE donor ENCDO877NVF; https://www.encodeproject.org/ENCDO877NVF/


title: Mint-ChIP-seq from brain (ENCLB759QOZ)

description:
https://www.encodeproject.org/experiments/ENCSR041JSH/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR041JSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB759QOZ
fragmentation methods: none

value: brain

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Paola Arlotta

value: ENCBS001KQF at ENCODE; https://www.encodeproject.org/ENCBS001KQF/

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


title: Control ChIP-seq from middle frontal area 46 (ENCLB541GYE)

description:
https://www.encodeproject.org/experiments/ENCSR105CRB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on middle frontal area 46 tissue male adult (90 or above years) with mild cognitive impairment.
experiment encode accession: ENCSR105CRB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-21
lab: Bradley Bernstein, Broad
library encode accession: ENCLB541GYE
size range: 200-600

value: middle frontal area 46

value: adult


title: dis3l2_ctr_1_4_rM

value: GV oocytes

value: ctr


title: Mint-ChIP-seq from brain (ENCLB818LKQ)

description:
https://www.encodeproject.org/experiments/ENCSR041JSH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR041JSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB818LKQ
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS219JHY at ENCODE; https://www.encodeproject.org/ENCBS219JHY/


title: dis3l2_ctr_1_2_rM


title: Mint-ChIP-seq from brain (ENCLB750DGP)

description:
https://www.encodeproject.org/experiments/ENCSR041JSH/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR041JSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB750DGP
fragmentation methods: none

value: ENCBS337FMJ at ENCODE; https://www.encodeproject.org/ENCBS337FMJ/


title: Control Mint-ChIP-seq from T-helper 17 cell (ENCLB606FFF)

description:
https://www.encodeproject.org/experiments/ENCSR104DYP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR104DYP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB606FFF

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

value: T-helper 17 cell

value: primary cell

value: 50 year

value: male

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from brain (ENCLB405UEW)

description:
https://www.encodeproject.org/experiments/ENCSR041JSH/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR041JSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB405UEW
fragmentation methods: none

value: brain

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Paola Arlotta


title: WT pAN6-rosR vs. WT pAN6-rep1

description:
WT pAN6-rosR vs. WT pAN6-rep1
Biological replicate 1 of 3
original platform:
GPL15451

source_name: WT pAN6-rosR

value: WT + overexpression

value: WT pAN6-rosR harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-04

source_name: WT pAN6

value: wild type + control

value: WT pAN6 harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-04


title: WT pAN6-rosR vs. WT pAN6-rep3

description:
WT pAN6-rosR vs. WT pAN6-rep3
Biological replicate 3 of 3
original platform:
GPL15451


title: dis3l2_ctr_1_1_rM

value: GV oocytes

value: ctr


title: WT pAN6-rosR vs. WT pAN6-rep2

description:
WT pAN6-rosR vs. WT pAN6-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: ∆rosR (anaerob) vs. WT (anaerob)-rep3

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

source_name: ∆rosR (anaerob)

value: deletion mutant

value: delta_rosR harvested during exponential growth phase, CGXII glucose, anaerobic cultivation, date of experiment:2007-08/2007-09

source_name: WT (anaerob)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, anaerobic cultivation, date of experiment:2007-08/2007-09


title: Mint-ChIP-seq from HCT116 (ENCLB694BND)

description:
https://www.encodeproject.org/experiments/ENCSR919YMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR919YMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB694BND

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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


title: ∆rosR (anaerob) vs. WT (anaerob)-rep2

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


title: Mint-ChIP-seq from HCT116 (ENCLB009JHK)

description:
https://www.encodeproject.org/experiments/ENCSR919YMZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR919YMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB009JHK


title: dis3l2_cKO_2_4_rM

value: cKO


title: Mint-ChIP-seq from H9 (ENCLB425AIB)

description:
https://www.encodeproject.org/experiments/ENCSR016RFN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR016RFN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB425AIB
fragmentation methods: none

source_name: Homo sapiens H9 cell line

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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

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


title: Histone ChIP-seq from ovary (ENCLB209UQZ)

description:
https://www.encodeproject.org/experiments/ENCSR509SNH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR509SNH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB209UQZ
size range: 200-600

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

value: ovary

value: tissue

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: Mint-ChIP-seq from H9 (ENCLB943ZUJ)

description:
https://www.encodeproject.org/experiments/ENCSR016RFN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR016RFN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB943ZUJ
fragmentation methods: none

value: cell line

value: Bradley Bernstein, Broad

value: ENCBS877WZR at ENCODE; https://www.encodeproject.org/ENCBS877WZR/


title: Mint-ChIP-seq from brain (ENCLB816ZQC)

description:
https://www.encodeproject.org/experiments/ENCSR041JSH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR041JSH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB816ZQC
fragmentation methods: none

value: brain

value: organoid

value: female

value: Paola Arlotta

value: ENCBS337FMJ at ENCODE; https://www.encodeproject.org/ENCBS337FMJ/


title: dis3l2_ctr_1_3_rM

value: GV oocytes

value: ctr


title: dis3l2_cKO_2_2_rM

value: cKO


title: Mint-ChIP-seq from H9 (ENCLB000VWI)

description:
https://www.encodeproject.org/experiments/ENCSR016RFN/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR016RFN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB000VWI
fragmentation methods: none

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

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

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


title: dis3l2_cKO_2_1_rM


title: ∆rosR (anaerob) vs. WT (anaerob)-rep1

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

value: deletion mutant

value: delta_rosR harvested during exponential growth phase, CGXII glucose, anaerobic cultivation, date of experiment:2007-08/2007-09

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, anaerobic cultivation, date of experiment:2007-08/2007-09


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

source_name: ∆rosR (CGXII, 4% glucose)

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

source_name: WT (CGXII, 4% glucose)

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