title: Mint-ChIP-seq from GM23338 (ENCLB004STF)

description:
https://www.encodeproject.org/experiments/ENCSR370JJY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR370JJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB004STF
fragmentation methods: none

value: cell line

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB660ULQ)

status: Public on Jun 15 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR116FVG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR116FVG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR034MTZ
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB660ULQ
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000,Illumina HiSeq 2500

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: description

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

tag: biosample encode accession

tag: Sex

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

tag: link

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 B cell (ENCLB180KBZ)

description:
https://www.encodeproject.org/experiments/ENCSR115FGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR115FGJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR499CKV
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB180KBZ
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

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

value: naive B cell

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

value: healthy

value: ENCBS644KFM at ENCODE; https://www.encodeproject.org/ENCBS644KFM/

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


title: Control ChIP-seq from K562 (ENCLB895ZTX)

description:
https://www.encodeproject.org/experiments/ENCSR207GLV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR207GLV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB895ZTX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting MBD1

tag: line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS764GDV at ENCODE; https://www.encodeproject.org/ENCBS764GDV/

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


title: Mint-ChIP-seq from naive B cell (ENCLB273JIL)

description:
https://www.encodeproject.org/experiments/ENCSR115FGJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR115FGJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR499CKV
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB273JIL
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500,Illumina NovaSeq 6000

value: primary cell

value: not collected

value: unknown

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from GM23338 (ENCLB703RKB)

description:
https://www.encodeproject.org/experiments/ENCSR370JJY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR370JJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB703RKB
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens GM23338 cell line

value: cell line

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

value: male

value: Paola Arlotta

value: ENCBS695QJS at ENCODE; https://www.encodeproject.org/ENCBS695QJS/

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


title: Mint-ChIP-seq from astrocyte (ENCLB999GKP)

description:
https://www.encodeproject.org/experiments/ENCSR020LAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived astrocyte
experiment encode accession: ENCSR020LAQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR731CEI
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB999GKP
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: George Church

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB622SXF)

description:
https://www.encodeproject.org/experiments/ENCSR112KIE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR112KIE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR622ZKD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622SXF
fragmentation methods: none

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

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

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

value: healthy

value: David Hafler

value: ENCBS235RVH at ENCODE; https://www.encodeproject.org/ENCBS235RVH/

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


title: Mint-ChIP-seq from GM23338 (ENCLB943UZR)

description:
https://www.encodeproject.org/experiments/ENCSR370JJY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR370JJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2020-07-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB943UZR
fragmentation methods: none

value: cell line

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB313UBV)

description:
https://www.encodeproject.org/experiments/ENCSR112KIE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR112KIE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR622ZKD
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB313UBV
fragmentation methods: none

value: primary cell

value: not collected

value: unknown


title: Mint-ChIP-seq from endodermal cell (ENCLB954CTS)

description:
https://www.encodeproject.org/experiments/ENCSR110OND/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR110OND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB954CTS
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: female

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 endodermal cell (ENCLB492NQB)

description:
https://www.encodeproject.org/experiments/ENCSR110OND/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR110OND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB492NQB
fragmentation methods: none

value: healthy

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


title: Control ChIP-seq from K562 (ENCLB998XIQ)

description:
https://www.encodeproject.org/experiments/ENCSR004LZA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR004LZA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB998XIQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting HMG20B

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS670TBR at ENCODE; https://www.encodeproject.org/ENCBS670TBR/

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


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB089WKR)

description:
https://www.encodeproject.org/experiments/ENCSR105REF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105REF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR761HQT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089WKR
fragmentation methods: none

source_name: Homo sapiens male adult (30 years) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: male

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS845PJM at ENCODE; https://www.encodeproject.org/ENCBS845PJM/

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB062HCW)

description:
https://www.encodeproject.org/experiments/ENCSR209TVI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq of CD8-positive, alpha-beta T cell male adult (21 years)
experiment encode accession: ENCSR209TVI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR820SXH
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062HCW
fragmentation methods: none

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

value: CD8-positive, alpha-beta T cell

value: 21 year

value: ENCBS832HZD at ENCODE; https://www.encodeproject.org/ENCBS832HZD/

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


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB435ZZJ)

description:
https://www.encodeproject.org/experiments/ENCSR365IQY/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR365IQY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB435ZZJ
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS747UFJ at ENCODE; https://www.encodeproject.org/ENCBS747UFJ/

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


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB136FPL)

description:
https://www.encodeproject.org/experiments/ENCSR365IQY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR365IQY
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB136FPL
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: primary cell


title: 21-0143_102R3

city: Columbus

first: Megann

middle: A.

last: Boone

state: OH

address: 700 Children's Drive, WA5011

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with a cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain: EF DBD+.
102_comb.bw

library_source: transcriptomic

data_processing:
FASTQC and Multiqc were used for raw sequence quality control.
Trim_galore was used to trim low-quality and overrepresented sequences.
Two-pass STAR appraoch (STAR version 2.5.2b) was used to align sequences to hg19 human reference genome.
RSeQC was used to evaluate post-mapping sequence quality.
DESeq2 was used to identify different analysis of genes.
Genome_build: hg19
Supplementary_files_format_and_content: Samples were pooled together after normalization to background and combined bigwig files were generated to depict expression of RNA-sequencing reads.

molecule: total RNA

growth_protocol: HEK-293EBNA cells were seeded at 50-70% confluency and left to adhere overnight.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and gDNA Eliminator columns (Qiagen) were used to remove residual genomic DNA. 3 ug of total RNA was used for library prep.
TruSeq Stranded mRNA Kit

treatment_protocol: HEK-293EBNA cells were transfected with cDNA-containing vectors, including an Empty Vector (197) control, type IV EWS/FLI (714), EWS/FLI containing just the DNA-binding domain of FLI (EF DBD; 85), and EWS/FLI containing a slightly larger portion of the FLI protein (EF DBD+; 102). Cells were collected 48 hours after transfection. Whole cell total RNA was extracted using a Qiagen RNeasy Extraction kit and genomic DNA was removed uisng Qiagen gDNA Eliminator columns.

tag: cell line

tag: transfection

value: cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain:EF DBD+


title: Mint-ChIP-seq from CD8-positive naive resting alpha-beta T cell (ENCLB116YCG)

description:
https://www.encodeproject.org/experiments/ENCSR105REF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR105REF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR761HQT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB116YCG
fragmentation methods: none

value: male

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS845PJM at ENCODE; https://www.encodeproject.org/ENCBS845PJM/


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB657KMP)

description:
https://www.encodeproject.org/experiments/ENCSR204EXQ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR204EXQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB657KMP

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

value: female

value: embryonic

value: 5 day

value: SESCC

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/

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


title: 21-0141_714R3

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with a cDNA vector containing full-length "type IV" EWS/FLI.
714_comb.bw


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB905AKK)

description:
https://www.encodeproject.org/experiments/ENCSR204EXQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR204EXQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB905AKK
fragmentation methods: none

value: healthy

value: Bradley Bernstein, Broad

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


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB339NIL)

description:
https://www.encodeproject.org/experiments/ENCSR204EXQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR204EXQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB339NIL
fragmentation methods: none


title: Mint-ChIP-seq from immature natural killer cell (ENCLB305IJY)

description:
https://www.encodeproject.org/experiments/ENCSR442OSV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR442OSV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305IJY
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

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

value: not collected

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 endodermal cell (ENCLB115CIQ)

description:
https://www.encodeproject.org/experiments/ENCSR110OND/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR110OND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB115CIQ
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

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


title: 21-0138_85R2

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with a cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain: EF DBD.
85_comb.bw

value: cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain:EF DBD


title: 21-0142_85R3


title: 21-0139_102R2

value: cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain:EF DBD+


title: Mint-ChIP-seq from type B pancreatic cell (ENCLB891IQD)

description:
https://www.encodeproject.org/experiments/ENCSR204EXQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR204EXQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR380ZKL
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB891IQD

value: type B pancreatic cell

value: WA09 derived insulin producing beta-like cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/

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


title: 21-0136_197R2

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with an Empty Vector control vector.
197_comb.bw

value: Empty Vector


title: Mint-ChIP-seq from T-cell (ENCLB555QAP)

description:
https://www.encodeproject.org/experiments/ENCSR006CYO/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27me3 Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR006CYO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB555QAP
fragmentation methods: none

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

value: T-cell

value: primary 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 (ENCLB533DZF)

description:
https://www.encodeproject.org/experiments/ENCSR006CYO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR006CYO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB533DZF
fragmentation methods: none


title: Mint-ChIP-seq from T-cell (ENCLB857BPE)

description:
https://www.encodeproject.org/experiments/ENCSR006CYO/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K27me3 Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR006CYO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB857BPE
fragmentation methods: none


title: 21-0137_714R2

value: cDNA vector containing full-length "type IV" EWS/FLI


title: Mint-ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB800FSC)

description:
https://www.encodeproject.org/experiments/ENCSR209TVI/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq of CD8-positive, alpha-beta T cell male adult (21 years)
experiment encode accession: ENCSR209TVI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR820SXH
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800FSC
fragmentation methods: none

value: CD8-positive, alpha-beta T cell

value: 21 year

value: Yijun Ruan, JAX

value: ENCBS832HZD at ENCODE; https://www.encodeproject.org/ENCBS832HZD/

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


title: Mint-ChIP-seq from naive B cell (ENCLB459NCI)

description:
https://www.encodeproject.org/experiments/ENCSR440ZMH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR440ZMH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR499CKV
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB459NCI
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: naive B cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS644KFM at ENCODE; https://www.encodeproject.org/ENCBS644KFM/

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


title: Mint-ChIP-seq from endodermal cell (ENCLB491ZFJ)

description:
https://www.encodeproject.org/experiments/ENCSR110OND/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR110OND
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB491ZFJ
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

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: 21-0132_197R1

value: Empty Vector


title: 21-0133_714R1

value: cDNA vector containing full-length "type IV" EWS/FLI


title: 21-0135_102R1

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with a cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain: EF DBD+.
102_comb.bw

value: cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain:EF DBD+


title: Mint-ChIP-seq from endothelial cell (ENCLB222WCE)

description:
https://www.encodeproject.org/experiments/ENCSR436KET/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived endothelial cell
experiment encode accession: ENCSR436KET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR759ZAX
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB222WCE
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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

value: endothelial cell

value: PGP1 derived endothelial cells

value: male

value: adult

value: 53 year

value: George Church

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB924BRT)

description:
https://www.encodeproject.org/experiments/ENCSR005BTU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR005BTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546UUS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB924BRT
fragmentation methods: none

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

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS872QPK at ENCODE; https://www.encodeproject.org/ENCBS872QPK/

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


title: Mint-ChIP-seq from endothelial cell (ENCLB917ELO)

description:
https://www.encodeproject.org/experiments/ENCSR436KET/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived endothelial cell
experiment encode accession: ENCSR436KET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR759ZAX
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB917ELO
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: endothelial cell

value: in vitro differentiated cells


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB853GOM)

description:
https://www.encodeproject.org/experiments/ENCSR532PXR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive thymus-derived CD4-positive, alpha-beta T cell
experiment encode accession: ENCSR532PXR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR899DXS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB853GOM
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

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

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


title: 21-0162_DBDplusR3

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ (DBDplus)) was expressed.
DBDplus_comb.bw

source_name: A673 cells

growth_protocol: Ewing sarcoma cells (A673) were seeded at 50-70% confluency and left to adhere overnight.

treatment_protocol: Endogenous EWS/FLI protein was knocked down in A673 cells using an shRNA targeting the 3'-UTR of the native transcript (iEF). cDNA constructs were used to rescue cells with empty vector control (Empty Vector), wild-type EWS/FLI (EF) cDNA, or one of four mutant EWS/FLI constructs (EF DBD, EF DBD+, EF DBD+ DN, or EF DBD+ DC). Antibiotic selection was used to select for cells expressing these constructs and cells were collected after 8 days.  Whole cell total RNA was extracted using a Qiagen RNeasy Extraction kit and genomic DNA was removed uisng Qiagen gDNA Eliminator columns.

tag: expression

value: EWS/FLI cDNA mutant (EF DBD+ (DBDplus))


title: Control Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB212WKG)

description:
https://www.encodeproject.org/experiments/ENCSR201SEO/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with 10 ng
experiment encode accession: ENCSR201SEO
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB212WKG

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: male

value: adult

value: 43 year

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: ENCBS677HEG at ENCODE; https://www.encodeproject.org/ENCBS677HEG/

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


title: Control Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB804OCW)

description:
https://www.encodeproject.org/experiments/ENCSR201SEO/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with 10 ng
experiment encode accession: ENCSR201SEO
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2021-04-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB804OCW

value: primary cell


title: Control Mint-ChIP-seq from T-cell (ENCLB415QBQ)

description:
https://www.encodeproject.org/experiments/ENCSR203XDG/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on T-cell male adult (38 years)
experiment encode accession: ENCSR203XDG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB415QBQ

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

value: T-cell

value: CD3+ unactivated cells from Stam Lab at Altius.

value: 38 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS059XUY at ENCODE; https://www.encodeproject.org/ENCBS059XUY/

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


title: 21-0161_DBDR3

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD (DBD)) was expressed.
DBD_comb.bw

value: EWS/FLI cDNA mutant (EF DBD (DBD))


title: 21-0155_DBDplusR2

value: EWS/FLI cDNA mutant (EF DBD+ (DBDplus))


title: 21-0157_DBDCR2

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ DC (DBDC)) was expressed.
DBDC_comb.bw

value: EWS/FLI cDNA mutant (EF DBD+ DC (DBDC))


title: 21-0140_197R3

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with an Empty Vector control vector.
197_comb.bw

value: Empty Vector


title: 21-0152_197R2

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down.
197_comb.bw


title: 21-0163_DBDNR3

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ DN (DBDN)) was expressed.
DBDN_comb.bw

value: EWS/FLI cDNA mutant (EF DBD+ DN (DBDN))


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB092FSV)

description:
https://www.encodeproject.org/experiments/ENCSR005BTU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive thymus-derived CD8-positive, alpha-beta T cell
experiment encode accession: ENCSR005BTU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR546UUS
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB092FSV
fragmentation methods: none

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS872QPK at ENCODE; https://www.encodeproject.org/ENCBS872QPK/

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


title: 21-0153_714R2

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (EF(714)) was expressed.
714_comb.bw

value: EWS/FLI cDNA (EF(714))


title: Mint-ChIP-seq from endodermal cell (ENCLB182YXF)

description:
https://www.encodeproject.org/experiments/ENCSR102GPT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR102GPT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182YXF
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

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

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


title: 21-0150_DBDCR1

value: EWS/FLI cDNA mutant (EF DBD+ DC (DBDC))


title: Control Mint-ChIP-seq from T-cell (ENCLB805VCK)

description:
https://www.encodeproject.org/experiments/ENCSR203XDG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on T-cell male adult (38 years)
experiment encode accession: ENCSR203XDG
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB805VCK

value: T-cell

value: primary cell

value: CD3+ unactivated cells from Stam Lab at Altius.

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos

value: ENCBS059XUY at ENCODE; https://www.encodeproject.org/ENCBS059XUY/

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


title: Mint-ChIP-seq from endodermal cell (ENCLB251RZY)

description:
https://www.encodeproject.org/experiments/ENCSR102GPT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR102GPT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251RZY
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: healthy


title: Mint-ChIP-seq from naive B cell (ENCLB873WMX)

description:
https://www.encodeproject.org/experiments/ENCSR440ZMH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR440ZMH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR499CKV
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB873WMX
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

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

value: naive B cell

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

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS644KFM at ENCODE; https://www.encodeproject.org/ENCBS644KFM/

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


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB355MFO)

description:
https://www.encodeproject.org/experiments/ENCSR003SWN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR003SWN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB355MFO
fragmentation methods: none

source_name: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: adult

value: 43 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS514SPI at ENCODE; https://www.encodeproject.org/ENCBS514SPI/

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


title: 21-0154_DBDR2

value: EWS/FLI cDNA mutant (EF DBD (DBD))


title: 21-0164_DBDCR3

value: EWS/FLI cDNA mutant (EF DBD+ DC (DBDC))


title: Mint-ChIP-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB943WYN)

description:
https://www.encodeproject.org/experiments/ENCSR003SWN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR003SWN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR176HLK
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB943WYN
fragmentation methods: none


title: 21-0159_197R3


title: 21-0156_DBDNR2

value: EWS/FLI cDNA mutant (EF DBD+ DN (DBDN))


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB101CAA)

description:
https://www.encodeproject.org/experiments/ENCSR417AIG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR417AIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365IQY
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB101CAA
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: healthy

value: unknown

value: ENCBS747UFJ at ENCODE; https://www.encodeproject.org/ENCBS747UFJ/

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


title: Mint-ChIP-seq from endodermal cell (ENCLB888CMY)

description:
https://www.encodeproject.org/experiments/ENCSR102GPT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR102GPT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB888CMY
fragmentation methods: none

value: endodermal cell

value: in vitro differentiated cells

value: WA09 derived endoderm cells

value: female

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

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

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


title: Mint-ChIP-seq from endodermal cell (ENCLB659DEA)

description:
https://www.encodeproject.org/experiments/ENCSR102GPT/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human H9 derived endodermal cell
experiment encode accession: ENCSR102GPT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR901NYG
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB659DEA
fragmentation methods: none


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB757BKX)

description:
https://www.encodeproject.org/experiments/ENCSR002UMT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on CD4-positive, alpha-beta memory T cell male adult (43 years)
experiment encode accession: ENCSR002UMT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR817QVK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB757BKX
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: primary 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: 21-0147_DBDR1

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD (DBD)) was expressed.
DBD_comb.bw

value: EWS/FLI cDNA mutant (EF DBD (DBD))


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB021GQX)

description:
https://www.encodeproject.org/experiments/ENCSR101USF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101USF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR426RVC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB021GQX
fragmentation methods: none

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

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: 21-0145_197R1


title: 21-0148_DBDplusR1

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ (DBDplus)) was expressed.
DBDplus_comb.bw

value: EWS/FLI cDNA mutant (EF DBD+ (DBDplus))


title: 21-0134_85R1

description:
RNA-sequencing was performed on HEK-293EBNA cells transfected with a cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain: EF DBD.
85_comb.bw

value: cDNA vector containing a mutant version of EWS/FLI with deletions of the FLI domain:EF DBD


title: Mint-ChIP-seq from T-cell (ENCLB568UQL)

description:
https://www.encodeproject.org/experiments/ENCSR006CYO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq of T-cell male adult (42 years)
experiment encode accession: ENCSR006CYO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR445KDW
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB568UQL
fragmentation methods: none

value: T-cell

value: primary cell

value: male

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: 21-0149_DBDNR1

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ DN (DBDN)) was expressed.
DBDN_comb.bw

value: EWS/FLI cDNA mutant (EF DBD+ DN (DBDN))


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB408TOK)

description:
https://www.encodeproject.org/experiments/ENCSR417AIG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR417AIG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365IQY
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB408TOK
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: CD14-positive monocyte

value: Monocyte CD3- CD14+ CD19-

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS747UFJ at ENCODE; https://www.encodeproject.org/ENCBS747UFJ/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB828WRI)

description:
https://www.encodeproject.org/experiments/ENCSR002UMT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on CD4-positive, alpha-beta memory T cell male adult (43 years)
experiment encode accession: ENCSR002UMT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR817QVK
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB828WRI
fragmentation methods: none

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

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: Mint-ChIP-seq from excitatory neuron (ENCLB634YEI)

description:
https://www.encodeproject.org/experiments/ENCSR327BWK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR327BWK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB634YEI
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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: male

value: 53 year

value: George Church

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

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


title: 21-0146_714R1

description:
RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (EF(714)) was expressed.
714_comb.bw

value: EWS/FLI cDNA (EF(714))


title: 19-1252_102R2: iEF + EF DBD+ (102) Replicate 2

description: RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ (102)) was expressed.

data_processing:
FASTQC and Multiqc were used for raw sequence quality control.
Trim_galore was used to trim low-quality and overrepresented sequences.
Two-pass STAR appraoch (STAR version 2.5.2b) was used to align sequences to hg19 human reference genome.
RSeQC was used to evaluate post-mapping sequence quality.
DESeq2 was used to identify different analysis of genes.
Genome_build: hg19
Supplementary_files_format_and_content: fastq files include raw reads of each samples; bigwig files are aligned, trimmed, normalized reads combined for each samples from separate replicates.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and gDNA Eliminator columns (Qiagen) were used to remove residual genomic DNA.  3 ug of total RNA was used for library prep.
TruSeq Stranded mRNA Kit

treatment_protocol: Endogenous EWS/FLI protein was knocked down in A673 cells using an shRNA targeting the 3'-UTR of the native transcript (iEF); iLuc (a shRNA targeting the firefly luciferase gene) was used as a control for knockdown. cDNA constructs were expressed: empty vector control (Empty Vector), EWS/FLI (EF), or two mutant EWS/FLI constructs (EF DBD and EF DBD+). Antiobiotic selection was used to select for cells expressing these constructs and cells were collected after 8 days.  Whole cell total RNA was extracted using a Qiagen RNeasy Extraction kit and genomic DNA was removed uisng Qiagen gDNA Eliminator columns.

tag: disease state of cells

value: Ewing sarcoma


title: Mint-ChIP-seq from excitatory neuron (ENCLB830EJF)

description:
https://www.encodeproject.org/experiments/ENCSR411ZUA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR411ZUA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830EJF
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from naive B cell (ENCLB543KLN)

description:
https://www.encodeproject.org/experiments/ENCSR200JRA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR200JRA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR119CTT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB543KLN
fragmentation methods: none

value: naive B cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS182GUX at ENCODE; https://www.encodeproject.org/ENCBS182GUX/

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


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB000FHW)

description:
https://www.encodeproject.org/experiments/ENCSR100CMZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with 10 ng
experiment encode accession: ENCSR100CMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB000FHW
fragmentation methods: none

source_name: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: male

value: adult

value: 43 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: ENCBS377CVF at ENCODE; https://www.encodeproject.org/ENCBS377CVF/

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


title: 19-1251_85R2: iEF + EF DBD (85) Replicate 2

description: RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD (85)) was expressed.

value: Ewing sarcoma


title: 19-1246_85R1: iEF + EF DBD (85) Replicate 1


title: Mint-ChIP-seq from excitatory neuron (ENCLB183KYR)

description:
https://www.encodeproject.org/experiments/ENCSR327BWK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR327BWK
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB183KYR
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

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: 102R2D8: iEF + EF DBD+ (102) Replicate 2

description: CUT&RUN was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ (102)) was expressed.

data_processing:
Library strategy: CUT&RUN
Pearson correlations were calculated to determine if they were sufficiently similar.
CUT&RUNTools was used to trim, de-duplicate, and align reads to hg19 reference genome.
Diffbind and macs2 was used to call peaks.
Bigwig files were normalized using "RPGC" (Reads per genomic content) using Deeptools.
ChIPpeakAnno and Genomic Ranges was used to analyze overlapping peaks.
Genome_build: hg19
Supplementary_files_format_and_content: fastq files include raw reads of each samples; bigwig files are aligned, trimmed, normalized reads combined from each replicate.

extract_protocol:
Cells were bound to magnetic beads and an antibody-directed micrococcal nuclease protein was used to localize and nick DNA specifically where the EWS/FLI constructs were bound. DNA was extracted using phenol/choloroform followed by an ethanol precipitation. All was done according to Henikoff lab CUT&RUN protocol (2019).
Library prep was performed using the NEB High-Fidelity PCR Master Mix with published index primers (Buenrostro et al, 2015). Libraries were purified using AMPure beads (Beckman Coulter). Two biological replicates for each sample were used to construct cDNA libraries; each library was submitted twice to acheive sufficient read-depth and combined for analysis.

treatment_protocol: Endogenous EWS/FLI protein was knocked down in A673 cells using an shRNA targeting the 3'-UTR of the native transcript (iEF); iLuc (a shRNA targeting the firefly luciferase gene) was used as a control for knockdown. cDNA constructs were expressed: empty vector control (Empty Vector), EWS/FLI (EF) cDNA, or two mutant EWS/FLI constructs (EF DBD and EF DBD+). Antibiotic selection was used to select for cells expressing these constructs and cells were collected after 8 days.

tag: disease state of cell line


title: 85R2D8: iEF + EF DBD (85) Replicate 2

description: CUT&RUN was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD (85)) was expressed.


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB729AWS)

description:
https://www.encodeproject.org/experiments/ENCSR200SSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of CD4-positive, alpha-beta memory T cell originated from CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR200SSJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR131SAQ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB729AWS
fragmentation methods: none

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

tag: antibody

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: dH1f_OSKM_DMSO_ATAC_3

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

description: dH1f_OSKM_DMSO_ATAC_123Avg_SeqDepthNorm_dedupblck.bigwig

data_processing:
Sequence reads were mapped to the most recent human reference genome (hg38) using bowtie (Langmead et al., 2009), allowing a maximum of 2 mismatches and only uniquely mapped reads. After mapping, reads with mapping quality score below 30 and blacklisted regions were filtered.
DeepTools (Ramírez et al., 2016) ComputeMatrix and plotProfile commands were used to generate aggregate ATAC plots.
For this, BigWig files were generated using deepTools bamCoverage command, eliminating duplicates and normalizing by sequencing depth and effective genome size.
Intersecting regions among fibroblast ChIP peaks for H3K27ac, H3K4me1 and H3K4me3 were identified using previously published fibroblast ChIP-seq data (Ebrahimi et al., 2019), calling the peaks using macs2 (Zhang et al., 2008) with the parameters --keep-dup 1 and –broad, and finding the intersecting regions using bedtools (Quinlan et al.,  2010) intersect.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: BigWig files, average of replicates and normalized by sequencing depth

source_name: fibroblast cells

extract_protocol:
Cell nuclei were isolated and transposes were used to tagment the DNA
Nextera Tagmentation perfrormed during the sample preperation

tag: cell type

tag: transduced with

value: OSKM

tag: treatment

value: DMSO


title: 21-0160_714R3

value: EWS/FLI cDNA (EF(714))


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB618ULG)

description:
https://www.encodeproject.org/experiments/ENCSR200SSJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac Mint-ChIP-seq of CD4-positive, alpha-beta memory T cell originated from CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR200SSJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR131SAQ
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB618ULG
fragmentation methods: none

tag: description

tag: biosample encode accession

tag: Sex

tag: health state


title: 102R1D8: iEF + EF DBD+ (102) Replicate 1

value: Ewing sarcoma


title: Mint-ChIP-seq from endothelial cell (ENCLB124PKV)

description:
https://www.encodeproject.org/experiments/ENCSR306WYL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived endothelial cell
experiment encode accession: ENCSR306WYL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR759ZAX
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB124PKV
fragmentation methods: none

value: endothelial cell

value: in vitro differentiated cells

value: PGP1 derived endothelial cells

value: male

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB199QUG)

description:
https://www.encodeproject.org/experiments/ENCSR509FRR/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR509FRR
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB199QUG
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

tag: link

value: ENCBS080GJD at ENCODE; https://www.encodeproject.org/ENCBS080GJD/

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


title: Mint-ChIP-seq from naive B cell (ENCLB407LHJ)

description:
https://www.encodeproject.org/experiments/ENCSR200JRA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR200JRA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR119CTT
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB407LHJ
fragmentation methods: none

value: naive B cell

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

value: healthy

value: unknown

value: David Hafler

value: ENCBS182GUX at ENCODE; https://www.encodeproject.org/ENCBS182GUX/

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


title: dH1f_dBRD9_ATAC_1

description: dH1f_dBRD9_ATAC_123Avg_SeqDepthNorm_dedupblck.bigwig

value: dBRD9 0.3 µM


title: Mint-ChIP-seq from GM23338 (ENCLB373LLS)

description:
https://www.encodeproject.org/experiments/ENCSR505OUT/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR505OUT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB373LLS
fragmentation methods: none

source_name: Homo sapiens GM23338 cell line

tag: line

value: cell line

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

value: male

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS695QJS at ENCODE; https://www.encodeproject.org/ENCBS695QJS/

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


title: Mint-ChIP-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB872XLP)

description:
https://www.encodeproject.org/experiments/ENCSR100CMZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq of activated CD4-positive, alpha-beta T cell male adult (43 years) treated with 10 ng
experiment encode accession: ENCSR100CMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR764JRB
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872XLP
fragmentation methods: none

value: primary cell

value: 43 year

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: ENCBS377CVF at ENCODE; https://www.encodeproject.org/ENCBS377CVF/

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


title: 102R2: iEF + EF DBD+ (102) Replicate 2

description: ATAC was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ (102)) was expressed.

data_processing:
ENCODE pipeline - trimming, alignment to hg19 reference genome, and peak calling on individual biological replicates.
RegioneR R package - permutation test and calculate p-values between ATAC peaks in different samples
EnrichedHeatmaps, ggplot2, ChIPpeakAnno, and GenomicRanges R packages were used to calculate overlapping regions between samples and create scatterplots, heatmaps, and Venn diagrams.
Differential ATAC peak analysis was performed using DiffBind and DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: fastq files include raw reads of each samples; bigwig files are aligned, trimmed, normalized reads combined from each replicate.

extract_protocol:
Transposition was performed using Tn5 enzyme (Illumina) and cells were lysed using a high-salt lysis buffer.
Library prep was performed using the NEB High-Fidelity PCR Master Mix with published index primers (Buenrostro et al, 2015). Libraries were purified using AMPure beads (Beckman Coulter).

treatment_protocol: Endogenous EWS/FLI protein was knocked down in A673 cells using an shRNA targeting the 3'-UTR of the native transcript (iEF); iLuc (a shRNA targeting the firefly luciferase gene) was used as a control for knockdown. cDNA constructs were expressed: empty vector control (Empty Vector), EWS/FLI (EF), or two mutant EWS/FLI constructs (EF DBD and EF DBD+). Antibiotic selection was used to select for cells expressing these constructs and cells were collected after 8 days.

tag: genetic tag

tag: disease state of cells

value: Ewing sarcoma

tag: cell line


title: 19-1247_102R1: iEF + EF DBD+ (102) Replicate 1

description: RNA-sequencing was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD+ (102)) was expressed.


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB984OMJ)

description:
https://www.encodeproject.org/experiments/ENCSR101USF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR101USF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR426RVC
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB984OMJ
fragmentation methods: none

tag: antibody

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

value: not collected

value: multiple sclerosis

value: unknown

value: David Hafler

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

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


title: 102R1: iEF + EF DBD+ (102) Replicate 1


title: Mint-ChIP-seq from excitatory neuron (ENCLB032IHO)

description:
https://www.encodeproject.org/experiments/ENCSR411ZUA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR411ZUA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508IYL
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB032IHO
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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/


title: dH1f_OSKM_DMSO_ATAC_2

tag: cell type

tag: transduced with

value: OSKM

value: DMSO


title: 85R1D8: iEF + EF DBD (85) Replicate 1

tag: disease state of cell line

value: Ewing sarcoma


title: dH1f_DMSO_ATAC_2

description: dH1f_DMSO_ATAC_123Avg_SeqDepthNorm_dedupblck.bigwig

tag: treatment


title: dH1f_OSKM_DMSO_ATAC_1


title: 714R2D8: iEF + EF (714) Replicate 2

description: CUT&RUN was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (EF(714)) was expressed.


title: dH1f_dBRD9_ATAC_3

value: dBRD9 0.3 µM


title: Mint-ChIP-seq from endothelial cell (ENCLB503GSA)

description:
https://www.encodeproject.org/experiments/ENCSR306WYL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human PGP1 derived endothelial cell
experiment encode accession: ENCSR306WYL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR759ZAX
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503GSA
fragmentation methods: none

value: endothelial cell

tag: description

value: PGP1 derived endothelial cells

tag: biosample encode accession

tag: Sex

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/

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


title: 714R1D8: iEF + EF (714) Replicate 1


title: dH1f_DMSO_ATAC_1


title: 714R1: iEF + EF (714) Replicate 1

description: ATAC was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA (EF(714)) was expressed.


title: iPSC_DMSO_RNA_3

data_processing:
Quality check of reads for all samples was carried out using FastQC version 0.11.5.
Reads were mapped to hg19 using HISAT2 version 2.1.0.
Raw read counts were generated using feautureCounts version 1.6.0.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimeted text files with raw counts for all samples.

source_name: pluripotent stem cells

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.
RNA libraries were prepared for sequencing using standard NEB protocols.

value: iPSC


title: 197R2: iEF + Empty vector (197) Replicate 2

description: ATAC was performed on A673 cells with endogenous EWS/FLI knocked-down.


title: Control Mint-ChIP-seq from CD14-positive monocyte (ENCLB315KQN)

description:
https://www.encodeproject.org/experiments/ENCSR509FRR/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR509FRR
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB315KQN
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: age

value: David Hafler

value: ENCBS080GJD at ENCODE; https://www.encodeproject.org/ENCBS080GJD/

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


title: 197R1: iEF + Empty vector (197) Replicate 1


title: dH1f_dBRD9_ATAC_2


title: 197R2D8: iEF + Empty vector (197) Replicate 2

description: CUT&RUN was performed on A673 cells with endogenous EWS/FLI knocked-down.


title: Control Mint-ChIP-seq from excitatory neuron (ENCLB716AVI)

description:
https://www.encodeproject.org/experiments/ENCSR508IYL/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR508IYL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB716AVI
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: male

value: adult

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: George Church

tag: link

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


title: iLucR2: iLuc + Empty vector (iLuc) Replicate 2

description: ATAC was performed on A673 cells containing the endogenous EWS/FLI protein.

tag: genetic tag

value: Ewing sarcoma


title: Control Mint-ChIP-seq from excitatory neuron (ENCLB136WTK)

description:
https://www.encodeproject.org/experiments/ENCSR508IYL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human PGP1 derived excitatory neuron
experiment encode accession: ENCSR508IYL
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB136WTK
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

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


title: 197R1D8: iEF + Empty vector (197) Replicate 1


title: iLucR1: iLuc + Empty vector (iLuc) Replicate 1

tag: disease state of cells


title: Mint-ChIP-seq from GM23338 (ENCLB208QCL)

description:
https://www.encodeproject.org/experiments/ENCSR505OUT/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR505OUT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB208QCL
fragmentation methods: none

tag: line

value: cell line

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

value: Paola Arlotta

value: ENCBS695QJS at ENCODE; https://www.encodeproject.org/ENCBS695QJS/


title: dH1f_iBRD9_ATAC_3

description: dH1f_iBRD9_ATAC_123Avg_SeqDepthNorm_dedupblck.bigwig

value: I-BRD9 1 µM


title: dH1f_sgBRD9_RNA_1

value: lentiCRISPRv2 (Cas9 and sgBRD9)


title: dH1f_sgNT1_RNA_3

value: lentiCRISPRv2 (Cas9 and sgNT1)


title: Mint-ChIP-seq from GM23338 (ENCLB812FQN)

description:
https://www.encodeproject.org/experiments/ENCSR505OUT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR505OUT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB812FQN
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: antibody

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/


title: dH1f_iBRD9_ATAC_2

tag: cell type


title: Mint-ChIP-seq from GM23338 (ENCLB892KWG)

description:
https://www.encodeproject.org/experiments/ENCSR505OUT/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR505OUT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB892KWG
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500


title: E85R2: iEF + EF DBD (E85) Replicate 2

description: ATAC was performed on A673 cells with endogenous EWS/FLI knocked-down and EWS/FLI cDNA mutant (EF DBD (85)) was expressed.

tag: cell line


title: dH1f_dBRD9_RNA_3

tag: transduced with

value: dBRD9 0.3 µM


title: E85R1: iEF + EF DBD (E85) Replicate 1


title: dH1f_iBRD9_ATAC_1

tag: treatment


title: RNAseq.M_WT_rep1

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
total RNA polyA-selected
RNAseq.read_count.txt

data_processing:
RNA-Seq data were aligned against reference genome (dm3) using STAR (v2.3.0e) with default parameters and maximum fragment size of 2kb ("--alignMatesGapMax 2000"). The resulting files were filtered for concordant, primary alignments using SAMtools (v1.1). The enrichment of different genomic regions were analyzed using RSeQC (v3.0.1). Reads were assigned to RefSeq genes using featureCounts (v1.6.2) and differential expression between groups were analyzed using DESeq2.
TT-seq data were pre-processed in similar ways as RNA-seq. Visualization tracks were also generated in the same way. When assigning reads to RefSeq genes, we included the whole gene body instead of only coding regions. Differential expression between groups were analyzed again using DESeq2.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

organism: Drosophila melanogaster

source_name: 3rd instar larval salivary gland

growth_protocol: Fly larvae grown in standard conditions. Male or female salivary glands were dissected from wandering 3rd instar larva from appropriate crosses (control or Mtor RNAi induction).

extract_protocol:
Total RNA was isolated using TRIzol (Ambion) from salivary glands (10-12 animals per sample is sufficient) vortexed at 4°C for 2 h, extracted with ethanol precipitation, subsequently purified with PureLink RNA Kit columns (Invitrogen).
RNA-seq libraries were constructed using the dUTP method (Parkhomchuk et al., 2009).

treatment_protocol: UAS-Mtor RNAi induced with Nubbin-Gal4, control is Nubbin-Gal4.

tag: tissue

value: 3rd instar larval salivary gland

tag: genotype/variation

value: Nub-Gal4 x w118

value: Male


title: dH1f_DMSO_ATAC_3

value: DMSO


title: CD15s.Neg_6

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description:
CD15s Neg Basophils from donor 6
readCounts_genes.txt
RHP4339

data_processing:
Paired-end reads were mapped to GRCm38 reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v1.6.0 and with GENCODE GRCh38 v27 gene annotation
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts for all samples

source_name: PBMC

extract_protocol:
Total RNA was isolated from CD15s enriched cells using ARCTURUS PicoPure RNA Isolation Kit (Applied Biosystems™ Thermo Fisher Scientific).
Reverse transcription and amplification were performed using Smart-seq2 method (Picelli et al., 2014). Briefly, cDNA was synthesized from 2 ng of purified total RNA using modified oligo(dT) primers along with array control RNA spikes (Ambion® Thermo Fisher Scientific). To generate sufficient quantities of cDNA for downstream library preparation steps, 13 cycles of PCR amplification were performed.  Pooled cDNA libraries were prepared (250 pg of cDNA per sample) using Nextera XT Kit (Illumina, San Diego, CA, USA) with dual indices for de-multiplexing. The libraries were quantified by qPCR (Kapa Biosystems) to ascertain the loading concentration. Samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000.

value: Basophils

tag: cell subset

value: CD15s Neg


title: Polydactyly_04

city: Seoul

first: Jong Hee

last: Lee

address: 81, Irwon-ro, Gangnam-gu

department: Department of Dermatology

country: South Korea

institute: Samsung Medical Center

description: Extra-digits from 6-12 months old patient were delivered to the dermatologic clinic immediately after the digit removal

data_processing:
Barcoded sequencing libraries were generated using Chromium Single Cell 3′ v2 Reagent Kits and sequenced across by a HiSeq 4000 platform targeting 25,000 reads per cell.
Sequencing data were aligned to the human reference genome (GRCh38) and processed using the CellRanger 3.1.0 pipeline (10x Genomics).
Genome_build: hg38
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Skin

extract_protocol:
Specimens were transferred to freshly prepared dissociation solution composed of 120 μl of Liberase TL (2 mg/ml; Sigma Aldrich) and 840 μl PBS and incubated at 37ºC for 45 min. The cells were collected through 70-μm cell strainer (#352340, Corning) and stored on ice. The tissue was transferred to dissociation solution for second round of dissociation as mentioned above followed by dissociation in Trypsin solution (350 μl PBS, 50 μl 0.25% Trypsin). Cells were washed once and re-suspended in 50-200 μl of freshly prepared PBS-bovine serum albumin (BSA; 1 x PBS and 0.04% BSA). Cell viability was assessed using LUNA-FL dual fluorescence cell counter (Logos biosysteomics).
Single cell dissociates were loaded into the Chromium system (10x Genomics) targeting 5,000 cells. The Chromium Single Cell 3’ Reagent Kit V2 (10x Genomics) was used to generate scRNA-seq libraries, according to the manufacturer’s instructions.Barcoded sequencing libraries were generated using Chromium Single Cell 3′ v2 Reagent Kits and sequenced across by a HiSeq 4000 platform targeting 25,000 reads per cell.
Single cell sequencing

value: 6-12 months old

tag: pathology

value: normal

tag: type

value: Extra-digit

value: Nail unit


title: iPSC_DMSO_RNA_2

value: iPSC


title: Polydactyly_02

tag: age


title: dH1f_dBRD9_RNA_1


title: 714R2: iEF + EF (714) Replicate 2

source_name: A673 cells

value: Ewing sarcoma


title: CD15s.Pos_6

description:
CD15s Pos Basophils from donor 6
readCounts_genes.txt
RHP4338

value: CD15s Pos


title: CD15s.Pos_5

description:
CD15s Pos Basophils from donor 5
readCounts_genes.txt
RHP4336


title: iPSC_DMSO_RNA_1


title: dH1f_IBRD9_RNA_3

value: I-BRD9 1 µM


title: dH1f_sgBRD9_RNA_3

value: lentiCRISPRv2 (Cas9 and sgBRD9)


title: dH1f_sgBRD9_RNA_2


title: dH1f_IBRD9_RNA_2


title: Polydactyly_03


title: dH1f_sgNT1_RNA_2

value: lentiCRISPRv2 (Cas9 and sgNT1)


title: RNAseq.M_WT_rep3

tag: Sex


title: CD15s.Pos_4

description:
CD15s Pos Basophils from donor 4
readCounts_genes.txt
RHP4334


title: dH1f_sgNT1_RNA_1


title: Polydactyly_01


title: CD15s.Neg_3

description:
CD15s Neg Basophils from donor 3
readCounts_genes.txt
RHO1219


title: RNAseq.M_WT_rep2


title: dH1f_BI7273_RNA_1


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB349CDQ)

description:
https://www.encodeproject.org/experiments/ENCSR283LWF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR283LWF
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB349CDQ
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

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

value: primary cell

tag: description

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

tag: biosample encode accession

value: not collected

tag: health state

value: multiple sclerosis

tag: dev stage

value: unknown

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: David Hafler

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

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


title: RNAseq.F_KD_rep2

value: 3rd instar larval salivary gland

value: Nub-Gal4 x Mtor RNAi

value: Female


title: dH1f_dBRD9_RNA_2

tag: cell type

value: dBRD9 0.3 µM


title: RNAseq.M_KD_rep3

value: Male


title: CD15s.Neg_5

description:
CD15s Neg Basophils from donor 5
readCounts_genes.txt
RHP4337

value: Basophils

value: CD15s Neg


title: RNAseq.M_KD_rep2


title: RNAseq.M_KD_rep1


title: RNAseq.F_WT_rep3

value: Nub-Gal4 x w118


title: dH1f_DMSO_RNA_3

value: DMSO


title: CD15s.Neg_4

description:
CD15s Neg Basophils from donor 4
readCounts_genes.txt
RHP4335


title: H3K36me2_NSD1_WT_rep2

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

data_processing:
Library strategy: CUT&RUN
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: All J1 mESCs were cultured in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% Glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM β-Mercaptoethanol, and 1,000 U/ml recombinant leukemia inhibitory factor (LIF). Cells were cultured on 0.1% gelatin coated plates with fresh medium.

extract_protocol:
RNA-seq: Total RNA from 10^6 cells was purified by RNeasy plus mini kit (Qiagen, Cat.# 74134). ATAC-seq: 10^6 mESCs were collected and lysed by lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40) and separated into 50 µl with 50,000 cells. CUT&RUN/CUT&Tag: mESCs were harvested and washed with Wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1X Roche Complete Protease Inhibitor EDTA-Free tablet), 10 μl pre-washed Concanavalin A coated beads in binding buffer (20 mM HEPES pH7.9, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) were added per sample.
RNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocols. Other libraries preparation was described previously(Kaya-Okur et al., 2019a).

tag: strain

value: untreated

tag: chip antibody

value: H3K36me2 (Cell Signaling Technology, Cat.# 2901)

tag: genotype

value: wild type


title: Control Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB506GQP)

description:
https://www.encodeproject.org/experiments/ENCSR283LWF/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR283LWF
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB506GQP
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

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

value: primary cell

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

value: not collected

value: multiple sclerosis

value: unknown

tag: link


title: H3K36me2_NSD1_KO2_rep2

tag: treatment


title: CD15s.Pos_1

description:
CD15s Pos Basophils from donor 1
readCounts_genes.txt
RHO1214

tag: cell subset

value: CD15s Pos


title: RNAseq.F_WT_rep2

tag: tissue

value: 3rd instar larval salivary gland

tag: genotype/variation

value: Female


title: CD15s.Pos_3

description:
CD15s Pos Basophils from donor 3
readCounts_genes.txt
RHO1218


title: delta lexA/delta sulA M9/rdm/glu input replicate 1

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: Input

data_processing:
Adapter removal using the common Illumina TruSeq adapter sequences with cutadapt 1.8.1.
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed.
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper.
RNA reads were subject to quantitation using kallisto v0.43 and differential expression calling using sleuth 0.30.0.
Genome_build: E. coli U00096.3
Supplementary_files_format_and_content: Important: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text Abundance.tsv files – kallisto output giving (among other information) gene names and tpm estimates. See the kallisto documentation for details of the file format.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Cultured cells

growth_protocol: Cells were grown to exponential phase (OD600=0.2) in M9/rdm/glu rich defined medium.

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, a 50 microliter input sample was diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50o C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup.

treatment_protocol: Cells were treated for 10 minutes with rifampicin, then crosslinked for 5 minutes with 1% formaldehyde, prior to quenching with excess glycine. The resulting pellets are washed with PBS and frozen.

value: delta lexA / delta sulA

tag: media

value: MOPS rich defined medium + glucose

tag: time of harvest

value: logarithmic phase


title: RNAseq.F_WT_rep1

value: Nub-Gal4 x w118

tag: Sex


title: dH1f_IBRD9_RNA_1

tag: transduced with

value: I-BRD9 1 µM


title: dH1f_BI7273_RNA_2


title: RNAseq.F_KD_rep3

value: Nub-Gal4 x Mtor RNAi


title: SF_DOX_8d_Screen_d0

city: Toronto

first: Micheal

middle: D

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

description:
sgRNA_read_counts.txt
sgRNAs PCR-amplified from genomic DNA

data_processing:
Reads were aligned using Bowtie2.2.5 in the forward direction only (--norc option) with otherwise default parameters and total read counts per sgRNA were tabulated.
Read counts from different sequencing lanes for the same sample were summed.
Genome_build: For Nalm-6 screens: EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), using only the core RefSeq gene-targeting sgRNA set of of the library.
Supplementary_files_format_and_content: Tab-separated sgRNA read counts per sample

source_name: Nalm-6 pre-B lymphoid cell line

growth_protocol: Nalm-6 cells were grown in 10% FBS (v/v) (Wisent) RPMI 1640 medium (Wisent) at 5% (v/v) CO2 and 37°C.

extract_protocol:
Genomic DNA was extracted and purified using the Gentra Cell Puregene kit (QIAGEN, cat. # 158388).
sgRNA libraries were prepared by PCR amplification to add sequencing adapters and indices followed by SPRI beads purification of sequencing-ready amplicons.

treatment_protocol: A Nalm-6 clone with inducible expression of Cas9 was thawed, and Cas9 expression induced with doxycycline at 2 µg/mL for 7 days (see Bertomeu et al., 2017 for details). The pooled EKO library was split in different T-75 flasks, compounds added, and propagated for 8 days. Fresh media and compound was added at each cell passage. The untreated control sample was grown in T-175 spinner flasks.

tag: sample type

value: pooled sgRNA library

value: Pre-treatment, post-doxycycline induction, control sample


title: SF_Screen_d8

value: No treatment control, day 8


title: CD15s.Neg_2

description:
CD15s Neg Basophils from donor 2
readCounts_genes.txt
RHO1217

value: Basophils

value: CD15s Neg


title: CD15s.Pos_2

description:
CD15s Pos Basophils from donor 2
readCounts_genes.txt
RHO1216


title: TG003_20uM

value: 20 uM TG003 for 8 days


title: KH-CB19_50uM

value: 50 uM KH-CB19 for 8 days


title: GPS167_0_813uM

value: 0.813 uM GPS167 for 8 days