title: fb_C4


title: Emerged haustoria-small RNAs bioreplicate 1

status: Public on Jul 22 2022

type: SRA

city: Uppsala

first: German

last: Martinez

state: Uppsala

address: Almas Allé 8

department: Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences

library_source: transcriptomic

data_processing:
sRNA libraries were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore)
Reads were aligned using bowtie (Langmead, et al. 2009) with the command “–v2” that allows two mismatches. The r0.32 version of the C. campestris genome (Vogel et al., 2018) and the miRbase version 21 (https://www.mirbase.org/) were used in this analysis. TE annotation for the r0.32 version of the C. campestris genome was retrieved from e!DAL (https://edal.ipk-gatersleben.de/)
Conserved miRNAs were identified using miRProf with only genome-matching sRNAs. New miRNAs were identified using miRCat and only considering new miRNAs with the following characteristics: 21-22 nt in length, detection of miRNA* complement, at least 10 reads in total and identification in multiple bioreplicates.
miRNA accumulation raw and normalized (in reads per million) values are shown in the miRNA_accumulation_values tabular file.
Genome_build: Cuscuta campestris r0.32; FASTA file with miRNA transcript sequences is available on the series record.

molecule: total RNA

organism: Cuscuta campestris

source_name: Emerged haustoria

growth_protocol: Seeds from C. campestris were harvested from a culture of the parasite that was grown in a glasshouse at the phytotron of the University of Tromsø, Norway, in 24 h of light at 21 °C on Pelargonium zonale L. as host. To increase germination percentage, the seeds were scarified with concentrated sulfuric acid (96% v/v) for 20 minutes before being rinsed with water and placed on moist sterile filter paper. Young seedlings were harvested when they were 3 to 6 cm long. For the non-infective parts of mature C. campestris vines, the top 3 cm measured from the growing tip were harvested directly from the C. campestris culture on P. zonale. Shoot segments with developing haustoria (prehaustorial stage and emerged haustoria, respectively) were harvested after induction by far-red light and a tactile stimulus as described by Olsen et al. (2016)

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life Technologies, Carlsbad, CA, USA). Small RNAs were gel purified in a 15% acrylamide/8M urea gel. Purified sRNAs were used as input to generate sRNA libraries using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) following the manufacturer instructions. This procedure is identical to the one described in Martinez et al. (2016). PARE libraries were constructed following the protocol described in Zhai et al. (2014).
sRNA libraries were generated using the standard NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) protocol. PARE libraries were constructed following the protocol described in Zhai et al. (2014) which, briefly, is based on the enrichment of 5'P-mRNA molecules that are ligated to an RNA adapter. After reverse transcription the adapter is used to generate 20 nt fragments using a restriction enzyme. These fragments are then ligated again to adapters that are compatible with standard sRNA Illumina primers and indexes.

tag: tissue

value: Emerged haustoria

tag: sample type

value: small RNA

tag: molecule subtype


title: fb_HD5

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

institute: Lund University

data_processing:
Mapping - RNAseq (STAR aligner (2.6.0))
Bam to bigwig - RNAseq (bamCompare; deeptools)
Quantification of reads mapping to genes - RNAseq (featureCounts from Subread (1.6.3))
Genome_build: GRCh38 v30
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: featureCounts

organism: Homo sapiens

growth_protocol: All cell culture work on fibroblasts cells and direct neuronal conversion was perfomed as described before (Drouin-Ouellet J, Lau S, Brattås PL, Rylander Ottosson D, Pircs K, Grassi DA, et al. REST suppression mediates neural conversion of adult human fibroblasts via microRNA-dependent and -independent pathways. EMBO Mol Med. 2017;9(8):1117-31.)

extract_protocol:
Total RNA was extracted from 10,000 cells/ sample with RNeasy micro kit (Qiagen) according to manufacturer’s protocol
cDNA was synthesized with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara/Clontech) and assessed with the Bioanalyzer high sensitivity DNA kit, followed by library preparation using Nextera XT (Illumina). The quality and concentration of the libraries was assessed with the Bioanalyzer high sensitivity DNA kit and Qubit dsDNA BR DNA assay kit, respectively.

treatment_protocol: 10,000 induced neurons were FACS sorted based on NCAM+ staining after 28 days as described before (Shrigley S, Pircs K, Barker RA, Parmar M, Drouin-Ouellet J. Simple Generation of a High Yield Culture of Induced Neurons from Human Adult Skin Fibroblasts. J Vis Exp. 2018(132).)

tag: cell type

value: Fibroblasts

tag: condition

value: Huntington


title: Prehaustoria-small RNAs bioreplicate 3

source_name: Prehaustoria

value: Prehaustoria


title: fb_C1

value: Control


title: Mint-ChIP-seq from HCT116 (ENCLB777SHR)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR743HTN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR743HTN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB777SHR

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: age

value: 48 year

tag: Sex

value: male

tag: health state

value: colorectal carcinoma

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Erez Aiden

tag: treatments

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

tag: link

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

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


title: Mint-ChIP-seq from dendritic cell (ENCLB358TMH)

description:
https://www.encodeproject.org/experiments/ENCSR753RMT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR753RMT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB358TMH

source_name: Homo sapiens male adult (51 years) dendritic primary cell

value: dendritic cell

value: primary cell

value: 51 year

value: Charles Lee

value: ENCBS682CBV at ENCODE; https://www.encodeproject.org/ENCBS682CBV/

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


title: ChrS-Ala245fs_vs_WT_2

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

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 16 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 7 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 7). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7).

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

organism: Corynebacterium glutamicum

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: pre-culture 1: in reaction tubes, 5 ml BHI, triplicates (3x WT, 3x ChrS-Ala245fs mutant), inoculated from a fresh agar plate, 30 C, 170 rpm, ~ 8 h; pre-culture 2: in 100 ml flasks, 2 ml of pre-culture 1 was transferred to 20 ml CGXII + 2% glucose + PCA + trace elements without any iron, 30 C, 120 rpm, over night;  main culture: 500 ml flasks, cells were pelleted so that they were inoculated at an OD of 1 in 50 ml CGXII + 2% glucose + PCA + trace elements without iron + 4 µM hemin;

extract_protocol: Harvesting: after 6 h of cultivation, mutant strains reached ~ OD 5 and WT ~ OD 2.5 were harvested in 25 ml ice falcons for later RNA Isolation. The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

treatment_protocol: see growth protocol

tag: genotype

value: WT


title: fb_C6

value: Fibroblasts

value: Control


title: in_C1

value: Induced neurons


title: Prehaustoria-PARE/Degradome bioreplicate 2

data_processing:
Library strategy: Degradome-seq
sRNA libraries were trimmed using Trim Galore (https://github.com/FelixKrueger/TrimGalore)
Reads were aligned using bowtie (Langmead, et al. 2009) with the command “–v2” that allows two mismatches. The r0.32 version of the C. campestris genome (Vogel et al., 2018) and the miRbase version 21 (https://www.mirbase.org/) were used in this analysis. TE annotation for the r0.32 version of the C. campestris genome was retrieved from e!DAL (https://edal.ipk-gatersleben.de/)
Conserved miRNAs were identified using miRProf with only genome-matching sRNAs. New miRNAs were identified using miRCat and only considering new miRNAs with the following characteristics: 21-22 nt in length, detection of miRNA* complement, at least 10 reads in total and identification in multiple bioreplicates.
miRNA accumulation raw and normalized (in reads per million) values are shown in the miRNA_accumulation_values tabular file.
Genome_build: Cuscuta campestris r0.32; FASTA file with miRNA transcript sequences is available on the series record.

tag: tissue

value: Prehaustoria

value: Degradome

value: 5'P RNA


title: Stem-small_RNAs_bioreplicate 1

source_name: Stem

value: Stem

tag: sample type

value: small RNA


title: fb_C3


title: Emerged haustoria-small RNAs bioreplicate 3

value: Emerged haustoria

tag: molecule subtype


title: Seedling-small_RNAs

source_name: Seedling

value: Seedling


title: fb_C5

tag: cell type


title: Prehaustoria-small RNAs bioreplicate 2


title: Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB669RSF)

description:
https://www.encodeproject.org/experiments/ENCSR918KMR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR918KMR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR368JDN
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669RSF

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

value: 33 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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

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


title: Mint-ChIP-seq from dendritic cell (ENCLB801PCX)

description:
https://www.encodeproject.org/experiments/ENCSR745BMJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR745BMJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB801PCX

value: dendritic cell

value: primary cell

value: 51 year

value: Charles Lee

value: ENCBS682CBV at ENCODE; https://www.encodeproject.org/ENCBS682CBV/

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


title: Prehaustoria-small RNAs bioreplicate 1

value: Prehaustoria

value: small RNA


title: Mint-ChIP-seq from dendritic cell (ENCLB581EKF)

description:
https://www.encodeproject.org/experiments/ENCSR748IOD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR748IOD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB581EKF


title: Stem-small_RNAs_bioreplicate 2

value: Stem


title: Mint-ChIP-seq from dendritic cell (ENCLB059RQZ)

description:
https://www.encodeproject.org/experiments/ENCSR753RMT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR753RMT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB059RQZ


title: Mint-ChIP-seq from HCT116 (ENCLB287YFM)

description:
https://www.encodeproject.org/experiments/ENCSR743HTN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR743HTN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB287YFM

value: cell line

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

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

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

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


title: Emerged haustoria-small RNAs bioreplicate 2

value: Emerged haustoria


title: Emerged haustoria-PARE/Degradome bioreplicate 2

value: Degradome

value: 5'P RNA


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB279BOP)

description:
https://www.encodeproject.org/experiments/ENCSR919UFE/
***************
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: ENCSR919UFE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB279BOP
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

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

value: primary cell

tag: description

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

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


title: MH20-22B ∆leuA vs. KK25 ∆leuA-rep1

description: Biological replicate 1 of 2

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.

source_name: production strain MH20-22B deletion mutant

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

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

tag: condition

value: MH20-22B delta_leuA harvested during exponential growth phase, CGXII glucose, date of experiment:2002-06

source_name: production strain KK25 deletion mutant

value: KK25 delta_leuA harvested during exponential growth phase, CGXII glucose, date of experiment:2002-06


title: Mint-ChIP-seq from dendritic cell (ENCLB069SQI)

description:
https://www.encodeproject.org/experiments/ENCSR748IOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR748IOD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB069SQI

tag: antibody

value: dendritic cell

value: 51 year

value: male

value: adult

value: Charles Lee

value: ENCBS682CBV at ENCODE; https://www.encodeproject.org/ENCBS682CBV/

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


title: MH20-22B vs. KK25-rep2

description: Biological replicate 2 of 2

source_name: production strain MH20-22B

value: MH20-22B harvested during exponential growth phase, CGXII glucose, date of experiment:2001-08/2002-08

source_name: production strain KK25

value: KK25 harvested during exponential growth phase, CGXII glucose, date of experiment:2001-08/2002-08


title: Mint-ChIP-seq from activated T-helper 17 cell (ENCLB315XLP)

description:
https://www.encodeproject.org/experiments/ENCSR742HMR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR742HMR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR122NDV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB315XLP

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

value: activated T-helper 17 cell

value: primary cell

tag: biosample encode accession

value: 50 year

value: John Stamatoyannopoulos

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

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

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


title: Mint-ChIP-seq from Caco-2 (ENCLB385DWN)

description:
https://www.encodeproject.org/experiments/ENCSR699FXX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR699FXX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR662AMW
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385DWN

source_name: Homo sapiens Caco-2 cell line

tag: line

value: cell line

tag: age

value: 72 year

value: colorectal adenocarcinoma

value: Bradley Bernstein, Broad

value: Mats Ljungman

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

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


title: Mint-ChIP-seq from dendritic cell (ENCLB924FCT)

description:
https://www.encodeproject.org/experiments/ENCSR745BMJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR745BMJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB924FCT

value: dendritic cell

value: 51 year

tag: Sex

value: male

value: adult

value: Charles Lee

value: ENCBS682CBV at ENCODE; https://www.encodeproject.org/ENCBS682CBV/

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


title: MH20-22B vs. KK25-rep1

description: Biological replicate 1 of 2

value: MH20-22B harvested during exponential growth phase, CGXII glucose, date of experiment:2001-08/2002-08

value: KK25 harvested during exponential growth phase, CGXII glucose, date of experiment:2001-08/2002-08


title: MH20-22B (stationary phase) vs. WT (stationary phase)-rep2

description: Biological replicate 2 of 2

value: MH20-22B harvested during stationary growth phase, CGXII glucose, date of experiment:2002-03

source_name: wild type

value: WT harvested during stationary growth phase, CGXII glucose, date of experiment:2002-03


title: MH20-22B ∆leuA vs. KK25 ∆leuA-rep2

description: Biological replicate 2 of 2

value: MH20-22B delta_leuA harvested during exponential growth phase, CGXII glucose, date of experiment:2002-06

value: KK25 delta_leuA harvested during exponential growth phase, CGXII glucose, date of experiment:2002-06


title: MH20-22B (late exponential phase) vs. WT (exponential phase)-rep1

description: Biological replicate 1 of 2

value: MH20-22B harvested during late exponential growth phase, CGXII glucose, date of experiment:2001-06

value: WT harvested during late exponential growth phase, CGXII glucose, date of experiment:2001-06


title: Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB064BDW)

description:
https://www.encodeproject.org/experiments/ENCSR918KMR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR918KMR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR368JDN
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB064BDW

value: primary cell

value: 33 year

tag: dev stage

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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

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


title: Mint-ChIP-seq from activated T-helper 17 cell (ENCLB316DXU)

description:
https://www.encodeproject.org/experiments/ENCSR742HMR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR742HMR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR122NDV
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB316DXU

value: activated T-helper 17 cell

value: 50 year

value: male

value: adult

tag: lab

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

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

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


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB161BOT)

description:
https://www.encodeproject.org/experiments/ENCSR917BHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR917BHP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR995LKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB161BOT

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

value: 36 year

tag: source

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

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


title: MH20-22B vs. WT-rep3

description: Biological replicate 3 of 3

value: MH20-22B harvested during exponential growth phase, CGXII glucose, date of experiment:2001-01/2001-08

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2001-01/2001-08


title: MH20-22B (late exponential phase) vs. WT (exponential phase)-rep2

description: Biological replicate 2 of 2

value: MH20-22B harvested during late exponential growth phase, CGXII glucose, date of experiment:2001-06

value: WT harvested during late exponential growth phase, CGXII glucose, date of experiment:2001-06


title: Mint-ChIP-seq from activated T-cell (ENCLB612RAH)

description:
https://www.encodeproject.org/experiments/ENCSR695HMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR695HMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR619MIA
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB612RAH

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: 43 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

tag: treatments

value: ENCBS496KUK at ENCODE; https://www.encodeproject.org/ENCBS496KUK/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB354YLA)

description:
https://www.encodeproject.org/experiments/ENCSR917BHP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR917BHP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR995LKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB354YLA

value: male

value: adult

tag: link


title: MH20-22B vs. WT-rep1

description: Biological replicate 1 of 3


title: Histone ChIP-seq from middle frontal area 46 (ENCLB641UNF)

description:
https://www.encodeproject.org/experiments/ENCSR691JHZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR691JHZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB641UNF
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

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

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


title: MH20-22B vs. WT-rep2

description: Biological replicate 2 of 3

value: MH20-22B harvested during exponential growth phase, CGXII glucose, date of experiment:2001-01/2001-08

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2001-01/2001-08


title: Mint-ChIP-seq from Caco-2 (ENCLB109MVB)

description:
https://www.encodeproject.org/experiments/ENCSR699FXX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR699FXX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR662AMW
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB109MVB

value: cell line

value: 72 year

tag: health state

value: colorectal adenocarcinoma

value: Mats Ljungman

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

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


title: Mint-ChIP-seq from activated T-cell (ENCLB853LRC)

description:
https://www.encodeproject.org/experiments/ENCSR695HMZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR695HMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR619MIA
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB853LRC

value: activated T-cell

value: primary cell

value: 43 year

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

value: ENCBS496KUK at ENCODE; https://www.encodeproject.org/ENCBS496KUK/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: Mint-ChIP-seq from HCT116 (ENCLB350VEA)

description:
https://www.encodeproject.org/experiments/ENCSR899DBQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR899DBQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR642FUX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB350VEA

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: 48 year

value: colorectal carcinoma

value: adult

value: Erez Aiden

value: ENCBS891BUF at ENCODE; https://www.encodeproject.org/ENCBS891BUF/

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


title: KK25 ∆leuA vs. KK25-rep4

description: Biological replicate 4 of 4

value: KK25 delta_leuA harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11

value: KK25 harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11


title: Histone ChIP-seq from middle frontal area 46 (ENCLB532HPE)

description:
https://www.encodeproject.org/experiments/ENCSR691JHZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR691JHZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB532HPE
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

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

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


title: LE4 vs. MH20-22B-rep2

description: Biological replicate 2 of 2

source_name: production strain LE4

value: LE4 harvested during exponential growth phase, CGXII glucose, date of experiment:2001-07/2001-08

value: MH20-22B harvested during exponential growth phase, CGXII glucose, date of experiment:2001-07/2001-08


title: Mint-ChIP-seq from HCT116 (ENCLB739LGZ)

description:
https://www.encodeproject.org/experiments/ENCSR899DBQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR899DBQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR642FUX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB739LGZ

value: cell line

value: 48 year

value: male

value: Bradley Bernstein, Broad


title: KK25 ∆leuA vs. KK25-rep2

description: Biological replicate 2 of 4


title: KK25 ∆leuA vs. KK25-rep1

description: Biological replicate 1 of 4


title: KK25 ∆leuA vs. KK25-rep3

description: Biological replicate 3 of 4


title: Control Mint-ChIP-seq from HCT116 (ENCLB298III)

description:
https://www.encodeproject.org/experiments/ENCSR898CSY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR898CSY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB298III

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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


title: LE4 vs. MH20-22B-rep1

description: Biological replicate 1 of 2


title: Control Mint-ChIP-seq from HCT116 (ENCLB689KWJ)

description:
https://www.encodeproject.org/experiments/ENCSR898CSY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR898CSY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB689KWJ

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


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB105ILF)

description:
https://www.encodeproject.org/experiments/ENCSR892XTV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR892XTV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR414ZUR
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB105ILF

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

value: primary cell

value: 36 year

value: John Stamatoyannopoulos

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

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

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


title: LE4 vs. WT-rep1

description: Biological replicate 1 of 2

value: LE4 harvested during exponential growth phase, CGXII glucose, date of experiment:2001-08

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2001-08


title: KK25 vs. WT-rep3

description: Biological replicate 3 of 3

value: KK25 harvested during exponential growth phase, CGXII glucose, date of experiment:2001-09/2001-11

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2001-09/2001-11


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB480TCU)

description:
https://www.encodeproject.org/experiments/ENCSR892XTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR892XTV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR414ZUR
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB480TCU

value: male

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from memory B cell (ENCLB298WUD)

description:
https://www.encodeproject.org/experiments/ENCSR891FJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR891FJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB298WUD

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

value: memory B cell

value: 40 year

value: adult

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

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


title: LE4 vs. WT-rep2

description: Biological replicate 2 of 2


title: Control ChIP-seq from placenta (ENCLB814OVC)

description:
https://www.encodeproject.org/experiments/ENCSR889ZOH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR889ZOH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB814OVC
size range: 200-600

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: unknown

value: female

value: embryonic

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

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


title: Histone ChIP-seq from lower lobe of right lung (ENCLB338UXZ)

description:
https://www.encodeproject.org/experiments/ENCSR690AFM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR690AFM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR454FJM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338UXZ
size range: 200-600

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

value: lower lobe of right lung

value: 60 year

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

value: Shin Lin

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

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


title: Control ChIP-seq from placenta (ENCLB724VDC)

description:
https://www.encodeproject.org/experiments/ENCSR889ZOH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR889ZOH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB724VDC
size range: 200-600

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos


title: KK25 vs. WT-rep2

description: Biological replicate 2 of 3

value: KK25 harvested during exponential growth phase, CGXII glucose, date of experiment:2001-09/2001-11

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2001-09/2001-11


title: DM1945 ∆cg1722-ldcCOPT STR2 (microaerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep4

description: Biological replicate 4 of 4

source_name: production strain DM1945

value: DM1945 delta_cg1722-ldcCOPT STR2 (microaerob) harvested during exponential growth, CGXII glucose, date of experiment:2015-05

value: DM1945 delta_act3-ldcCOPT STR2 (microaerob) harvested during exponential growth, CGXII glucose, date of experiment:2015-05


title: KK25 vs. WT-rep1

description: Biological replicate 1 of 3


title: DM1945 ∆cg1722-ldcCOPT STR2 (microaerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep3

description: Biological replicate 3 of 4


title: DM1945 ∆cg1722-ldcCOPT STR2 (microaerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep2

description: Biological replicate 2 of 4


title: Histone ChIP-seq from middle frontal area 46 (ENCLB014PPK)

description:
https://www.encodeproject.org/experiments/ENCSR888EEH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR888EEH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR846OTK
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB014PPK
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 89 year

value: adult

value: Rush University

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

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


title: DM1945 ∆cg1722-ldcCOPT STR2 (microaerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep1

description: Biological replicate 1 of 4


title: Mint-ChIP-seq from HCT116 (ENCLB347EHJ)

description:
https://www.encodeproject.org/experiments/ENCSR686VUZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR686VUZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB347EHJ

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: Erez Aiden

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

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


title: DM1945 ∆act3-ldcCOPT STR1 (aerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep4

description: Biological replicate 4 of 4

value: DM1945 delta_act3-ldcCOPT STR1  harvested during exponential growth, CGXII glucose, date of experiment:2015-05

value: DM1945 delta_act3-ldcCOPT harvested during exponential growth, CGXII glucose, date of experiment:2015-05


title: Mint-ChIP-seq from memory B cell (ENCLB853VMJ)

description:
https://www.encodeproject.org/experiments/ENCSR891FJY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR891FJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB853VMJ

value: memory B cell

value: primary cell

value: 40 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from HCT116 (ENCLB167NER)

description:
https://www.encodeproject.org/experiments/ENCSR686VUZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR686VUZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR500IKB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB167NER

value: adult


title: DM1945 ∆act3-ldcCOPT STR1 (aerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep2

description: Biological replicate 2 of 4

value: DM1945 delta_act3-ldcCOPT STR1  harvested during exponential growth phase, CGXII glucose, date of experiment:2015-05


title: Mint-ChIP-seq from memory B cell (ENCLB962YMY)

description:
https://www.encodeproject.org/experiments/ENCSR886LDA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR886LDA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB962YMY


title: Inactivated pta vs. WT-rep3

description: Biological replicate 3 of 3

source_name: deletion mutant

value: inactivated pta harvested during exponential growth phase, CGXII glucose acetate, date of experiment:2002-11

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


title: Histone ChIP-seq from lower lobe of right lung (ENCLB238OOO)

description:
https://www.encodeproject.org/experiments/ENCSR690AFM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR690AFM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR454FJM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB238OOO
size range: 200-600

value: lower lobe of right lung

value: tissue

value: 60 year

value: male

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

value: Shin Lin

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

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB028DAS)

description:
https://www.encodeproject.org/experiments/ENCSR686HFA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR686HFA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB028DAS
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

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

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


title: Mint-ChIP-seq from memory B cell (ENCLB191UXT)

description:
https://www.encodeproject.org/experiments/ENCSR886LDA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR886LDA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR430DND
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB191UXT

value: memory B cell

value: 40 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB958QMN)

description:
https://www.encodeproject.org/experiments/ENCSR686HFA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR686HFA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283QZJ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB958QMN
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB406GYR)

description:
https://www.encodeproject.org/experiments/ENCSR919UFE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR919UFE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406GYR
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

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

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

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

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

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


title: Control ChIP-seq from right lobe of liver (ENCLB419JML)

description:
https://www.encodeproject.org/experiments/ENCSR886ATT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR886ATT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB419JML
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 middle frontal area 46 (ENCLB637LVZ)

description:
https://www.encodeproject.org/experiments/ENCSR888EEH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR888EEH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR846OTK
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB637LVZ
size range: 200-600

value: middle frontal area 46

value: 89 year

value: adult

value: Rush University

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

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


title: DM1945 ∆act3-ldcCOPT STR1 (aerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep1

description: Biological replicate 1 of 4

value: DM1945 delta_act3-ldcCOPT STR1  harvested during exponential growth phase, CGXII glucose, date of experiment:2015-05

value: DM1945 delta_act3-ldcCOPT harvested during exponential growth, CGXII glucose, date of experiment:2015-05


title: DM1945 ∆act3-ldcCOPT STR1 (aerob) vs. DM1945 ∆act3-ldcCOPT (aerobic)-rep3

description: Biological replicate 3 of 4


title: Control Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB799GEN)

description:
https://www.encodeproject.org/experiments/ENCSR885JZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR885JZJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB799GEN

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

value: primary cell

value: 50 year

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

value: ENCBS572PDL at ENCODE; https://www.encodeproject.org/ENCBS572PDL/

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


title: Control Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB795WJF)

description:
https://www.encodeproject.org/experiments/ENCSR885JZJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR885JZJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB795WJF


title: Mint-ChIP-seq from MCF 10A (ENCLB703KDX)

description:
https://www.encodeproject.org/experiments/ENCSR884WUC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR884WUC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB703KDX

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: 36 year

value: female

value: fibrocystic disease

value: Mats Ljungman

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

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


title: Control ChIP-seq from right lobe of liver (ENCLB058XAD)

description:
https://www.encodeproject.org/experiments/ENCSR886ATT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR886ATT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB058XAD
size range: 200-600

value: right lobe of liver

value: tissue

value: 47 year

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

value: adult

value: Shin Lin

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

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


title: Inactivated pta vs. WT-rep1

description: Biological replicate 1 of 3

value: inactivated pta harvested during exponential growth phase, CGXII glucose acetate, date of experiment:2002-11

source_name: wild type

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


title: ∆clpC vs. WT-rep2

description: Biological replicate 2 of 3

value: delta_clpC harvested during exponential growth phase, LB glucose, date of experiment:2001-06/2002_11

value: WT harvested during exponential growth phase, LB glucose, date of experiment:2001-06/2002_11


title: ∆clpC vs. WT-rep1

description: Biological replicate 1 of 3


title: Mint-ChIP-seq from MCF 10A (ENCLB300BZA)

description:
https://www.encodeproject.org/experiments/ENCSR884WUC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR884WUC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB300BZA

value: MCF 10A

value: cell line

value: 36 year

value: female

value: Bradley Bernstein, Broad


title: ∆phoSR vs WT (P-Poor 30 min, 0,005 g/l KH2PO4, 0,01 g/l K2HPO4)-rep1

description: Biological replicate 1 of 3

value: delta_phoSR harvested during exponential growth phase 30 min after switch to phosphate starvation, CGXII glucose 0,005 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-07/2002-08

value: WT harvested during exponential growth phase 30 min after switch to phosphate starvation, CGXII glucose 0,005 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-07/2002-08


title: Mint-ChIP-seq from MCF 10A (ENCLB896BSE)

description:
https://www.encodeproject.org/experiments/ENCSR685JSL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR685JSL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB896BSE

value: fibrocystic disease

value: Mats Ljungman

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

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


title: Inactivated pta vs. WT-rep2

description: Biological replicate 2 of 3


title: ∆phoSR vs WT (P-Poor 30 min, 0,005 g/l KH2PO4, 0,01 g/l K2HPO4)-rep2

description: Biological replicate 2 of 3


title: ∆phoSR vs WT (P-Poor 30 min, 0,005 g/l KH2PO4, 0,01 g/l K2HPO4)-rep3

description: Biological replicate 3 of 3


title: ∆clpC vs. WT-rep3

description: Biological replicate 3 of 3


title: Mint-ChIP-seq from activated T-cell (ENCLB020DTW)

description:
https://www.encodeproject.org/experiments/ENCSR882EIQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR882EIQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR798SDW
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB020DTW

source_name: Homo sapiens female adult (21 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: 21 year

value: adult

value: John Stamatoyannopoulos

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

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

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


title: Mint-ChIP-seq from MCF 10A (ENCLB795KWE)

description:
https://www.encodeproject.org/experiments/ENCSR685JSL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR685JSL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB795KWE

value: MCF 10A

value: cell line

value: 36 year


title: Mint-ChIP-seq from activated T-cell (ENCLB351CUA)

description:
https://www.encodeproject.org/experiments/ENCSR882EIQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR882EIQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR798SDW
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB351CUA

value: female

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from HCT116 (ENCLB295NTE)

description:
https://www.encodeproject.org/experiments/ENCSR879YQX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR879YQX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR071RJS
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB295NTE

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: 48 year

value: male

value: colorectal carcinoma

value: Erez Aiden

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

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


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB264QRL)

description:
https://www.encodeproject.org/experiments/ENCSR684HLM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR684HLM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB264QRL

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: 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: ∆phoSR vs WT (P-Limit 60 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep4

description: Biological replicate 4 of 5

value: delta_phoSR harvested during exponential growth phase 60 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: WT harvested during exponential growth phase 60 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR vs WT (P-Limit 60 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep1

description: Biological replicate 1 of 5


title: ∆phoSR vs WT (P-Limit 30 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep2

description: Biologicial replicate 2 of 2

value: delta_phoSR harvested during exponential growth phase 30 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: WT harvested during exponential growth phase 30 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR vs WT (P-Limit 60 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep3

description: Biological replicate 3 of 5


title: ∆phoSR vs WT (P-Limit 60 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep5

description: Biological replicate 5 of 5


title: Histone ChIP-seq from middle frontal area 46 (ENCLB370MAW)

description:
https://www.encodeproject.org/experiments/ENCSR875PYX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years)
experiment encode accession: ENCSR875PYX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR772LYM
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB370MAW
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 83 year

value: adult

value: Bradley Bernstein, Broad

value: Rush University

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

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB118UDW)

description:
https://www.encodeproject.org/experiments/ENCSR684GKG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR684GKG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR569JUB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB118UDW

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

value: primary cell

value: 36 year

value: male

value: John Stamatoyannopoulos

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

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


title: ∆phoSR (P-Limit 30 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)  vs. ∆phoRS-rep2

description: Biological replicate 2 of 3

value: delta_phoSR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-04


title: ∆phoSR (P-Limit 30 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)  vs. ∆phoRS-rep3

description: Biological replicate 3 of 3

value: delta_phoSR harvested during exponential growth phase 30 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB234CJH)

description:
https://www.encodeproject.org/experiments/ENCSR684GKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR684GKG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR569JUB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB234CJH


title: Mint-ChIP-seq from HCT116 (ENCLB195QEO)

description:
https://www.encodeproject.org/experiments/ENCSR879YQX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR879YQX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR071RJS
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB195QEO

value: cell line

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

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

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


title: Mint-ChIP-seq from stimulated activated naive B cell (ENCLB782YQZ)

description:
https://www.encodeproject.org/experiments/ENCSR684HLM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR684HLM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546DAT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB782YQZ

value: stimulated activated naive B cell

value: 39 year

value: female

value: adult

value: Bradley Bernstein, Broad

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

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB793OUY)

description:
https://www.encodeproject.org/experiments/ENCSR875PYX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on middle frontal area 46 tissue male adult (83 years)
experiment encode accession: ENCSR875PYX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR772LYM
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB793OUY
size range: 200-600

value: middle frontal area 46

value: tissue

value: 83 year

value: male

value: Rush University

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

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


title: ∆phoSR vs WT (P-Limit 60 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep2

description: Biological replicate 2 of 5

value: delta_phoSR harvested during exponential growth phase 60 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: WT harvested during exponential growth phase 60 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR vs WT (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep4

description: Biological replicate 4 of 5

value: delta_phoSR harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: WT harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)  vs. ∆phoRS-rep3

description: Biological replicate 3 of 3

value: delta_phoSR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-04


title: Mint-ChIP-seq from HCT116 (ENCLB916RUY)

description:
https://www.encodeproject.org/experiments/ENCSR295BJE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR295BJE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR099TYF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB916RUY

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

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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

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


title: ∆phoSR (P-Limit 30 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)  vs. ∆phoRS-rep1

description: Biological replicate 1 of 3

value: delta_phoSR harvested during exponential growth phase 30 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR vs WT (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep3

description: Biological replicate 3 of 5


title: Control ChIP-seq from right lobe of liver (ENCLB450NKG)

description:
https://www.encodeproject.org/experiments/ENCSR683VJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR683VJG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB450NKG
size range: 200-600

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

value: right lobe of liver

value: tissue

value: 16 year

value: female

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

value: child

value: Bradley Bernstein, Broad

value: Shin Lin

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

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


title: Control ChIP-seq from right lobe of liver (ENCLB855IDZ)

description:
https://www.encodeproject.org/experiments/ENCSR683VJG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR683VJG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB855IDZ
size range: 200-600


title: Mint-ChIP-seq from HCT116 (ENCLB927VHY)

description:
https://www.encodeproject.org/experiments/ENCSR873SVP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR873SVP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927VHY

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

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


title: Control Mint-ChIP-seq from natural killer cell (ENCLB757HSO)

description:
https://www.encodeproject.org/experiments/ENCSR294RLP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR294RLP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB757HSO

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

value: natural killer cell

value: primary cell

value: 41 year

value: adult

value: John Stamatoyannopoulos

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

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


title: ∆phoSR vs WT (P-Limit 30 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep1

description: Biologicial replicate 1 of 2

value: delta_phoSR harvested during exponential growth phase 30 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: WT harvested during exponential growth phase 30 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: Control Mint-ChIP-seq from natural killer cell (ENCLB817GXX)

description:
https://www.encodeproject.org/experiments/ENCSR294RLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR294RLP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB817GXX

value: female

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from HCT116 (ENCLB985RZA)

description:
https://www.encodeproject.org/experiments/ENCSR295BJE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR295BJE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR099TYF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB985RZA

value: Erez Aiden

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

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

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


title: Mint-ChIP-seq from stimulated activated CD8-positive, alpha-beta memory T cell (ENCLB422MUR)

description:
https://www.encodeproject.org/experiments/ENCSR294HTM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR294HTM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466PQY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB422MUR

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

value: male

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS039WVH at ENCODE; https://www.encodeproject.org/ENCBS039WVH/

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


title: Control Mint-ChIP-seq from HCT116 (ENCLB215FWB)

description:
https://www.encodeproject.org/experiments/ENCSR873HRN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR873HRN
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB215FWB

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

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

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


title: Control Mint-ChIP-seq from HCT116 (ENCLB470CUU)

description:
https://www.encodeproject.org/experiments/ENCSR873HRN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR873HRN
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB470CUU

value: Bradley Bernstein, Broad


title: Inactivated ack (50 mM glucose, 50 mM acetate) vs. WT (50 mM glucose, 50 mM acetate)-rep4

description: Biological replicate 4 of 4

source_name: inactivation

value: Inactivated ack harvested during exponential growth phase, CGXII 50 mM glucose, 50 mM acetate, date of experiment:2002-11/2002-12

value: WT harvested during exponential growth phase, CGXII 50 mM glucose, 50 mM acetate, date of experiment:2002-11/2002-12


title: Inactivated ack (50 mM glucose, 50 mM acetate) vs. WT (50 mM glucose, 50 mM acetate)-rep3

description: Biological replicate 3 of 4


title: ∆phoSR (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)  vs. ∆phoRS-rep2

description: Biological replicate 2 of 3

source_name: deletion mutant

value: delta_phoSR harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: delta_phoSR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-04


title: Inactivated ack (50 mM glucose, 50 mM acetate) vs. WT (50 mM glucose, 50 mM acetate)-rep2

description: Biological replicate 2 of 4


title: Histone ChIP-seq from middle frontal area 46 (ENCLB819DQC)

description:
https://www.encodeproject.org/experiments/ENCSR872YGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR872YGQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR846OTK
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB819DQC
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 89 year

value: female

value: Rush University

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

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


title: ∆phoSR vs WT (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep5

description: Biological replicate 5 of 5

value: WT harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR  vs. WT-rep1

description: Biologicial replicate 1 of 2

value: delta_phoSR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11

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


title: ∆phoSR vs WT (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep1

description: Biological replicate 1 of 5


title: Inactivated ack (50 mM glucose, 50 mM acetate) vs. WT (50 mM glucose, 50 mM acetate)-rep1

description: Biological replicate 1 of 4


title: ∆clgR (10 min after heatshock, 50°C) vs. ∆clgR-rep3

description: Biological replicate 3 of 3

value: delta_clgR harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2003-04

value: delta_clgR harvested during exponential growth phase, CGXII glucose, date of experiment:2003-04


title: Mint-ChIP-seq from HCT116 (ENCLB120QUY)

description:
https://www.encodeproject.org/experiments/ENCSR873SVP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR873SVP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR801URS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB120QUY

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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

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

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


title: Mint-ChIP-seq from stimulated activated CD8-positive, alpha-beta memory T cell (ENCLB229PJN)

description:
https://www.encodeproject.org/experiments/ENCSR294HTM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR294HTM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466PQY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB229PJN

value: primary cell

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS039WVH at ENCODE; https://www.encodeproject.org/ENCBS039WVH/

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


title: ∆phoSR vs WT (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)-rep2

description: Biological replicate 2 of 5

value: delta_phoSR harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: WT harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04


title: ∆phoSR  vs. WT-rep2

description: Biologicial replicate 2 of 2

value: delta_phoSR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11

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


title: ∆clgR vs. WT PCR-Product-rep2

description: Biological replicate 2 of 3

value: delta_clgR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11/2003-3

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11/2003-3


title: ∆clgR vs. WT PCR-Product-rep1

description: Biological replicate 1 of 3


title: Mint-ChIP-seq from HCT116 (ENCLB956IDB)

description:
https://www.encodeproject.org/experiments/ENCSR871TIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR871TIY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR846UXS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB956IDB

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB854EOY)

description:
https://www.encodeproject.org/experiments/ENCSR496LKR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR496LKR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB854EOY

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB184ZFG)

description:
https://www.encodeproject.org/experiments/ENCSR872YGQ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease
experiment encode accession: ENCSR872YGQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR846OTK
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB184ZFG
size range: 200-600

value: middle frontal area 46

value: tissue

value: 89 year

value: female

value: Rush University

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

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB560MZV)

description:
https://www.encodeproject.org/experiments/ENCSR496LKR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR496LKR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB560MZV

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from HCT116 (ENCLB753IVN)

description:
https://www.encodeproject.org/experiments/ENCSR871TIY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR871TIY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR846UXS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753IVN

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

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

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

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


title: MH20-22B (stationary phase) vs. WT (stationary phase)-rep1

description: Biological replicate 1 of 2

source_name: production strain MH20-22B

value: MH20-22B harvested during stationary growth phase, CGXII glucose, date of experiment:2002-03

source_name: wild type

value: WT harvested during stationary growth phase, CGXII glucose, date of experiment:2002-03


title: Mint-ChIP-seq from T-cell (ENCLB838XKO)

description:
https://www.encodeproject.org/experiments/ENCSR498DCY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR498DCY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB838XKO

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

value: T-cell

value: primary cell

value: 21 year

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB651KBA)

description:
https://www.encodeproject.org/experiments/ENCSR293IGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR293IGW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB651KBA

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: 33 year

value: Bradley Bernstein, Broad

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: ∆phoSR (P-Limit 10 min, 0,01 g/l KH2PO4, 0,01 g/l K2HPO4)  vs. ∆phoRS-rep1

description: Biological replicate 1 of 3

value: delta_phoSR harvested during exponential growth phase 10 min after switch to phosphate limitation, CGXII glucose 0,01 g/l KH2PO4, 0,01 g/l K2HPO4, date of experiment:2002-04

value: delta_phoSR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-04


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB516NVK)

description:
https://www.encodeproject.org/experiments/ENCSR293IGW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR293IGW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB516NVK

value: male

value: adult


title: ∆clgR vs. WT PCR-Product-rep3

description: Biological replicate 3 of 3

value: delta_clgR harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11/2003-3

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2002-11/2003-3


title: ∆acnR (4% glucose, 20 mM glutamate) vs. WT (4% glucose, 20 mM glutamate)-rep3

description: Biological replicate 3 of 13

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

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


title: Control ChIP-seq from Calu3 (ENCLB030UCW)

description:
https://www.encodeproject.org/experiments/ENCSR871UJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR871UJG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB030UCW
size range: 200-600

source_name: Homo sapiens Calu3 cell line

value: cell line

value: 25 year

value: Lung adenocarcinoma

value: Mats Ljungman

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

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


title: Histone ChIP-seq from placenta (ENCLB895ZVR)

description:
https://www.encodeproject.org/experiments/ENCSR681RQP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR681RQP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR889ZOH
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895ZVR
size range: 200-600

source_name: Homo sapiens female embryo placenta tissue

value: placenta

value: tissue

value: unknown

value: female

value: embryonic

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from T-cell (ENCLB839QOJ)

description:
https://www.encodeproject.org/experiments/ENCSR498DCY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR498DCY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB839QOJ

value: T-cell

value: primary cell

value: 21 year

value: adult

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

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


title: ∆clgR (10 min after heatshock, 50°C) vs. ∆clgR-rep2

description: Biological replicate 2 of 3

value: delta_clgR harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2003-04

value: delta_clgR harvested during exponential growth phase, CGXII glucose, date of experiment:2003-04


title: Control ChIP-seq from Calu3 (ENCLB489EVC)

description:
https://www.encodeproject.org/experiments/ENCSR871UJG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR871UJG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB489EVC
size range: 200-600

value: cell line

value: 25 year

value: male

value: Lung adenocarcinoma

value: Mats Ljungman

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

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


title: ∆clgR (10 min after heatshock, 50°C) vs. ∆clgR-rep1

description: Biological replicate 1 of 3


title: WT pMV1-lysG (CGXII, 4% myo-inositol) vs. WT pMV1 (CGXII, 4% myo-inositol)-rep2

description: Biological replicate 2 of 2

source_name: wild type + overexpression

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

source_name: wild type + control

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


title: ∆acnR (4% glucose, 20 mM glutamate) vs. WT (4% glucose, 20 mM glutamate)-rep4

description: Biological replicate 4 of 13

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

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


title: ∆acnR (4% glucose, 40 mM glutamate, 500 µM FeSO4) vs. ∆acnR (4% glucose, 40 mM glutamate)-rep5

description: Biological replicate 5 of 5

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

value: WT harvested during exponential growth phase, CGXII glucose, 40 mM glutamate, 500 µM FeSO4, date of experiment:2002-12/2003-05