title: Control ChIP-seq from K562 (ENCLB816QIR)

description:
https://www.encodeproject.org/experiments/ENCSR825BVU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR825BVU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB816QIR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF3

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS782THZ at ENCODE; https://www.encodeproject.org/ENCBS782THZ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: PkaCoe_r2_hr14

status: Public on Jun 15 2021

type: SRA

city: Houston

first: Gad

last: Shaulsky

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
After demultiplexing and filtering illumina adapter sequences, the data was mapped to the D. discoideum genome with bowtie version 1.0.0. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_rc.tab" contain raw expression values while files ending with "_nor.tab" contain normalized expression values.

molecule: total RNA

organism: Dictyostelium discoideum

growth_protocol: Twenty strains were cultured axenically in HL5.

extract_protocol:
At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.
We prepared Illumina multiplexed libraries of all samples. 434 individual libraries were separately prepared and divided to 22 sets. We added a unique barcode to each library in each set at the final step of PCR amplification. We pooled equal amounts of DNA from each library and sequenced those pools by Illumina HiSeq2500 (single-end sequencing, read length = 50 or 100 bases) or (paired-end sequencing, read length = 93 or 100 bases) or by NovaSeq6000 (paired-end sequencing, read length = 150 bases).

treatment_protocol: Cells were washed with PDF and plated on nitrocellulse filter on filter paper saturated in PDF at 1.8x106 cells/cm2.

tag: strain

value: PkaCoe

tag: phenotype group

value: precocious development

tag: replicate

tag: developmental time


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB662JWZ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR536AYF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR536AYF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB662JWZ
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

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

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: healthy

tag: dev stage

value: unknown

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

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

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


title: Control Mint-ChIP-seq from T-cell (ENCLB562VDM)

description:
https://www.encodeproject.org/experiments/ENCSR445KDW/
***************
biological replicate number: 1
technical replicate number: 3
description: Control Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR445KDW
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562VDM

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

value: T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: PkaCoe_r2_hr00

value: PkaCoe

value: precocious development


title: Control Mint-ChIP-seq from IgD-negative memory B cell (ENCLB198SUI)

description:
https://www.encodeproject.org/experiments/ENCSR354FME/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell
experiment encode accession: ENCSR354FME
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB198SUI

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

value: IgD-negative memory B cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: ENCBS091EUT at ENCODE; https://www.encodeproject.org/ENCBS091EUT/

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


title: PkaCoe_r2_hr08


title: PkaCoe_r2_hr04


title: Control ChIP-seq from SK-N-SH (ENCLB975AAK)

description:
https://www.encodeproject.org/experiments/ENCSR922UWH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR922UWH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB975AAK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line treated with 6 uM all-trans-retinoic acid for 48 hours

tag: line

value: SK-N-SH

value: cell line

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS736WLO at ENCODE; https://www.encodeproject.org/ENCBS736WLO/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: PkaCoe_r1_hr24

value: PkaCoe

value: precocious development


title: PkaCoe_r1_hr18


title: PkaCoe_r1_hr20


title: PkaCoe_r1_hr16


title: Control Mint-ChIP-seq from IgD-negative memory B cell (ENCLB851ZSD)

description:
https://www.encodeproject.org/experiments/ENCSR354FME/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell
experiment encode accession: ENCSR354FME
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB851ZSD

value: IgD-negative memory B cell

value: primary cell

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

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler


title: PkaCoe_r1_hr14


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB493DFJ)

description:
https://www.encodeproject.org/experiments/ENCSR534UDS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with 10 ng
experiment encode accession: ENCSR534UDS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR779CPT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB493DFJ
fragmentation methods: none

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: male

value: adult

value: 20 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: ENCBS736STX at ENCODE; https://www.encodeproject.org/ENCBS736STX/

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


title: PkaCoe_r1_hr12

value: PkaCoe


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB200RVW)

description:
https://www.encodeproject.org/experiments/ENCSR534UDS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with 10 ng
experiment encode accession: ENCSR534UDS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR779CPT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200RVW
fragmentation methods: none


title: PkaCoe_r1_hr04

value: precocious development


title: PkaCoe_r1_hr08


title: AX4_PE_r4_hr24

value: WT


title: Mint-ChIP-seq from activated T-cell (ENCLB256ZVC)

description:
https://www.encodeproject.org/experiments/ENCSR439XYT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR439XYT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB256ZVC
fragmentation methods: none

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell

value: activated T-cell

value: primary cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS693BEC at ENCODE; https://www.encodeproject.org/ENCBS693BEC/

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


title: PkaCoe_r1_hr00


title: AX4_PE_r4_hr20


title: Mint-ChIP-seq from activated T-cell (ENCLB165TCP)

description:
https://www.encodeproject.org/experiments/ENCSR439XYT/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR439XYT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB165TCP
fragmentation methods: none

value: male

value: adult

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from activated T-cell (ENCLB169GPQ)

description:
https://www.encodeproject.org/experiments/ENCSR439XYT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR439XYT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB169GPQ
fragmentation methods: none

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/


title: Mint-ChIP-seq from H9 (ENCLB584PNA)

description:
https://www.encodeproject.org/experiments/ENCSR352HOU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR352HOU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584PNA
fragmentation methods: none

source_name: Homo sapiens H9 cell line originated from H9

value: cell line

value: WA09 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

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


title: Control ChIP-seq from K562 (ENCLB525SKV)

description:
https://www.encodeproject.org/experiments/ENCSR816YLP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR816YLP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB525SKV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF655

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS767DWU at ENCODE; https://www.encodeproject.org/ENCBS767DWU/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: AX4_PE_r4_hr00

value: WT


title: AX4_PE_r3_hr24


title: AX4_PE_r4_hr04


title: AX4_PE_r4_hr08


title: AX4_PE_r4_hr12


title: Mint-ChIP-seq from H9 (ENCLB509TQC)

description:
https://www.encodeproject.org/experiments/ENCSR352HOU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR352HOU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB509TQC
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: AX4_PE_r3_hr16


title: AX4_PE_r3_hr20


title: AX4_PE_r3_hr12


title: Mint-ChIP-seq from H9 (ENCLB669VXM)

description:
https://www.encodeproject.org/experiments/ENCSR352HOU/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR352HOU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669VXM
fragmentation methods: none

value: cell line

value: WA09 ES cells


title: AX4_PE_r3_hr08


title: AX4_PE_r3_hr04


title: WGS from HepG2 (ENCLB183WVA)

description:
https://www.encodeproject.org/experiments/ENCSR350RUO/
***************
biological replicate number: 1
technical replicate number: 1
description: These data correspond to shotgun PE151 Illumina sequencing done on long insert fragmented gDNA from the HepG2 cell line.
experiment encode accession: ENCSR350RUO
assay title: WGS
assembly: hg19
possible controls: ENCSR276ECO
encode release date: 2019-02-26
lab: Alexander Urban, Stanford
library encode accession: ENCLB183WVA
fragmentation methods: chemical (Nextera tagmentation)
size range: 3062-3062
nucleic acid starting quantity: 2
nucleic acid starting quantity units: µg

source_name: Homo sapiens HepG2 cell line

extract_protocol:
pipeline protocol: https://www.encodeproject.org/documents/0a14f50a-5674-4f33-9b5d-2d169750c8aa/@@download/attachment/Supplementary%20Figure%201_duplicate.pdf
general protocol: https://www.encodeproject.org/documents/d084c0e6-5818-4c54-b8dd-cbe9963981c6/@@download/attachment/updated2_Experiment%20accession%20ENCSR350RUO.pdf
general protocol: https://www.encodeproject.org/documents/8ef877c4-63d9-46b3-a7a4-0473de1a130a/@@download/attachment/ENCSR350RUO_file_details.pdf
extraction method: QIAGEN DNeasy Blood & Tissue Kit
extraction protocol: https://www.encodeproject.org/documents/95ebdfee-474e-4b23-83f4-a6fcb9bbe235/@@download/attachment/nextera_mate_pair_sample_prep_guide_15035209_d.pdf

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Alexander Urban, Stanford

value: Michael Snyder

tag: passage number

value: ENCBS760ISV at ENCODE; https://www.encodeproject.org/ENCBS760ISV/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: AX4_PE_r3_hr00

tag: strain


title: AX4_FD_r2_hr22

description:
GSM1517257
GEO: GSE61914
Filter development, replicate 2, hour 22
AX4_FD_r2_hr22

data_processing:
After demultiplexing and filtering illumina adapter sequences, the data was mapped to the D. discoideum genome with bowtie version 1.0.0 through the web application dictyExpress GenBoard or Genialis platform. Read qualities were used. Other parameters: seed length = 28, allowed mismatches = 2, allowed up to 1 alignment per read, with bowtie options -a, --strata, --best. Unmapped reads were trimmed from 3' by 2 nucleotides, which was repeated 5 times.
Raw expression values were computed as the number of reads that were uniquely mapped to gene exons.
Normalized expression were scaled with mappable exon lengths. This normalization is similar to the RPKM normalization (Reads Per Kilobase of exon per Megabase of library size), but instead of dividing by exon lengths we used the uniquely mappable parts of the exon. To obtain uniquely mappable parts, all possible subsequences of the reference genome (of the same length as reads in raw data) are mapped back to the reference genome, obtaining the number of uniquely mapped sequences to the exons (Exon_mappable). As a library size we used the total number of all uniquely mapped reads from the experiment, excluding the non-polyadenylated genes (N_unique). Normalized expressions were computed as follows: Exp = 10^9*raw/(N_unique * Exon_mappable).
Genome_build: D. discoideum Chromosomal DNA: 1,2,3,4,5,6,M, and floating contigs (created: 05-13-2009 13:53) from the DictyBase (chromosomes 1,2,3,4,5,6 and mitochondrial DNA are the same as on NCBI assembly "dicty_2.7"). Regions [3016085, 3768655] from chr2, [64985, 72996] from chrBF and [42801, 78150] from chrR were masked.
Supplementary_files_format_and_content: Processed data files are tab-separated files with two columns: the first containing gene names and the second its expression. Files ending with "_rc.tab" contain raw expression values while files ending with "_nor.tab" contain normalized expression values.

molecule: polyA RNA

growth_protocol: Dictyostelium discoideum cells were grown in nutrient media (HL-5)

extract_protocol: At each time point, we harvested the cells directly into 1 mL of Trizol® (life technologies, CA, USA) and extracted total RNA according to the manufacturer’s recommended protocol. We performed two rounds of poly-A selection and fragmented 100 ng of the resulting mRNA into approximately 200 bases fragments. We prepared cDNA and the second strand.

tag: phenotype group


title: AX4_PE_r4_hr16

tag: replicate


title: Control ChIP-seq from K562 (ENCLB136AGN)

description:
https://www.encodeproject.org/experiments/ENCSR915XAG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR915XAG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB136AGN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF830

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS507QZG at ENCODE; https://www.encodeproject.org/ENCBS507QZG/


title: AX4_FD_r2_hr20

description:
GSM1517256
GEO: GSE61914
Filter development, replicate 2, hour 20
AX4_FD_r2_hr20

value: WT

tag: developmental time


title: AX4_FD_r2_hr24

description:
GSM1517258
GEO: GSE61914
Filter development, replicate 2, hour 24
AX4_FD_r2_hr24


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB610BWY)

description:
https://www.encodeproject.org/experiments/ENCSR348YRH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of naive thymus-derived CD8-positive, alpha-beta T cell originated from naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR348YRH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR426RVC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB610BWY
fragmentation methods: none

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

tag: antibody

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS671UYD at ENCODE; https://www.encodeproject.org/ENCBS671UYD/

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


title: Mint-ChIP-seq from activated T-cell (ENCLB880KAG)

description:
https://www.encodeproject.org/experiments/ENCSR439XYT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR439XYT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB880KAG
fragmentation methods: none

value: activated T-cell

tag: description

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: male

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/

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


title: AX4_FD_r2_hr18

description:
GSM1517255
GEO: GSE61914
Filter development, replicate 2, hour 18
AX4_FD_r2_hr18

value: WT


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB964FUG)

description:
https://www.encodeproject.org/experiments/ENCSR348YRH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of naive thymus-derived CD8-positive, alpha-beta T cell originated from naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR348YRH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR426RVC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB964FUG
fragmentation methods: none

value: primary cell

tag: biosample encode accession


title: AX4_FD_r2_hr14

description:
GSM1517253
GEO: GSE61914
Filter development, replicate 2, hour 14
AX4_FD_r2_hr14


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB751VME)

description:
https://www.encodeproject.org/experiments/ENCSR347NUR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR347NUR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB751VME
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) type B pancreatic in vitro differentiated cells originated from type B pancreatic cell

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

tag: Sex

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/

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


title: AX4_FD_r2_hr12

description:
GSM1517252
GEO: GSE61914
Filter development, replicate 2, hour 12
AX4_FD_r2_hr12


title: AX4_FD_r2_hr11

description:
GSM1517251
GEO: GSE61914
Filter development, replicate 2, hour 11
AX4_FD_r2_hr11


title: AX4_FD_r2_hr09

description:
GSM1517249
GEO: GSE61914
Filter development, replicate 2, hour 09
AX4_FD_r2_hr09


title: AX4_FD_r2_hr10

description:
GSM1517250
GEO: GSE61914
Filter development, replicate 2, hour 10
AX4_FD_r2_hr10


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB829TWV)

description:
https://www.encodeproject.org/experiments/ENCSR347NUR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR347NUR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB829TWV
fragmentation methods: none

tag: health state

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from T-cell (ENCLB987WPF)

description:
https://www.encodeproject.org/experiments/ENCSR343NGK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR343NGK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB987WPF
fragmentation methods: none

value: T-cell

value: male

tag: dev stage

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: AX4_FD_r2_hr07

description:
GSM1517247
GEO: GSE61914
Filter development, replicate 2, hour 07
AX4_FD_r2_hr07

value: WT


title: AX4_FD_r2_hr08

description:
GSM1517248
GEO: GSE61914
Filter development, replicate 2, hour 08
AX4_FD_r2_hr08


title: AX4_FD_r2_hr03

description:
GSM1517243
GEO: GSE61914
Filter development, replicate 2, hour 03
AX4_FD_r2_hr03


title: AX4_FD_r2_hr04

description:
GSM1517244
GEO: GSE61914
Filter development, replicate 2, hour 04
AX4_FD_r2_hr04


title: AX4_FD_r2_hr06

description:
GSM1517246
GEO: GSE61914
Filter development, replicate 2, hour 06
AX4_FD_r2_hr06


title: Mint-ChIP-seq from T-cell (ENCLB132KSJ)

description:
https://www.encodeproject.org/experiments/ENCSR343NGK/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR343NGK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB132KSJ
fragmentation methods: none

value: primary cell

tag: age


title: Mint-ChIP-seq from H9 (ENCLB305AZQ)

description:
https://www.encodeproject.org/experiments/ENCSR352HOU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR352HOU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR931GAK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305AZQ
fragmentation methods: none

value: cell line

value: WA09 ES cells

value: female

value: healthy

tag: lab

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: Control ChIP-seq from K562 (ENCLB856KRV)

description:
https://www.encodeproject.org/experiments/ENCSR906GHW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR906GHW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB856KRV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting GTF2I

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

tag: source

value: ATCC

value: ENCBS948GVT at ENCODE; https://www.encodeproject.org/ENCBS948GVT/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: AX4_FD_r2_hr02

description:
GSM1517242
GEO: GSE61914
Filter development, replicate 2, hour 02
AX4_FD_r2_hr02


title: AX4_FD_r2_hr16

description:
GSM1517254
GEO: GSE61914
Filter development, replicate 2, hour 16
AX4_FD_r2_hr16


title: AX4_FD_r2_hr01

description:
GSM1517241
GEO: GSE61914
Filter development, replicate 2, hour 01
AX4_FD_r2_hr01


title: AX4_FD_r2_hr00

description:
GSM1517240
GEO: GSE61914
Filter development, replicate 2, hour 00
AX4_FD_r2_hr00


title: AX4_FD_r1_hr24

description:
GSM1517239
GEO: GSE61914
Filter development, replicate 1, hour 24
AX4_FD_r1_hr24


title: AX4_FD_r1_hr22

description:
GSM1517238
GEO: GSE61914
Filter development, replicate 1, hour 22
AX4_FD_r1_hr22


title: Mint-ChIP-seq from T-cell (ENCLB504MCE)

description:
https://www.encodeproject.org/experiments/ENCSR343NGK/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR343NGK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504MCE
fragmentation methods: none

value: T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

tag: link


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB378NLU)

description:
https://www.encodeproject.org/experiments/ENCSR435MSB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR435MSB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034MTZ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB378NLU
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS512HTQ at ENCODE; https://www.encodeproject.org/ENCBS512HTQ/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB927ECX)

description:
https://www.encodeproject.org/experiments/ENCSR435MSB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR435MSB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034MTZ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927ECX
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500


title: AX4_FD_r1_hr20

description:
GSM1517237
GEO: GSE61914
Filter development, replicate 1, hour 20
AX4_FD_r1_hr20

value: WT


title: AX4_FD_r1_hr18

description:
GSM1517236
GEO: GSE61914
Filter development, replicate 1, hour 18
AX4_FD_r1_hr18


title: AX4_FD_r1_hr16

description:
GSM1517235
GEO: GSE61914
Filter development, replicate 1, hour 16
AX4_FD_r1_hr16


title: AX4_FD_r2_hr05

description:
GSM1517245
GEO: GSE61914
Filter development, replicate 2, hour 05
AX4_FD_r2_hr05


title: AX4_FD_r1_hr14

description:
GSM1517234
GEO: GSE61914
Filter development, replicate 1, hour 14
AX4_FD_r1_hr14


title: Control ChIP-seq from NCI-H929 (ENCLB336EAL)

description:
https://www.encodeproject.org/experiments/ENCSR698TWO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human NCI-H929
experiment encode accession: ENCSR698TWO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-03-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB336EAL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens NCI-H929 cell line

tag: line

value: cell line

value: female

value: IgAk myeloma

value: 62 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS896UQM at ENCODE; https://www.encodeproject.org/ENCBS896UQM/

value: Derived from ENCODE donor ENCDO220OYR; https://www.encodeproject.org/ENCDO220OYR/


title: AX4_FD_r1_hr12

description:
GSM1517233
GEO: GSE61914
Filter development, replicate 1, hour 12
AX4_FD_r1_hr12


title: AX4_FD_r1_hr10

description:
GSM1517231
GEO: GSE61914
Filter development, replicate 1, hour 10
AX4_FD_r1_hr10


title: AX4_FD_r1_hr11

description:
GSM1517232
GEO: GSE61914
Filter development, replicate 1, hour 11
AX4_FD_r1_hr11


title: AX4_FD_r1_hr06

description:
GSM1517227
GEO: GSE61914
Filter development, replicate 1, hour 06
AX4_FD_r1_hr06


title: AX4_FD_r1_hr08

description:
GSM1517229
GEO: GSE61914
Filter development, replicate 1, hour 08
AX4_FD_r1_hr08


title: AX4_FD_r1_hr07

description:
GSM1517228
GEO: GSE61914
Filter development, replicate 1, hour 07
AX4_FD_r1_hr07


title: Mint-ChIP-seq from endodermal cell (ENCLB650VQI)

description:
https://www.encodeproject.org/experiments/ENCSR531CWB/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR531CWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB650VQI
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) endodermal in vitro differentiated cells originated from endodermal cell

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB050FXX)

description:
https://www.encodeproject.org/experiments/ENCSR426RVC/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of naive thymus-derived CD8-positive, alpha-beta T cell originated from naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR426RVC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB050FXX

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS671UYD at ENCODE; https://www.encodeproject.org/ENCBS671UYD/

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


title: Mint-ChIP-seq from T-cell (ENCLB744CDW)

description:
https://www.encodeproject.org/experiments/ENCSR343NGK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR343NGK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744CDW
fragmentation methods: none

value: T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB202KKC)

description:
https://www.encodeproject.org/experiments/ENCSR426RVC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of naive thymus-derived CD8-positive, alpha-beta T cell originated from naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR426RVC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB202KKC

value: primary cell


title: AX4_FD_r1_hr03

description:
GSM1517224
GEO: GSE61914
Filter development, replicate 1, hour 03
AX4_FD_r1_hr03

value: WT


title: AX4_FD_r1_hr04

description:
GSM1517225
GEO: GSE61914
Filter development, replicate 1, hour 04
AX4_FD_r1_hr04


title: AX4_FD_r1_hr02

description:
GSM1517223
GEO: GSE61914
Filter development, replicate 1, hour 02
AX4_FD_r1_hr02


title: AX4_FD_r1_hr05

description:
GSM1517226
GEO: GSE61914
Filter development, replicate 1, hour 05
AX4_FD_r1_hr05


title: AX4_FD_r1_hr09

description:
GSM1517230
GEO: GSE61914
Filter development, replicate 1, hour 09
AX4_FD_r1_hr09


title: Mint-ChIP-seq from endodermal cell (ENCLB885ONA)

description:
https://www.encodeproject.org/experiments/ENCSR531CWB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR531CWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB885ONA
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/

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


title: Mint-ChIP-seq from activated T-cell (ENCLB375XGR)

description:
https://www.encodeproject.org/experiments/ENCSR530YQK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR530YQK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB375XGR
fragmentation methods: none

value: activated T-cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: male

value: adult

value: 38 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS693BEC at ENCODE; https://www.encodeproject.org/ENCBS693BEC/

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


title: Mint-ChIP-seq from endodermal cell (ENCLB596WRP)

description:
https://www.encodeproject.org/experiments/ENCSR531CWB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR531CWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB596WRP
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells


title: Mint-ChIP-seq from activated T-cell (ENCLB821OTA)

description:
https://www.encodeproject.org/experiments/ENCSR530YQK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR530YQK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB821OTA
fragmentation methods: none

value: primary cell

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/


title: Mint-ChIP-seq from activated T-cell (ENCLB398KLL)

description:
https://www.encodeproject.org/experiments/ENCSR530YQK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR530YQK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB398KLL
fragmentation methods: none


title: AX4_FD_r1_hr00

description:
GSM1517221
GEO: GSE61914
Filter development, replicate 1, hour 00
AX4_FD_r1_hr00

value: WT


title: Mint-ChIP-seq from activated T-cell (ENCLB410ACR)

description:
https://www.encodeproject.org/experiments/ENCSR530YQK/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K9me3 ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR530YQK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB410ACR
fragmentation methods: none


title: Control ChIP-seq from K562 (ENCLB181MLA)

description:
https://www.encodeproject.org/experiments/ENCSR682TOC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR682TOC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB181MLA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF518B

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS941SED at ENCODE; https://www.encodeproject.org/ENCBS941SED/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: AX4_FD_r1_hr01

description:
GSM1517222
GEO: GSE61914
Filter development, replicate 1, hour 01
AX4_FD_r1_hr01


title: Control ChIP-seq from A549 (ENCLB311QMO)

description:
https://www.encodeproject.org/experiments/ENCSR676KGV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR676KGV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB311QMO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting RARB

value: male

value: adult

value: 58 year

value: ENCBS315BZU at ENCODE; https://www.encodeproject.org/ENCBS315BZU/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: microRNA-seq from excitatory neuron (ENCLB155EAK)

description:
https://www.encodeproject.org/experiments/ENCSR425WZE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation PGP1 excitatory cortical neurons microRNA-seq from Mortazavi
experiment encode accession: ENCSR425WZE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-01-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB155EAK
size range: <30

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells, preserved by cryopreservation

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB726BLM)

description:
https://www.encodeproject.org/experiments/ENCSR421FPZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR421FPZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR521SOP
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726BLM
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

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

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/

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


title: Mint-ChIP-seq from endodermal cell (ENCLB572EEG)

description:
https://www.encodeproject.org/experiments/ENCSR531CWB/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR531CWB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572EEG
fragmentation methods: none

value: endodermal cell

value: WA09 derived endoderm cells

value: female

value: embryonic

value: 5 day

value: SESCC

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/

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


title: microRNA-seq from excitatory neuron (ENCLB403WPE)

description:
https://www.encodeproject.org/experiments/ENCSR425WZE/
***************
biological replicate number: 1
technical replicate number: 2
description: RNA Evaluation PGP1 excitatory cortical neurons microRNA-seq from Mortazavi
experiment encode accession: ENCSR425WZE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2020-01-24
lab: Ali Mortazavi, UCI
library encode accession: ENCLB403WPE
size range: <30

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: male

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

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


title: WGS from transverse colon (ENCLB659IQW)

description:
https://www.encodeproject.org/experiments/ENCSR420NDH/
***************
biological replicate number: 1
technical replicate number: 2
description: The data contained in this experiment correspond to Illumina-based whole genome shotgun sequencing of EN-TEX donor ENCDO271OUW, a 51 year old female. There are two libraries: PCR-based (9-cycle, ENCLB659IQW) and PCR-free (ENCLB898JVB), both sequenced on multiple lanes to a combined depth of ~ 60X in PE125 format.
experiment encode accession: ENCSR420NDH
assay title: WGS
assembly: GRCh38
encode release date: 2016-04-18
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB659IQW
fragmentation methods: see document

source_name: Homo sapiens transverse colon tissue female adult (51 year)

value: transverse colon

value: tissue

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 51 year

value: Thomas Gingeras, CSHL

value: ENCBS999VTF at ENCODE; https://www.encodeproject.org/ENCBS999VTF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB082DSB)

description:
https://www.encodeproject.org/experiments/ENCSR421FPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR421FPZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR521SOP
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB082DSB
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/

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


title: Control ChIP-seq from SK-N-SH (ENCLB021JZI)

description:
https://www.encodeproject.org/experiments/ENCSR670GWL/
***************
biological replicate number: 1
technical replicate number: 1
description: SK-N-SH immortalized cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing C-terminal eGFP-ZSCAN18 fusion protein.
experiment encode accession: ENCSR670GWL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB021JZI
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting ZSCAN18 treated with 6 uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

value: SK-N-SH cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZSCAN18.

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: 4 year

value: Michael Snyder, Stanford

value: Michael Snyder

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS169KNY at ENCODE; https://www.encodeproject.org/ENCBS169KNY/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: Mint-ChIP-seq from naive B cell (ENCLB282ISL)

description:
https://www.encodeproject.org/experiments/ENCSR530AVK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR530AVK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR163IRW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282ISL
fragmentation methods: none

source_name: Homo sapiens naive B primary cell with multiple sclerosis, preserved by cryopreservation

value: naive B cell

value: primary cell

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

value: not collected

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: ENCBS345AAH at ENCODE; https://www.encodeproject.org/ENCBS345AAH/

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


title: Mint-ChIP-seq from immature natural killer cell (ENCLB292DFL)

description:
https://www.encodeproject.org/experiments/ENCSR338LJG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR338LJG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB292DFL
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

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

value: healthy

value: unknown

value: David Hafler

value: ENCBS497KWS at ENCODE; https://www.encodeproject.org/ENCBS497KWS/

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


title: Mint-ChIP-seq from naive B cell (ENCLB785AUB)

description:
https://www.encodeproject.org/experiments/ENCSR530AVK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR530AVK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR163IRW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785AUB
fragmentation methods: none


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB958WAY)

description:
https://www.encodeproject.org/experiments/ENCSR334BPI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on CD4-positive, alpha-beta memory T cell male adult (43 years)
experiment encode accession: ENCSR334BPI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR817QVK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB958WAY
fragmentation methods: none

source_name: Homo sapiens male adult (43 years) CD4-positive, alpha-beta memory T primary cell

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

value: male

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS050OWF at ENCODE; https://www.encodeproject.org/ENCBS050OWF/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: Control ChIP-seq from lung (ENCLB129NND)

description:
https://www.encodeproject.org/experiments/ENCSR645ZNG/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse lung (fragmentation date 05-28-14)
experiment encode accession: ENCSR645ZNG
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB129NND
fragmentation methods: sonication (generic)

organism: Mus musculus

source_name: Mus musculus strain B6NCrl lung tissue postnatal (0 days)

value: lung

value: tissue

value: pulverized lungs pooled from multiple dissections of postnatal 0 day mice

value: postnatal

value: 0 day

value: not collected

value: Richard Myers, HAIB

value: ENCBS307DXQ at ENCODE; https://www.encodeproject.org/ENCBS307DXQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB499VKS)

description:
https://www.encodeproject.org/experiments/ENCSR333JIO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR333JIO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR674JPB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB499VKS
fragmentation methods: none

source_name: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 20 year

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS896OLN at ENCODE; https://www.encodeproject.org/ENCBS896OLN/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB477YRI)

description:
https://www.encodeproject.org/experiments/ENCSR334BPI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on CD4-positive, alpha-beta memory T cell male adult (43 years)
experiment encode accession: ENCSR334BPI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR817QVK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB477YRI
fragmentation methods: none

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

value: male

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta T cell (ENCLB396ZLT)

description:
https://www.encodeproject.org/experiments/ENCSR333JIO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (20 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR333JIO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR674JPB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB396ZLT
fragmentation methods: none


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB682ZIT)

description:
https://www.encodeproject.org/experiments/ENCSR331WMS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR331WMS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR899DXS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB682ZIT
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

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

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS067WEN at ENCODE; https://www.encodeproject.org/ENCBS067WEN/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB055VBF)

description:
https://www.encodeproject.org/experiments/ENCSR331WMS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR331WMS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR899DXS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB055VBF
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

value: not collected


title: Mint-ChIP-seq from T-cell (ENCLB867YSN)

description:
https://www.encodeproject.org/experiments/ENCSR330OUU/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR330OUU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB867YSN
fragmentation methods: none

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

value: T-cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: Control ChIP-seq from K562 (ENCLB414MTA)

description:
https://www.encodeproject.org/experiments/ENCSR673WPR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR673WPR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB414MTA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting GABPB2

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS708AHL at ENCODE; https://www.encodeproject.org/ENCBS708AHL/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control Mint-ChIP-seq from IgD-negative memory B cell (ENCLB082KJI)

description:
https://www.encodeproject.org/experiments/ENCSR519VQC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell
experiment encode accession: ENCSR519VQC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB082KJI

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

value: IgD-negative memory B cell

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

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS318ZNB at ENCODE; https://www.encodeproject.org/ENCBS318ZNB/

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


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB251KKJ)

description:
https://www.encodeproject.org/experiments/ENCSR521SOP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR521SOP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251KKJ
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

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

value: not collected

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/


title: Mint-ChIP-seq from T-cell (ENCLB785UTT)

description:
https://www.encodeproject.org/experiments/ENCSR330OUU/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR330OUU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785UTT
fragmentation methods: none

value: T-cell

value: male

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS038FPK at ENCODE; https://www.encodeproject.org/ENCBS038FPK/

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


title: Mint-ChIP-seq from T-cell (ENCLB667TXV)

description:
https://www.encodeproject.org/experiments/ENCSR330OUU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR330OUU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB667TXV
fragmentation methods: none


title: Control Mint-ChIP-seq from IgD-negative memory B cell (ENCLB331CLV)

description:
https://www.encodeproject.org/experiments/ENCSR519VQC/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of IgD-negative memory B cell originated from IgD-negative memory B cell
experiment encode accession: ENCSR519VQC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB331CLV

value: IgD-negative memory B cell

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

value: healthy

value: unknown


title: Mint-ChIP-seq from T-cell (ENCLB762ZAO)

description:
https://www.encodeproject.org/experiments/ENCSR330OUU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330OUU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB762ZAO
fragmentation methods: none


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB503SUK)

description:
https://www.encodeproject.org/experiments/ENCSR330CQU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq of CD4-positive, alpha-beta memory T cell originated from CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR330CQU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR131SAQ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503SUK
fragmentation methods: none

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

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

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

value: multiple sclerosis

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS702KJW at ENCODE; https://www.encodeproject.org/ENCBS702KJW/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB266QCS)

description:
https://www.encodeproject.org/experiments/ENCSR330CQU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq of CD4-positive, alpha-beta memory T cell originated from CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR330CQU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR131SAQ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB266QCS
fragmentation methods: none

value: primary cell

value: not collected


title: Control ChIP-seq from liver (ENCLB431KGQ)

description:
https://www.encodeproject.org/experiments/ENCSR270KSY/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on postnatal 0 day mouse liver (fragmentation date 05-28-14)
experiment encode accession: ENCSR270KSY
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2016-01-14
lab: Richard Myers, HAIB
library encode accession: ENCLB431KGQ
fragmentation methods: sonication (generic)

source_name: Mus musculus strain B6NCrl liver tissue postnatal (0 days)

value: liver

value: tissue

value: pulverized livers pooled from multiple dissections of postnatal 0 day mice

value: postnatal

value: 0 day

value: Richard Myers, HAIB

value: ENCBS152FNH at ENCODE; https://www.encodeproject.org/ENCBS152FNH/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: total RNA-seq from macrophage (ENCLB991BZH)

description:
https://www.encodeproject.org/experiments/ENCSR171WZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Ribo depletion RNA-seq on chromatin fraction RNA which is part of BMDM cell pre-treated with 100 ng/ml Lipid A 12 hours, washed out for 12 hours, and stimulated with 100 ng/ml Lipid A for 35 minute.
experiment encode accession: ENCSR171WZJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2018-11-20
lab: Alexander Hoffmann, UCLA
library encode accession: ENCLB991BZH
fragmentation methods: see document
size range: 250-400
nucleic acid starting quantity: 1
nucleic acid starting quantity units: µg

source_name: Mus musculus strain C57BL/6J macrophage primary cell chromatin fraction

value: macrophage

value: unknown

value: Alexander Hoffmann, UCLA

value: Alexander Hoffmann

tag: subcellular fraction term name

value: chromatin

value: ENCBS037SLJ at ENCODE; https://www.encodeproject.org/ENCBS037SLJ/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: WGS from transverse colon (ENCLB506OMA)

description:
https://www.encodeproject.org/experiments/ENCSR410ALS/
***************
biological replicate number: 1
technical replicate number: 1
description: The library contained in this Experiment corresponds to 10X Genomics Chromium prepared WGS.
experiment encode accession: ENCSR410ALS
assay title: WGS
assembly: GRCh38
encode release date: 2017-08-01
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB506OMA

source_name: Homo sapiens transverse colon tissue male adult (37 years)

value: transverse colon

value: Transverse colon tissue aliquot received by the Gingeras lab to conduct RNA-Seq assays on.

value: 37 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS767MGS at ENCODE; https://www.encodeproject.org/ENCBS767MGS/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB485MHB)

description:
https://www.encodeproject.org/experiments/ENCSR338LJG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR338LJG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB485MHB
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

value: primary cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS497KWS at ENCODE; https://www.encodeproject.org/ENCBS497KWS/

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB103BCG)

description:
https://www.encodeproject.org/experiments/ENCSR516CKJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR516CKJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR231SVU
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB103BCG
fragmentation methods: none

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

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

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

value: multiple sclerosis

value: unknown

value: ENCBS347VRW at ENCODE; https://www.encodeproject.org/ENCBS347VRW/

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB664NUG)

description:
https://www.encodeproject.org/experiments/ENCSR410QNO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR410QNO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB664NUG
fragmentation methods: none

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

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

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


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB739ROD)

description:
https://www.encodeproject.org/experiments/ENCSR322VEH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR322VEH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519VQC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB739ROD
fragmentation methods: none

value: IgD-negative memory B cell

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

value: ENCBS318ZNB at ENCODE; https://www.encodeproject.org/ENCBS318ZNB/


title: ApcMin/+/14-3-3σ-/- adenoma 12176

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

description: NG-23101_12176ApcMin_SfnKO_lib365288_6590_6

data_processing:
CLC Genomics Workbench 20 software was used
Sequenced reads were mapped to mm10 genome using CLC Workbench default parameters
Reads were normalized using RUVs
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with RUVs normalized count values for each Sample

source_name: ApcMin/+/14-3-3σ-/- adenoma

extract_protocol:
Total RNA from murine adenomas was isolated using the RNeasy Plus Total RNA Isolation Kit (Qiagen) according to manufacturer’s instructions.
Strand-specific cDNA libraries were prepared using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: 144 days

tag: tissue

value: small intestine adenoma


title: ApcMin/+/14-3-3σ-/- adenoma 12174

description: NG-23101_12174ApcMin_SfnKO_lib365287_6590_5

value: 144 dyas


title: ApcMin/+ adenoma 11623

description: NG-23849_11623ApcMin_SfnWT_lib392224_6770_1

source_name: ApcMin/+ adenoma

value: ApcMin/+

value: 256 days


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB859XDY)

description:
https://www.encodeproject.org/experiments/ENCSR322VEH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR322VEH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR519VQC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB859XDY
fragmentation methods: none

value: primary cell

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

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


title: ApcMin/+ adenoma 11545

description: NG-23101_11545ApcMin_SfnWT_lib365284_6590_5

value: 266 days


title: ApcMin/+ adenoma 11618

description: NG-23849_11618ApcMin_SfnWT_lib392225_6770_1


title: Control Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB290CNO)

description:
https://www.encodeproject.org/experiments/ENCSR521SOP/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR521SOP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB290CNO
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

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

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

value: unknown

value: ENCBS892TKW at ENCODE; https://www.encodeproject.org/ENCBS892TKW/


title: WGS from HepG2 (ENCLB152EFM)

description:
https://www.encodeproject.org/experiments/ENCSR319QHO/
***************
biological replicate number: 1
technical replicate number: 1
description: The data contained in this Experiment come from 10X Chromium Genomics WGS of HepG2 cell line
experiment encode accession: ENCSR319QHO
assay title: WGS
assembly: hg19
encode release date: 2019-02-26
lab: Alexander Urban, Stanford
library encode accession: ENCLB152EFM
instrument models: Illumina NextSeq 500,HiSeq X Ten

source_name: Homo sapiens HepG2 cell line

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Alexander Urban, Stanford

value: Michael Snyder

tag: passage number

value: ENCBS760ISV at ENCODE; https://www.encodeproject.org/ENCBS760ISV/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: 3d_off_dox_1

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

data_processing:
Data quality was queried using a suite of custom perl and R scriptsto calculate the mean quality score at each position read as well as calculate the relative abundance of each nucleotide.
Following quality control, sequences were trimmed for adaptor sequence and were matched to ensure that the same read was present in both the forward and reverse fastq files.
Reads were mapped against Bowtie build index of NCBI 37.1 mouse reference genome using Tophat
Cufflinks was used for quantitation and normalization
Cuffcompare/cuffdiff was used to identify differentially expressed genes and splicing events
Genome_build: NCBI 37.1
Supplementary_files_format_and_content: Excel file containing log2FC expression results

source_name: heart tissue

extract_protocol:
RNA was extracted using a Qiagen kit according to manufacturer's instructions.
Total RNA samples were sent to Viginia Bioinformatics Institute at Virginia Tech for library preparation (poly A enrichment) and Illumina-based paired-end sequencing.

value: heart ventricles

tag: strain

tag: gender

value: 6-8 weeks

tag: treatment

value: 3 days off doxycycline


title: 3d_off_dox_2


title: 3d_off_dox_3


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB080PKX)

description:
https://www.encodeproject.org/experiments/ENCSR314IFB/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR314IFB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB080PKX
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

value: healthy

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS497KWS at ENCODE; https://www.encodeproject.org/ENCBS497KWS/

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


title: on_dox_1

value: male

tag: age

value: on doxycycline


title: on_dox_2


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB298IFV)

description:
https://www.encodeproject.org/experiments/ENCSR315MYP/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR315MYP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283LWF
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB298IFV
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

tag: antibody

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

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

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: lab

value: ENCBS812ZCI at ENCODE; https://www.encodeproject.org/ENCBS812ZCI/

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


title: on_dox_3

value: heart ventricles

value: 6-8 weeks


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB537WEO)

description:
https://www.encodeproject.org/experiments/ENCSR315MYP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR315MYP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR283LWF
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB537WEO
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

tag: source

tag: link


title: ApcMin/+/14-3-3σ-/- adenoma 12193

description: NG-23101_12193ApcMin_SfnKO_lib365289_6590_6

tag: strain background

value: 148 days

value: small intestine adenoma


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB647UGC)

description:
https://www.encodeproject.org/experiments/ENCSR314IFB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR314IFB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB647UGC
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

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

value: not collected

value: healthy

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB296IYX)

description:
https://www.encodeproject.org/experiments/ENCSR516CKJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR516CKJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR231SVU
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB296IYX
fragmentation methods: none

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

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

value: David Hafler

value: ENCBS347VRW at ENCODE; https://www.encodeproject.org/ENCBS347VRW/

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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB164MFE)

description:
https://www.encodeproject.org/experiments/ENCSR410QNO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR410QNO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR310ZGH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB164MFE
fragmentation methods: none

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

value: unknown

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

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


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB665YWI)

description:
https://www.encodeproject.org/experiments/ENCSR310ZGH/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR310ZGH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB665YWI

value: primary cell


title: ApcMin/+/14-3-3σ-/- adenoma 11624

description: NG-23101_11624ApcMin_SfnKO_lib365286_6590_5

tag: genotype/variation

value: 146 days


title: ApcMin/+ adenoma 11319

description: NG-23101_11319ApcMin_SfnWT_lib365283_6590_5

value: ApcMin/+

value: 282 days

tag: tissue

value: small intestine adenoma


title: Mint-ChIP-seq from activated T-cell (ENCLB515THY)

description:
https://www.encodeproject.org/experiments/ENCSR407QDX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR407QDX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515THY
fragmentation methods: none

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell

value: activated T-cell

value: Activated with 1:1 ratio of CD3, CD28 beads for 24 hours by Stam lab at Altius.

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS833ENP at ENCODE; https://www.encodeproject.org/ENCBS833ENP/

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


title: Mint-ChIP-seq from activated T-cell (ENCLB469PWB)

description:
https://www.encodeproject.org/experiments/ENCSR407QDX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR407QDX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469PWB
fragmentation methods: none

value: Bradley Bernstein, Broad

value: ENCBS693BEC at ENCODE; https://www.encodeproject.org/ENCBS693BEC/


title: Mint-ChIP-seq from activated T-cell (ENCLB754CHP)

description:
https://www.encodeproject.org/experiments/ENCSR407QDX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR407QDX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB754CHP
fragmentation methods: none


title: Control Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB788XQJ)

description:
https://www.encodeproject.org/experiments/ENCSR310ZGH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR310ZGH
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB788XQJ

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

value: not collected

value: healthy

value: unknown

value: David Hafler

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


title: Mint-ChIP-seq from activated T-cell (ENCLB358PER)

description:
https://www.encodeproject.org/experiments/ENCSR407QDX/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac ChIP-seq on activated T-cell male adult (38 years)
experiment encode accession: ENCSR407QDX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR897COL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB358PER
fragmentation methods: none

value: primary cell


title: Control ChIP-seq from WTC11 (ENCLB616XYF)

description:
https://www.encodeproject.org/experiments/ENCSR712UWN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR712UWN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB616XYF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line

tag: line

value: cell line

value: 30 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS078VZT at ENCODE; https://www.encodeproject.org/ENCBS078VZT/

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


title: Mint-ChIP-seq from astrocyte (ENCLB842RSJ)

description:
https://www.encodeproject.org/experiments/ENCSR510CNG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human PGP1 derived astrocyte
experiment encode accession: ENCSR510CNG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731CEI
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB842RSJ
fragmentation methods: none

source_name: Homo sapiens male adult (53 years) astrocyte in vitro differentiated cells originated from astrocyte, preserved by cryopreservation

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: adult

value: 53 year

value: George Church

value: ENCBS534DJA at ENCODE; https://www.encodeproject.org/ENCBS534DJA/

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


title: Mint-ChIP-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB646JIL)

description:
https://www.encodeproject.org/experiments/ENCSR303SQG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (30 years) treated with 10 ng
experiment encode accession: ENCSR303SQG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466PQY
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB646JIL
fragmentation methods: none

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: Yijun Ruan, JAX

value: AllCells

tag: treatments

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 ChIP-seq from K562 (ENCLB851DUS)

description:
https://www.encodeproject.org/experiments/ENCSR706XZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR706XZJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB851DUS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ELF2

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS084AQI at ENCODE; https://www.encodeproject.org/ENCBS084AQI/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: Control ChIP-seq from K562 (ENCLB800ZYD)

description:
https://www.encodeproject.org/experiments/ENCSR706RMI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR706RMI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB800ZYD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting RHOXF2B

value: adult

value: ENCBS847TGF at ENCODE; https://www.encodeproject.org/ENCBS847TGF/


title: Mint-ChIP-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB185TUX)

description:
https://www.encodeproject.org/experiments/ENCSR303SQG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq of activated CD8-positive, alpha-beta T cell male adult (30 years) treated with 10 ng
experiment encode accession: ENCSR303SQG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR466PQY
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB185TUX
fragmentation methods: none

value: primary cell

value: male

value: 30 year


title: Mint-ChIP-seq from astrocyte (ENCLB857LFL)

description:
https://www.encodeproject.org/experiments/ENCSR510CNG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human PGP1 derived astrocyte
experiment encode accession: ENCSR510CNG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731CEI
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB857LFL
fragmentation methods: none

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS534DJA at ENCODE; https://www.encodeproject.org/ENCBS534DJA/

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB718KUP)

description:
https://www.encodeproject.org/experiments/ENCSR507CIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR507CIJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB718KUP
fragmentation methods: none

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

value: not collected

value: healthy

value: unknown

value: David Hafler

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

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


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB699RDH)

description:
https://www.encodeproject.org/experiments/ENCSR507CIJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR507CIJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR688UBO
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB699RDH
fragmentation methods: none

value: primary cell


title: ELST#17

type: genomic

city: Berlin

first: Felix

last: Thierfelder

address: Charitépl. 1

institute: Charite

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip and Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
using R (version 4.0.2) minfi_1.36.0 package
arrays from different plattforms were combined using combineArrays function; beta values were normalized using minfi PreprocessFunnorm function; detection p-values was calculated using detectionP function; for methylated and unmethylated signals preprocessIllumina function was used for normalization

label: Cy3, Cy5

source_name: endolymphatic sac tumors

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tumor samples using Tissue DNA Purification Kit (Promega) according to the manufacturer´s protocol

tag: gender

value: f

value: endolymphatic sac tumors

tag: group

value: von Hippel-Lindau syndrome associated


title: Control ChIP-seq from K562 (ENCLB814DAW)

description:
https://www.encodeproject.org/experiments/ENCSR705NCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR705NCQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB814DAW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF551

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS339ETK at ENCODE; https://www.encodeproject.org/ENCBS339ETK/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ELST#22


title: ELST#21

value: m


title: ELST#20


title: ELST#18


title: ELST#11

value: sporadic


title: ELST#12


title: ELST#9