title: ChIP-seq from SK-N-SH (ENCLB555ACQ)

description:
https://www.encodeproject.org/experiments/ENCSR000FCU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACQ
size range: 200-500

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: 4 year

value: child

value: Peggy Farnham, USC

value: ENCBS495AAA at ENCODE; https://www.encodeproject.org/ENCBS495AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

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

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-11.aspx


title: ChIP-seq from SK-N-SH (ENCLB275IFZ)

status: Public on Oct 14 2016

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/ENCSR000FDA/
***************
biological replicate number: 1
technical replicate number: 1,2
description: Control ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR000FDA
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB275IFZ
size range: 200-500

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens SK-N-SH immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/5aaf2e58-de7c-451b-b6d7-747b82278bc3/@@download/attachment/Farnham_TF_ChIP_Library_Protocol_130201.docx.pdf

tag: antibody

value: Control

tag: line

tag: description

tag: biosample encode accession

tag: age

tag: dev stage

tag: Sex

value: female

tag: lab

tag: link

value: ENCBS490AAA at ENCODE; https://www.encodeproject.org/ENCBS490AAA/


title: ChIP-seq from fibroblast of arm (ENCLB919DQK)

description:
https://www.encodeproject.org/experiments/ENCSR007YOT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR007YOT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919DQK
size range: 200-600
nucleic acid starting quantity: 26
nucleic acid starting quantity units: ng

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: ChIP-seq from OCI-LY3 (ENCLB882ULO)

description:
https://www.encodeproject.org/experiments/ENCSR548PZS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR548PZS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB882ULO
size range: 200-600

source_name: Homo sapiens OCI-LY3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

value: immortalized cell line

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

tag: health state

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS018GXW at ENCODE; https://www.encodeproject.org/ENCBS018GXW/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: ChIP-seq from HCT116 (ENCLB555ABU)

description:
https://www.encodeproject.org/experiments/ENCSR000FCQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 HCT116 ChIP-Seq
experiment encode accession: ENCSR000FCQ
assay title: ChIP-seq
possible controls: ENCSR000EUX
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABU
size range: 200-500

source_name: Homo sapiens HCT116 immortalized cell line

value: colorectal carcinoma (PMID:7214343)

value: unknown

value: colorectal carcinoma

value: Peggy Farnham, USC

value: ENCBS471AAA at ENCODE; https://www.encodeproject.org/ENCBS471AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ENCODE dbxrefs HCT-116; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HCT-116

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-247.aspx


title: DNase-seq from Karpas-422 (ENCLB246IPC)

description:
https://www.encodeproject.org/experiments/ENCSR019JDO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR019JDO
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB246IPC

source_name: Homo sapiens Karpas-422 immortalized cell line

value: immortalized cell line

value: 73 year

value: adult

value: female

value: human B cell non-Hodgkin's lymphoma

value: John Stamatoyannopoulos, UW

value: ENCBS992KXS at ENCODE; https://www.encodeproject.org/ENCBS992KXS/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: ChIP-seq from SK-N-SH (ENCLB555ACP)

description:
https://www.encodeproject.org/experiments/ENCSR000FCT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACP
size range: 200-500

value: SK-N-SH

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: 4 year

value: child

value: ENCBS490AAA at ENCODE; https://www.encodeproject.org/ENCBS490AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

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

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-11.aspx


title: ChIP-seq from HCT116 (ENCLB555ABT)

description:
https://www.encodeproject.org/experiments/ENCSR000FCP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 HCT116 ChIP-Seq
experiment encode accession: ENCSR000FCP
assay title: ChIP-seq
possible controls: ENCSR000EUX
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABT
size range: 200-500

value: immortalized cell line

value: colorectal carcinoma (PMID:7214343)

value: unknown

value: male

value: colorectal carcinoma

value: Peggy Farnham, USC

value: ENCBS472AAA at ENCODE; https://www.encodeproject.org/ENCBS472AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ENCODE dbxrefs HCT-116; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HCT-116

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-247.aspx


title: ChIP-seq from OCI-LY7 (ENCLB173GMJ)

description:
https://www.encodeproject.org/experiments/ENCSR005SXO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005SXO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB173GMJ
size range: 200-600

source_name: Homo sapiens OCI-LY7 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: adult

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS886BJZ at ENCODE; https://www.encodeproject.org/ENCBS886BJZ/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: ChIP-seq from SUDHL6 (ENCLB582ITD)

description:
https://www.encodeproject.org/experiments/ENCSR511OIE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR511OIE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB582ITD
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: ENCBS401ZBX at ENCODE; https://www.encodeproject.org/ENCBS401ZBX/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: ChIP-seq from HCT116 (ENCLB555ABV)

description:
https://www.encodeproject.org/experiments/ENCSR000FCQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 HCT116 ChIP-Seq
experiment encode accession: ENCSR000FCQ
assay title: ChIP-seq
possible controls: ENCSR000EUX
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABV
size range: 200-500

value: colorectal carcinoma (PMID:7214343)

value: unknown

value: male

value: colorectal carcinoma

value: Peggy Farnham, USC

value: ENCBS472AAA at ENCODE; https://www.encodeproject.org/ENCBS472AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291


title: ChIP-seq from SUDHL6 (ENCLB365GAB)

description:
https://www.encodeproject.org/experiments/ENCSR494LJG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR494LJG
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB365GAB
size range: 200-600

value: adult

value: large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS136LHJ at ENCODE; https://www.encodeproject.org/ENCBS136LHJ/


title: ChIP-seq from OCI-LY7 (ENCLB538YXG)

description:
https://www.encodeproject.org/experiments/ENCSR005SXO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR005SXO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB538YXG
size range: 200-600
nucleic acid starting quantity: 22.4
nucleic acid starting quantity units: ng

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b4b48e6e-d14b-4359-96de-5e8c782c7bcf/@@download/attachment/TF_ChIP_Protocol_from_Shawn.pdf

value: immortalized cell line

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: B cell lymphoma

value: ENCBS006VZG at ENCODE; https://www.encodeproject.org/ENCBS006VZG/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: ChIP-seq from Panc1 (ENCLB555ABR)

description:
https://www.encodeproject.org/experiments/ENCSR000FCO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on human PANC1
experiment encode accession: ENCSR000FCO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EXM
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABR
size range: 200-500

source_name: Homo sapiens Panc1 immortalized cell line

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: 56 year

value: unknown

value: male

value: pancreatic carcinoma

value: ENCBS470AAA at ENCODE; https://www.encodeproject.org/ENCBS470AAA/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/

value: ENCODE dbxrefs Cellosaurus CVCL_0480; http://web.expasy.org/cellosaurus/CVCL_0480

value: ENCODE dbxrefs PANC-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PANC-1

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1469.aspx


title: ChIP-seq from SK-N-SH (ENCLB555ACM)

description:
https://www.encodeproject.org/experiments/ENCSR000FCS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACM
size range: 200-500

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: 4 year

value: child

value: female

value: Peggy Farnham, USC

value: ENCBS491AAA at ENCODE; https://www.encodeproject.org/ENCBS491AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

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

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-11.aspx


title: ChIP-seq from Panc1 (ENCLB555ABQ)

description:
https://www.encodeproject.org/experiments/ENCSR000FCO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on human PANC1
experiment encode accession: ENCSR000FCO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EXM
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABQ
size range: 200-500

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: 56 year

value: unknown

value: male

value: pancreatic carcinoma

value: ENCBS467AAA at ENCODE; https://www.encodeproject.org/ENCBS467AAA/


title: ChIP-seq from fibroblast of arm (ENCLB528CWH)

description:
https://www.encodeproject.org/experiments/ENCSR479HKJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR479HKJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB528CWH
size range: 200-600
nucleic acid starting quantity: 125.75
nucleic acid starting quantity units: ng

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: ChIP-seq from MCF-7 (ENCLB388RTX)

description:
https://www.encodeproject.org/experiments/ENCSR493NBY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR493NBY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB388RTX
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: ChIP-seq from SUDHL6 (ENCLB735PSW)

description:
https://www.encodeproject.org/experiments/ENCSR511OIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR511OIE
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB735PSW
size range: 200-600

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: male

value: ENCBS401ZBX at ENCODE; https://www.encodeproject.org/ENCBS401ZBX/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: ChIP-seq from Panc1 (ENCLB499BUK)

description:
https://www.encodeproject.org/experiments/ENCSR000EXM/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human PANC-1
experiment encode accession: ENCSR000EXM
assay title: ChIP-seq
encode release date: 2011-11-28
lab: Peggy Farnham, USC
library encode accession: ENCLB499BUK

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/7e85e27a-1b03-493d-b73f-db4ce2246318/@@download/attachment/wgEncodeSydhHistone.release3.html.pdf, general protocol: https://www.encodeproject.org/documents/0612f0bf-3665-47f8-af5d-09aab3d4ca24/@@download/attachment/wgEncodeSydhTfbs.release3.html.pdf

value: Control

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: 56 year

value: unknown

value: pancreatic carcinoma

value: Peggy Farnham, USC

value: ENCBS729QZR at ENCODE; https://www.encodeproject.org/ENCBS729QZR/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/

value: ENCODE dbxrefs Cellosaurus CVCL_0480; http://web.expasy.org/cellosaurus/CVCL_0480

value: ENCODE dbxrefs PANC-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PANC-1

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1469.aspx


title: ChIP-seq from OCI-LY7 (ENCLB361JAZ)

description:
https://www.encodeproject.org/experiments/ENCSR389WWC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR389WWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361JAZ
size range: 200-600

value: immortalized cell line

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: adult

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS304FAI at ENCODE; https://www.encodeproject.org/ENCBS304FAI/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: microRNA-seq from GM12878 (ENCLB051ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation GM12878 micro RNA-seq  from Mortazavi
experiment encode accession: ENCSR000AEK
assay title: microRNA-seq
encode release date: 2014-11-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB051ZZZ
size range: <30

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
general protocol: https://www.encodeproject.org/documents/9fb8e06c-d145-447a-a606-e7f3dc44b549/@@download/attachment/HA_Myers_miRNA-seq_Protocol_2013-05-02.pdf
extraction method: Ambion mirVana

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: female

value: Ali Mortazavi, UCI

value: ENCBS089RNA at ENCODE; https://www.encodeproject.org/ENCBS089RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: DNase-seq from OCI-LY7 (ENCLB753TXB)

description:
https://www.encodeproject.org/experiments/ENCSR489NAM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR489NAM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB753TXB
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: immortalized cell line

value: male

value: John Stamatoyannopoulos, UW

value: ENCBS141AMI at ENCODE; https://www.encodeproject.org/ENCBS141AMI/


title: ChIP-seq from HCT116 (ENCLB555ABS)

description:
https://www.encodeproject.org/experiments/ENCSR000FCP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 HCT116 ChIP-Seq
experiment encode accession: ENCSR000FCP
assay title: ChIP-seq
possible controls: ENCSR000EUX
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABS
size range: 200-500

value: colorectal carcinoma (PMID:7214343)

value: colorectal carcinoma

value: Peggy Farnham, USC

value: ENCBS471AAA at ENCODE; https://www.encodeproject.org/ENCBS471AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ENCODE dbxrefs HCT-116; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HCT-116

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-247.aspx


title: ChIP-seq from OCI-LY7 (ENCLB822NPD)

description:
https://www.encodeproject.org/experiments/ENCSR389WWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR389WWC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB822NPD
size range: 200-600

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

value: 48 year

value: adult

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS699NWP at ENCODE; https://www.encodeproject.org/ENCBS699NWP/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: ChIP-seq from HCT116 (ENCLB879CKK)

description:
https://www.encodeproject.org/experiments/ENCSR000EUX/
***************
biological replicate number: 1,2
technical replicate number: 1
description: Control ChIP-seq on human HCT-116
experiment encode accession: ENCSR000EUX
assay title: ChIP-seq
encode release date: 2012-06-15
lab: Peggy Farnham, USC
library encode accession: ENCLB879CKK

value: Control

value: immortalized cell line

value: unknown

value: male

value: ENCBS409MTT at ENCODE; https://www.encodeproject.org/ENCBS409MTT/


title: microRNA-seq from GM12878 (ENCLB052ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AEK/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation GM12878 micro RNA-seq  from Mortazavi
experiment encode accession: ENCSR000AEK
assay title: microRNA-seq
encode release date: 2014-11-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB052ZZZ
size range: <30

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: female

value: Ali Mortazavi, UCI

value: ENCBS090RNA at ENCODE; https://www.encodeproject.org/ENCBS090RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from Karpas-422 (ENCLB170BJG)

description:
https://www.encodeproject.org/experiments/ENCSR367UDO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367UDO
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB170BJG
size range: 200-600

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: adult

value: human B cell non-Hodgkin's lymphoma

value: ENCBS301UOD at ENCODE; https://www.encodeproject.org/ENCBS301UOD/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: DNase-seq from OCI-LY7 (ENCLB763ZVD)

description:
https://www.encodeproject.org/experiments/ENCSR489NAM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR489NAM
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB763ZVD
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: immortalized cell line

value: 48 year

value: B cell lymphoma

value: John Stamatoyannopoulos, UW

value: ENCBS581USS at ENCODE; https://www.encodeproject.org/ENCBS581USS/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: microRNA-seq from K562 (ENCLB069ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AET/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation K562 micro RNA-seq from Mortazavi
experiment encode accession: ENCSR000AET
assay title: microRNA-seq
encode release date: 2014-11-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB069ZZZ
size range: <30

source_name: Homo sapiens K562 immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 1.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS087RNA at ENCODE; https://www.encodeproject.org/ENCBS087RNA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from OCI-LY3 (ENCLB981KMQ)

description:
https://www.encodeproject.org/experiments/ENCSR361GKY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR361GKY
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB981KMQ
size range: 300-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

value: Control

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: adult

value: male

value: Bradley Bernstein, Broad

value: ENCBS757GPD at ENCODE; https://www.encodeproject.org/ENCBS757GPD/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: ChIP-seq from SK-N-SH (ENCLB555ACN)

description:
https://www.encodeproject.org/experiments/ENCSR000FCS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCS
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACN
size range: 200-500

value: SK-N-SH

value: immortalized cell line

value: neuroblastoma, newly promoted to tier 2:not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.

value: 4 year

value: child

value: Peggy Farnham, USC

value: ENCBS492AAA at ENCODE; https://www.encodeproject.org/ENCBS492AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531

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

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-11.aspx


title: shMBNL1-1_rep2

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
Single-end reads were trimmed (cutadapt version 1.8) and alighned to human transcriptome (hg19) using Tophat-2.0.12.
Transcript abundance was quantified using Cuffilnks-2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: Text file listing differential gene expression in MBNL1 knock-down cells (cuffdiff output)

source_name: MDA-MB-231 cells expressing MBNL1-targeting shRNA 1

growth_protocol: MDA-MB-231 cells were maintained at 37 degrees C, 5% CO2 and grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 1mM sodium pyruvate, 100 units/mL penicillin, 100 ug/mL streptomycin and 1ug/mL amphotericin B.

extract_protocol:
Total RNA was extracted with a spin-column based total RNA isolation kit (Norgen Biotek) including on-column DNase I treatment according to the manufacturer's protocol. Ribosomal RNA was depleted from the total RNA samples using the RiboZero kit (Illumina) according to the manufacturer's protocol.
Libraries were prepared using the ScriptSeq v2 kit (Epicentre) according to the manufacturer's instructions.

value: female

tag: cell type

value: breast cancer

tag: cell line


title: polyA mRNA RNA-seq from HeLa-S3 (ENCLB555ASI)

description:
https://www.encodeproject.org/experiments/ENCSR000CPR/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASI
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HeLa-S3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8170d791-0e6d-4dc3-a826-850fb4af58bc/@@download/attachment/LID16633.pdf

value: Cervical adenocarcinoma

value: 31 year

value: adult

value: cervical adenocarcinoma

value: Thomas Gingeras, CSHL

value: ENCBS737AAA at ENCODE; https://www.encodeproject.org/ENCBS737AAA/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: shMBNL1-2_rep2

source_name: MDA-MB-231 cells expressing MBNL1-targeting shRNA 2


title: ChIP-seq from Karpas-422 (ENCLB980ZHA)

description:
https://www.encodeproject.org/experiments/ENCSR306VSH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR306VSH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB980ZHA
size range: 200-600

value: immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS301UOD at ENCODE; https://www.encodeproject.org/ENCBS301UOD/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: ChIP-seq from Panc1 (ENCLB555ABN)

description:
https://www.encodeproject.org/experiments/ENCSR000FCM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 PANC1 ChIP-Seq
experiment encode accession: ENCSR000FCM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EXM
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABN
size range: 200-500

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: 56 year

value: unknown

value: male

value: pancreatic carcinoma

value: Peggy Farnham, USC

value: ENCBS466AAA at ENCODE; https://www.encodeproject.org/ENCBS466AAA/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/

value: ENCODE dbxrefs Cellosaurus CVCL_0480; http://web.expasy.org/cellosaurus/CVCL_0480

value: ENCODE dbxrefs PANC-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PANC-1

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1469.aspx


title: shMBNL1-2_rep1

value: female

value: breast cancer


title: shCTRL_rep2

source_name: MDA-MB-231 cells expressing a control shRNA


title: ChIP-seq from Panc1 (ENCLB555ABM)

description:
https://www.encodeproject.org/experiments/ENCSR000FCM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 PANC1 ChIP-Seq
experiment encode accession: ENCSR000FCM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EXM
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABM
size range: 200-500

value: immortalized cell line

value: ENCBS465AAA at ENCODE; https://www.encodeproject.org/ENCBS465AAA/


title: shCTRL_rep1


title: ChIP-seq from HCT116 (ENCLB497WAJ)

description:
https://www.encodeproject.org/experiments/ENCSR198WIH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR198WIH
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB497WAJ
size range: 200-600

extract_protocol: not provided

value: Control

value: cells obtained from ATCC

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS847SOB at ENCODE; https://www.encodeproject.org/ENCBS847SOB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from Panc1 (ENCLB555ABP)

description:
https://www.encodeproject.org/experiments/ENCSR000FCN/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 PANC1 ChIP-Seq
experiment encode accession: ENCSR000FCN
assay title: ChIP-seq
possible controls: ENCSR000EXM
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABP
size range: 200-500

value: pancreatic carcinoma, (PMID:1140870) PANC-1 was established from a pancreatic carcinoma, which was extracted via pancreatico-duodenectomy specimen from a 56-year-old Caucasian individual. Malignancy of this cell line was verified via in vitro and in vivo assays.

value: 56 year

value: unknown

value: male

value: pancreatic carcinoma

value: Peggy Farnham, USC

value: ENCBS466AAA at ENCODE; https://www.encodeproject.org/ENCBS466AAA/


title: ChIP-seq from Panc1 (ENCLB555ABO)

description:
https://www.encodeproject.org/experiments/ENCSR000FCN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 PANC1 ChIP-Seq
experiment encode accession: ENCSR000FCN
assay title: ChIP-seq
possible controls: ENCSR000EXM
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ABO
size range: 200-500

value: immortalized cell line

value: ENCBS467AAA at ENCODE; https://www.encodeproject.org/ENCBS467AAA/

value: Derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/

value: ENCODE dbxrefs Cellosaurus CVCL_0480; http://web.expasy.org/cellosaurus/CVCL_0480

value: ENCODE dbxrefs PANC-1; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=PANC-1

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1469.aspx


title: polyA mRNA RNA-seq from HeLa-S3 (ENCLB555ASJ)

description:
https://www.encodeproject.org/experiments/ENCSR000CPR/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPR
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ASJ
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/aaad5383-6b11-46a8-9a5b-2852e1475842/@@download/attachment/LID16634.pdf

value: Cervical adenocarcinoma

value: 31 year

value: adult

value: female

value: cervical adenocarcinoma

value: Thomas Gingeras, CSHL

value: ENCBS740AAA at ENCODE; https://www.encodeproject.org/ENCBS740AAA/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058

value: ENCODE dbxrefs HeLa-S3; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HeLa-S3

value: ATCC sample source; http://www.atcc.org/products/all/CCL-2.2.aspx


title: C2C12 MyoD ChIP-seq KlfKO

city: Bunkyo

first: Yumiko

last: Oishi

state: Tokyo

address: 1-5-45, Yushima

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Tokyo Medical and Dental University

description: formaldehyde cross-linked

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using RNA-Star. Aligned read files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif- and other analyses in the study.
Genome_build: mm9

organism: Mus musculus

source_name: C2C12 myoblast

growth_protocol: C2C12 cells were purchased from ATCC (Rockville, MD) and cultured in DMEM (Nakarai) containing 10% FBS and 1% penicillin-streptomycin at sub-confluent densities.

extract_protocol: ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles, size selected by gel extraction and sequenced on a Hi-Seq 2500 (Illumina) for 51 cycles.

treatment_protocol: C2C12 cells were differentiated into myotubes by replacing Growth Medium with media containing 2% horse serum with antibiotics (differentiation medium, DM). For knockdown Klf5 in C2C12 cells, siKlf5 (Thermo scientific, Dharmacon, siRNA-SMARTpool, M-062477-01-0005) treatment were performed with RNAiMAX (Life Technologies) according to manufacturer’s instructions.

value: C2C12 myoblast

tag: differentiation stage


title: MBNL1_CLIP_rep2

description: MBNL1-bound RNA

data_processing:
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
CIMS was then used to identify the MBNL1 CLIP tags (Zhang & Darnell, 2001, Nat. Biotech. 29:607). Tags between the replicates were then overlapped between the two biological replicates.
MBNL1 binding sites were then used to generate shuffled sequences, based on a 1st order Markov model, for motif comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: Idntfied MBNL1 binding sites in BED format

source_name: MDA-MB-231 cells

extract_protocol:
Isolation of MBNL1-bound RNA was carried out using a previously published protocol (Moore et al. 2014. Nat Protoc. 9:263-293.)
Library of isolated MBNL1-bound RNA was carried out using a previously published protocol (Moore et al. 2014. Nat Protoc. 9:263-293.)

treatment_protocol: MDA-MB-231 cells were washed twice with ice cold PBS and irradiated with 400 mJ/cm2 254 nm UV before lysate preparation.

value: breast cancer


title: DNase-seq from fibroblast of arm (ENCLB358EUZ)

description:
https://www.encodeproject.org/experiments/ENCSR217TAW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR217TAW
assay title: DNase-seq
assembly: GRCh38, hg19
encode release date: 2015-06-17
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB358EUZ
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: MBNL1_CLIP_rep1

description: MBNL1-bound RNA

value: female


title: ChIP-seq from SK-N-SH (ENCLB339LAI)

description:
https://www.encodeproject.org/experiments/ENCSR185OHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR185OHN
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB339LAI
size range: 200-600

source_name: Homo sapiens SK-N-SH immortalized cell line

value: Control

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

value: Bradley Bernstein, Broad

value: ENCBS500EWH at ENCODE; https://www.encodeproject.org/ENCBS500EWH/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531


title: ChIP-seq from OCI-LY1 (ENCLB780YNK)

description:
https://www.encodeproject.org/experiments/ENCSR189AGR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR189AGR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB780YNK
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: adult

value: B cell lymphoma

value: ENCBS899DSB at ENCODE; https://www.encodeproject.org/ENCBS899DSB/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: C2C12 ChIP-input

description: formaldehyde cross-linked

value: C2C12 myoblast


title: shMBNL1-1_rep1

value: female

value: breast cancer


title: polyA mRNA RNA-seq from K562 (ENCLB555AKN)

description:
https://www.encodeproject.org/experiments/ENCSR000CPH/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPH
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AKN
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/58553067-8146-48c9-aa19-2e6751a451df/@@download/attachment/LID16627.pdf

value: immortalized cell line

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Thomas Gingeras, CSHL

value: ENCBS723AAA at ENCODE; https://www.encodeproject.org/ENCBS723AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/products/all/CCL-243.aspx


title: polyA mRNA RNA-seq from HepG2 (ENCLB555AQC)

description:
https://www.encodeproject.org/experiments/ENCSR000CPE/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQC
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/bf6e8b18-2787-4c45-8a55-4c38f7cb2431/@@download/attachment/LID16636.pdf

value: hepatocellular carcinoma

value: 15 year

value: child

value: male

value: ENCBS746AAA at ENCODE; https://www.encodeproject.org/ENCBS746AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: ChIP-seq from SUDHL6 (ENCLB190DEU)

description:
https://www.encodeproject.org/experiments/ENCSR316KHQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR316KHQ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB190DEU
size range: 200-600

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: adult

value: Bradley Bernstein, Broad

value: ENCBS401ZBX at ENCODE; https://www.encodeproject.org/ENCBS401ZBX/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: C2C12 Klf5 ChIP-seq day5

description: formaldehyde cross-linked

value: C2C12 myoblast


title: ChIP-seq from OCI-LY1 (ENCLB170FWB)

description:
https://www.encodeproject.org/experiments/ENCSR189AGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189AGR
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB170FWB
size range: 200-600

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: B cell lymphoma

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from SUDHL6 (ENCLB944MPB)

description:
https://www.encodeproject.org/experiments/ENCSR179YLS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR179YLS
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB944MPB
size range: 200-600

value: Control

value: male

value: large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma

value: ENCBS136LHJ at ENCODE; https://www.encodeproject.org/ENCBS136LHJ/


title: C2C12 Klf5 ChIP-seq day0

description: formaldehyde cross-linked


title: H3_input

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing:
library strategy: m6A-seq
Base calling was performed using CASAVA 1.3
Alignment was done by TopHat v2.0.14
Peak calling was done by customized algorithm
Genome_build: hg38; panTro4; rheMac2(Mmul_051212)
Supplementary_files_format_and_content: Peaks were generated by customized algorithm, enrichment score of each peak file represented the ratio of reads between m6A-enriched mRNA and intact mRNA.

source_name: LCL

growth_protocol: LCLs were cultured in RPMI1640 media with 15% FBS and Penicillin-Streptomycin

extract_protocol:
Regular RNA isolation
Illumina TruSeq stranded total RNA protocol

treatment_protocol: mRNA was fragmented to ~100nt, and enriched by m6A specific antibody

value: lymphoblastoid cell line (LCL)

tag: ip antibody

value: none (input)


title: polyA mRNA RNA-seq from GM12878 (ENCLB555AQG)

description:
https://www.encodeproject.org/experiments/ENCSR000COQ/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQG
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c3388b65-d800-42db-a660-796c9f4716f2/@@download/attachment/LID16629.pdf

value: immortalized cell line

value: B-lymphoblastoid cell line

value: unknown

value: adult

value: female

value: Thomas Gingeras, CSHL

value: ENCBS095RNA at ENCODE; https://www.encodeproject.org/ENCBS095RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: microRNA-seq from K562 (ENCLB070ZZZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AET/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation K562 micro RNA-seq from Mortazavi
experiment encode accession: ENCSR000AET
assay title: microRNA-seq
encode release date: 2014-11-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB070ZZZ
size range: <30

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 2.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Brenton Graveley, UConn

value: ENCBS088RNA at ENCODE; https://www.encodeproject.org/ENCBS088RNA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: polyA mRNA RNA-seq from A549 (ENCLB555AUK)

description:
https://www.encodeproject.org/experiments/ENCSR000CON/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CON
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUK
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens A549 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/9c9235b2-6944-47e2-b285-ac3751fac0d7/@@download/attachment/LID8964.pdf

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: 58 year

value: male

value: ENCBS445ENC at ENCODE; https://www.encodeproject.org/ENCBS445ENC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-185.aspx


title: C2C12 MyoD ChIP-seq control

description: formaldehyde cross-linked

value: C2C12 myoblast


title: polyA mRNA RNA-seq from HepG2 (ENCLB555AQD)

description:
https://www.encodeproject.org/experiments/ENCSR000CPE/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HepG2. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPE
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQD
size range: >200
spikeins used: /references/ENCSR402QNO/

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/0405eeb5-77b9-47a2-accb-31601a002993/@@download/attachment/LID16635.pdf

value: hepatocellular carcinoma

value: 15 year

value: child

value: Thomas Gingeras, CSHL

value: ENCBS743AAA at ENCODE; https://www.encodeproject.org/ENCBS743AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ENCODE dbxrefs HepG2; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=HepG2

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: H1_input

value: lymphoblastoid cell line (LCL)

value: none (input)


title: H2_IP

value: m6A specific antibody (SYSY, CAT#202003, LOT#42)


title: H3_IP


title: P-KO 89P

status: Public on Oct 13 2016

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description: H9 poly(A)+ RNA SPA paternal deletion

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map to mouse genome hg19 using Tophat(v 2.0.9)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
For each gene, we first merged all exons from different isoforms, then counted the mapping reads and normalized as RPKM values.
MISO tool (Katz et al., 2010) was used to estimate inclusion levels of exons.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

molecule: polyA RNA

source_name: H9 SPA P-KO cells

growth_protocol: HESCs were cultured on plates coated with growth-factor-depleted Matrigel (BD Biosciences, San Jose, CA) in either serum-free, defined mTeSR medium (StemCell Technologies Inc, Vancouver, BC, Canada) or fibroblast-conditioned medium (CM) with irradiation inactivated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF) (Life Technologies, Rockville, MD). Cultured H9 cells were regularly evaluated for Oct3/4 expression every 3-4 weeks and passaged every 6-7 days.

extract_protocol:
Total RNAs were prepared using Trizol Reagent. After treatment with DNase I, total RNAs were used for RNA-Seq libraries preparation with Illumina TruSeq RNA Sample Preparation Kits according to the manufacturer's instructions.
cDNA libraries were constructed according to Illumina's instructions using the Illumina® TruSeq® RNA Sample Preparation Kit v2. Briefly, the first step in the workflow involves purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis follows, using DNA Polymerase I and RNase H. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library which were subjected to Illumina HiSeq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

tag: type

value: Poly(A)+ RNA

tag: treatment

value: Embryonic stem cells


title: H2_input


title: WT

description: H9 poly(A)+ RNA WT

source_name: H9 cells


title: Fib IP

description: PA1 Fib IP

data_processing:
Basecalling using Illumina Casava1.8.2 software
Map to mouse genome hg19 using Tophat(v 2.0.9)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
We used cufflinks de novo assembly to annotate transcripts, then counted the mapping reads and normalized as RPKM values. Fib enrichment was calculated between input and Fib IP samples. Details in manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: PA1 cells

growth_protocol: Embryonal carcinoma (EC) cell line PA-1 was cultured using standard protocols provided by ATCC.

extract_protocol:
RNA-protein immunoprecipitations were carried out in PA1 cells as previously described (Chen et al., 2008) with rabbit anti-Fibrillarin (A gift from Joan Steitz at Yale). Immunoprecipitated RNAs were prepared using Trizol Reagent. After treatment with DNase I, RNAs were used for RNA-Seq libraries preparation with Illumina TruSeq RNA Sample Preparation Kits according to the manufacturer's instructions.
cDNA libraries were constructed according to Illumina's instructions using the Illumina® TruSeq® RNA Sample Preparation Kit v2 with some modifications. Briefly, the first step is fragmenting immunoprecipitated RNAs into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis follows, using DNA Polymerase I and RNase H. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library which were subjected to Illumina HiSeq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

value: Human embryonal carcinoma (EC)

tag: antibody

value: anti-Fibrillarin


title: P-KO 90P

description: H9 poly(A)+ RNA SPA paternal deletion

source_name: H9 P-KO cells


title: MW2 MH liquid 37C Bioreplicate1 without RppH

status: Public on Oct 15 2016

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

description: processed data file: EMOTE_Saureus_unambiguous.tsv.gz

data_processing:
Library strategy: TSS-EMOTE
FASTQ files for each EMOTE sample is obtained by demultiplexing the original FASTQ file according to the EMOTE-barcode detected in the reads. Demultiplexing is performed by EMOTEconv program, allowing for 1 mismatch in the EMOTE recognition sequence.
EMOTE reads are parsed from the FASTQ files to extract the UMI sequence, and the mapping sequence. This step is performed by EMOTEconv program.
The mapping sequence of each read is aligned to the corresponding bacterial genome using Bowtie. Reads aligning to multiple position on the genome are ignored to keep only unambiguously mapped reads.
For each position on the genome, Emoteconv quantify the number of read whose first base align at this position (N value). In a second it corrects for potential PCR bias by removing duplicated reads (that have the same UMI sequence), and quantify again (Q value).
Supplementary_files_format_and_content: EMOTE_Saureus_unambiguous.tsv.gz: abundance measurements across S. aureus genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Eaerogenes_unambiguous.tsv.gz: abundance measurements across E. aerogenes genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Sepidermidis_unambiguous.tsv.gz: abundance measurements across S. epidermidis genome (tab separated text file)
Supplementary_files_format_and_content: EMOTE_Abaumannii_unambiguous.tsv.gz: abundance measurements across A. baumannii genome (tab separated text file)

organism: Staphylococcus aureus

source_name: exponentially growing culture

extract_protocol:
RNA extraction protocol not provided.
EMOTE, as described in associated paper

tag: growth conditions

value: 37°C, MH liquid

value: without RppH

tag: strain

tag: emote library

tag: emote barcode

value: CGTC


title: Input

description:
Ribo- RNA
PA1 input


title: polyA mRNA RNA-seq from GM12878 (ENCLB555AQH)

description:
https://www.encodeproject.org/experiments/ENCSR000COQ/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line GM12878. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000COQ
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AQH
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens GM12878 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/c3a0ed67-0d67-4a1d-b326-80a047d669dd/@@download/attachment/LID16630.pdf

tag: line

value: immortalized cell line

tag: description

value: B-lymphoblastoid cell line

tag: biosample encode accession

tag: age

value: unknown

tag: dev stage

value: adult

value: female

value: ENCBS096RNA at ENCODE; https://www.encodeproject.org/ENCBS096RNA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: P-KO hnRNP M iCLIP replicate1

description: P-KO hnRNP M iCLIP replicate1

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 4-nt experimental barcodes.
5-nt barcodes for identifying PCR duplicates were registered and removed, followed by trimming relevant sequencing adapters.
Trimmed reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using Bowtie1
Mapped reads with same genomic locations and the same 5-nt barcode were combined.
Peak calling and the false discovery rate (FDR) calculating were determined according previous work(Konig et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: peak/bed file

source_name: H9 SPA PKO cells

extract_protocol:
The UV-crosslinked cells were resuspended in lysis buffer and sonicated for 20s x 4 times on 25% duty. After centrifugation at 14,000rpm at 4?, the supernatant were incubated with 8?g anti-TDP43 or anti-RBFOX2 or anti-hnRNP M antibodies and 100?l DynaBeads G at 4? for 2 hours.
Then the protein-RNA complexes were treated with 5 Kunz U/ml of micrococcal nuclease with 5 ?g yeast tRNAs for 5 min at 37°C, and RNA 3’ ends were dephosphorylated by PNK at pH6.5. Then pre-adenylated linker L3 (3’ modification with biotin) was linked to 3’ end of RNA at 16°C overnight. 5’ end of RNA was labeled with [?-32P] ATP and eluted with 1x Nupage loading buffer (Invitrogen) at 70°C for 10 min. Complexes were separated on 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane and exposure to a Fuji film at -80?. Protein-RNA complexes were digested with proteinase K, and RNA were reverse transcribed by Superscript III reverse transcriptase (Invitrogen) with Rclip primers. cDNAs were separated on 6% TBE-urea gel, then three bands were cut at 120-200 nt (high), 85-120 nt (medium) and 70-85 nt (low).cDNAs were circularized by Circligase II (Epicentre). Single-stranded cDNAs were hybridized with cut_oligo, and then digested by BamHI. Linearized cDNAs were PCR amplified and purified on PAGEs to obtain iCLIP libraries, which were subjected to Illumina HiSeq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: WT and P-KO cells were washed with cold 1xPBS, then UV cross-linked at 400mJ/cm2 and collected by scraper.

value: anti-hnRNP M1-4 (1D8)

tag: antibody manufacturer

value: Santa Cruz Biotechnology, Inc.

tag: antibody catalog #

tag: antibody lot #

tag: barcode

value: NNNCAATNN


title: WT hnRNP M iCLIP replicate2

description: WT hnRNP M iCLIP replicate2

source_name: H9 WT cells

tag: cell line

value: NNNGGTTNN


title: ChIP-seq from SK-N-SH (ENCLB134GES)

description:
https://www.encodeproject.org/experiments/ENCSR185OHN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR185OHN
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB134GES
size range: 200-600

value: Control

value: SK-N-SH

value: 4 year

value: child

tag: Sex

tag: passage number

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS018DDZ at ENCODE; https://www.encodeproject.org/ENCBS018DDZ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531


title: P-KO TDP43 iCLIP replicate1

description: P-KO TDP43 iCLIP replicate1

tag: antibody

value: Proteintech


title: WT hnRNP M iCLIP replicate1

description: WT hnRNP M iCLIP replicate1

value: NNNAATGNN


title: H1_IP

value: lymphoblastoid cell line (LCL)

tag: ip antibody

value: m6A specific antibody (SYSY, CAT#202003, LOT#42)


title: ChIP-seq from fibroblast of arm (ENCLB522ZLN)

description:
https://www.encodeproject.org/experiments/ENCSR007YOT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007YOT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB522ZLN
size range: 200-600
nucleic acid starting quantity: 510
nucleic acid starting quantity units: ng

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: P-KO 31P

description: H9 poly(A)+ RNA SPA paternal deletion

tag: type

value: Poly(A)+ RNA

tag: treatment

value: Embryonic stem cells


title: WT TDP43 iCLIP replicate2

description: WT TDP43 iCLIP replicate2

value: Proteintech

value: NNNCAATNN


title: WT TDP43 iCLIP replicate1

description: WT TDP43 iCLIP replicate1


title: P-KO TDP43 iCLIP replicate2

description: P-KO TDP43 iCLIP replicate2

value: NNNGCCGNN


title: P-KO Fox2 iCLIP replicate1

description: P-KO Fox2 iCLIP replicate1

value: anti-RBM9 (RBFOX2)

value: Bethyl

value: NNNCGGANN


title: WT Fox2 iCLIP replicate2

description: WT Fox2 iCLIP replicate2


title: P-KO Fox2 iCLIP replicate2

description: P-KO Fox2 iCLIP replicate2


title: Farage.DMSO.12h.R3

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

description: mRNA isolated from DMSO-treated (12 hours) human GCB-DLBCL Farage cells

data_processing:
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long single-end reads were mapped to the reference human genome sequence, hg19, using Tophat2 aligner (Daehwan et al, Genome Biology 2013,14:R36) with the default parameters. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515) in the Tophat2 package.
Genome_build: hg19

source_name: GCB-DLBCL cell line Farage, treated with DMSO for 24 hours,  replicate 3

growth_protocol: cultured cells, RPMI1640+10%FBS

extract_protocol:
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared using the Illumina RNA-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

tag: cell type

value: diffuse large B-cell lymphoma cell line


title: Farage.BCL6.inh.12h.R2

description: mRNA isolated from BCL6-inhibitor-treated (12 hours) human GCB-DLBCL Farage cells

source_name: GCB-DLBCL cell line Farage, treated with BCL6 inhibitor for 24 hours,  replicate 2


title: Farage.DMSO.12h.R1

source_name: GCB-DLBCL cell line Farage, treated with DMSO for 24 hours,  replicate 1


title: Farage.BCL6.inh.12h.R3

source_name: GCB-DLBCL cell line Farage, treated with BCL6 inhibitor for 24 hours,  replicate 3


title: Farage.BCL6.inh.12h.R1

source_name: GCB-DLBCL cell line Farage, treated with BCL6 inhibitor for 24 hours,  replicate 1


title: SUDHL4.BCL6.inh.12h.R2

description: mRNA isolated from BCL6-inhibitor-treated (12 hours) human GCB-DLBCL SUDHL4 cells

source_name: GCB-DLBCL cell line SUDHL4, treated with BCL6 inhibitor for 24 hours,  replicate 2


title: WT Fox2 iCLIP replicate1

description: WT Fox2 iCLIP replicate1

value: NNNGGTCNN


title: SUDHL4.DMSO.12h.R3

description: mRNA isolated from DMSO-treated (12 hours) human GCB-DLBCL SUDHL4 cells

source_name: GCB-DLBCL cell line SUDHL4, treated with DMSO for 24 hours,  replicate 3


title: polyA mRNA RNA-seq from K562 (ENCLB555ALR)

description:
https://www.encodeproject.org/experiments/ENCSR000CPH/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line K562. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CPH
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555ALR
size range: >200
spikeins used: /references/ENCSR402QNO/

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/59ae107f-f8e4-40eb-9220-a155e8faf323/@@download/attachment/LID16628.pdf

tag: line

value: immortalized cell line

tag: description

value: leukemia, The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

tag: biosample encode accession

value: 53 year

value: adult

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: ENCBS726AAA at ENCODE; https://www.encodeproject.org/ENCBS726AAA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

value: ATCC sample source; http://www.atcc.org/products/all/CCL-243.aspx


title: SUDHL4.BCL6.inh.12h.R3

source_name: GCB-DLBCL cell line SUDHL4, treated with BCL6 inhibitor for 24 hours,  replicate 3


title: SUDHL4.DMSO.12h.R2

source_name: GCB-DLBCL cell line SUDHL4, treated with DMSO for 24 hours,  replicate 2


title: SUDHL4.BCL6.inh.12h.R1

source_name: GCB-DLBCL cell line SUDHL4, treated with BCL6 inhibitor for 24 hours,  replicate 1


title: SUDHL4.DMSO.12h.R1

source_name: GCB-DLBCL cell line SUDHL4, treated with DMSO for 24 hours,  replicate 1


title: SUDHL6.BCL6.inh.12h.R3

description: mRNA isolated from BCL6-inhibitor-treated (12 hours) human GCB-DLBCL SUDHL6 cells

source_name: GCB-DLBCL cell line SUDHL6, treated with BCL6 inhibitor for 24 hours,  replicate 3


title: SUDHL6.DMSO.12h.R3

description: mRNA isolated from DMSO-treated (12 hours) human GCB-DLBCL SUDHL6 cells

source_name: GCB-DLBCL cell line SUDHL6, treated with DMSO for 24 hours,  replicate 3


title: SUDHL6.BCL6.inh.12h.R2

source_name: GCB-DLBCL cell line SUDHL6, treated with BCL6 inhibitor for 24 hours,  replicate 2


title: SUDHL6.DMSO.12h.R2

source_name: GCB-DLBCL cell line SUDHL6, treated with DMSO for 24 hours,  replicate 2


title: SUDHL6.DMSO.12h.R1

source_name: GCB-DLBCL cell line SUDHL6, treated with DMSO for 24 hours, replicate 1


title: P-KO hnRNP M iCLIP replicate2

description: P-KO hnRNP M iCLIP replicate2

source_name: H9 SPA PKO cells

value: anti-hnRNP M1-4 (1D8)

tag: antibody manufacturer

value: Santa Cruz Biotechnology, Inc.

tag: antibody catalog #

value: NNNGCCGNN


title: Farage.DMSO.12h.R2

source_name: GCB-DLBCL cell line Farage, treated with DMSO for 24 hours,  replicate 2


title: MD901 cells with scramble shRNA control, replicate 2

description:
MD901_ctrl_2
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with scramble shRNA

data_processing:
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long paired-end reads were mapped to the reference human genome sequence, hg19, using Tophat2 aligner (Daehwan et al, Genome Biology 2013,14:R36) with the default parameters and --library-type fr-firststrand. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515) in the Tophat2 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file with FPKM values.

source_name: MD901 cells with scramble shRNA control

growth_protocol: cultured cells, IMDM+10%FBS

extract_protocol:
not provided.
Libraries were prepared according to a version of Illumina's TruSeq Stranded Total RNA with Ribo-depletion protocol (Illumina, CA)


title: MD901 cells with scramble shRNA control, replicate 3

description:
MD901_ctrl_3
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with scramble shRNA


title: MD901 cells with shCREBBP.572, replicate 3

description:
MD901_572_3
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.572

source_name: MD901 cells with shCREBBP.572


title: MD901 cells with shCREBBP.3753, replicate 3

description:
MD901_3753_3
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.3753

source_name: MD901 cells with shCREBBP.3753


title: MD901 cells with shCREBBP.1027, replicate 3

description:
MD901_11027_3
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.11027

source_name: MD901 cells with shCREBBP.1027


title: MD901 cells with shCREBBP.572, replicate 2

description:
MD901_572_2
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.572


title: MD901 cells with shCREBBP.3753, replicate 1

description:
MD901_3753_1
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.3753


title: MD901 cells with scramble shRNA control, replicate 1

description:
MD901_ctrl_1
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with scramble shRNA


title: MD901 cells with shCREBBP.1027, replicate 2

description:
MD901_11027_2
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.11027


title: MD901 cells with shCREBBP.3753, replicate 2

description:
MD901_3753_2
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.3753


title: MD901 cells with shCREBBP.572, replicate 1

description:
MD901_572_1
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.572


title: MD901 cells with shCREBBP.1027, replicate 1

description:
MD901_11027_1
total RNA > 200 nt
mRNA isolated from human GCB-DLBCL MD901 cells treated with shCREBBP.11027


title: md901_ctrl_1_input

description: input DNA for H3K27Ac ChIPseq in MD901 with scramble shRNA.ctrl_1

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats

source_name: MD901 cells

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with H3K27ac antibody (abcam 4729) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.
Libraries were prepared using the Illumina Truseq ChIPseq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

tag: genotype/variation

value: CREBBP wild-type

tag: chip antibody


title: md901_ctrl_2_K27ac

description: H3K27Ac ChIPseq in MD901 with scramble shRNA.ctrl_2

value: diffuse large B-cell lymphoma cell line

value: H3K27Ac (ab4729, Rabbit, 2 ug)


title: md901_ctrl_3_input

description: input DNA for H3K27Ac ChIPseq in MD901 with scramble shRNA.ctrl_3


title: md901_ctrl_3_K27ac

description: H3K27Ac ChIPseq in MD901 with scramble shRNA.ctrl_3


title: md901_3752_2_input

description: input DNA for H3K27Ac ChIPseq in MD901 with shCREBBP.3752_2

value: CREBBP knock-down


title: md901_3752_3_K27ac

description: H3K27Ac ChIPseq in MD901 with shCREBBP.3752_3


title: md901_3752_1_K27ac

description: H3K27Ac ChIPseq in MD901 with shCREBBP.3752_1


title: md901_ctrl_2_input

description: input DNA for H3K27Ac ChIPseq in MD901 with scramble shRNA.ctrl_2


title: md901_3752_3_input

description: input DNA for H3K27Ac ChIPseq in MD901 with shCREBBP.3752_3


title: md901_ctrl_1_K27ac

description: H3K27Ac ChIPseq in MD901 with scramble shRNA.ctrl_1


title: SUDHL6.BCL6.inh.12h.R1

description: mRNA isolated from BCL6-inhibitor-treated (12 hours) human GCB-DLBCL SUDHL6 cells

source_name: GCB-DLBCL cell line SUDHL6, treated with BCL6 inhibitor for 24 hours,  replicate 1


title: md901_11027_3_input

description: input DNA for H3K27Ac ChIPseq in MD901 with shCREBBP.11027_3


title: md901_11027_2_K27ac

description: H3K27Ac ChIPseq in MD901 with shCREBBP.11027_2


title: md901_11027_3_K27ac

description: H3K27Ac ChIPseq in MD901 with shCREBBP.11027_3


title: md901_11027_1_input

description: input DNA for H3K27Ac ChIP in MD901 with shCREBBP.11027_1


title: mouse cells with shCrebbp AO229_3

description:
total RNA > 200 nt
mRNA isolated from mouse cells treated with shCrebbp

data_processing:
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long paired-end reads were mapped to the reference mouse genome sequence, mm10, using Tophat2 aligner (Daehwan et al, Genome Biology 2013,14:R36) with the default parameters and --library-type fr-firststrand. The mRNA expression level for each gene was represented as FPKM (fragments per kilobase of transcript per million fragments mapped), called by Cufflinks (Trapnell et al, Nat Biotech 2010, 28: 511–515) in the Tophat2 package.
Genome_build: mm10
Supplementary_files_format_and_content: excel file with FPKM values.

source_name: splenic B220+ GFP+ lymphocytes_shCrebbp

growth_protocol: Cells were isolated from mouse spleens upon sacrifice.

extract_protocol:
Total RNA was extracted based on Trizol protocol (Invitrogen)
Libraries were prepared according to a version of Illumina's TruSeq Stranded Total RNA with Ribo-depletion protocol (Illumina, CA)

value: lymphoma cells

tag: tissue

value: spleen


title: HCT116 p53-/- IgG (Mock)

city: Pune

first: Samit

last: Chattopadhyay

state: Maharashtra

address: Ganeshkhind

department: Chromatin and disease biology lab

country: India

institute: National Centre For Cell Science

data_processing:
Base calling was performed using "Real Time Analysis (RTA)", a primary analysis software on Illumina GAIIx with "Consensus Assessment of Sequence and Variation (CASAVA)" software V1.8
Adapter trimming and  read quality  confirmation was performed using Cutadapt v1.2.1 and FastQC v0.10.1, respectively.
Good quality reads were aligned to human genome (hg19 build) using Bowtie 2 v2.2.1 . Downstream processing of alignment files was done using SAMtools v0.1.19.
Peak calling was performed using MACS v1.4.2.
Genome_build: Human Reference Genome hg19 build
Supplementary_files_format_and_content: All processed files are in .bed format and represents peak coordinates

source_name: HCT116 p53-/- cell line

growth_protocol: HCT116 p53+/+ and HCT116 p53-/- cells were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and antibiotic and antimycotic (1X, Gibco) at 37°C with 5% CO2.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed using ChIP assay kit (Upstate Biotechnology) following the manufacturer’s instructions.  Lysates obtained after sonication were subjected to pull down with antibody.
ChIP enriched DNA was subjected to library construction using Illumina's "Preparing samples for ChIP sequencing of DNA" kit. Briefly, DNA ends were repaired and phosphorylated. 3'-dA overhangs were generated using Klenow (exo-) and dATP. Thereafter, the adaptors were ligated. PCR amplification for 18 cycles and size selection was performed.

treatment_protocol: No treatment

tag: cell line

value: Human colorectal carcinoma

value: Normal Rabbit IgG (Santa Cruz Biotechnology, sc-2027)


title: Adipocyte precursor cells, Untreated

city: New Haven

first: Valerie

last: Horsley

state: CT

address: 266 Whitney avenue

department: MCDB

institute: Yale University

data_processing:
Illumina HiSeq2000 software used for basecalling.
Tophat (Version 2.0.2) to align reads to mm9 using default parameters
Cuffmerge (Version 2.0.2) to assemble the final transcriptome using default parameters
Cuffdiff (version 2.0.2) to quantify differential expression using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output

source_name: Dermis

growth_protocol: Adipocyte precursor cells were grown to 50% confluency in 10% FBS DMEM media at 37oC 5% CO2

extract_protocol:
Extraction of RNA was done using a combination of Trizol and Rneasy mini kit by Qiagen
illumina Truseq mRNA library prep protocol

treatment_protocol: When cells reached 50% confluency they were switched to 0.5% FBS DMEM overnight and treated with 30ng/ml of mouse Pdgfa

tag: strain

tag: Sex

value: male

tag: age

value: 6 week old

value: Dermis

value: adipocyte precursor cells


title: HCT116 p53-/- SMAR1 (Immune)

value: SMAR1/BANP (Bethyl Laboratories, A300-279A)


title: Adipocyte precursor cells, Pdgfa 1h


title: Adipocyte precursor cells, Pdgfa 2h


title: HCT116 p53+/+ SMAR1 (Immune)

source_name: HCT116 p53+/+ cell line


title: md901_11027_1_K27ac

description: H3K27Ac ChIPseq in MD901 with shCREBBP.11027_1


title: HCT116 p53+/+ IgG (Mock)


title: mouse cells with shCrebbp AO229_2


title: mouse cells with shCrebbp AO228_4


title: md901_3752_2_K27ac

description: H3K27Ac ChIPseq in MD901 with shCREBBP.3752_2


title: mouse cells with shCrebbp AO228_3


title: 24.Mef2.IR

city: London

first: Marc

last: Dionne

address: Level 0, Flowers Building

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: Mef2 knockdown replicate 4

data_processing:
Illumina RTA software was used for basecalling.
Sequenced reads were demultiplexed and adaper trimmed using Illumina bcl2fastq software, then mapped to Drosophila melanogaster genome version 6.26 using STAR 2.4.0j. Command line: STAR  --outSJfilterCountUniqueMin 5   2   2   2     --outSJfilterCountTotalMin 5   2   2   2      --outFilterType BySJout
Mapped reads were associated with genes using the FeatureCounts command in Rsubread. Differentially-expressed genes were identified using Limma.
Genome_build: BDGP6.26
Supplementary_files_format_and_content: tab-delimited text spreadsheet of non-normalized counts mapping to genes

organism: Drosophila melanogaster

source_name: whole adult male flies

extract_protocol:
For each sample, 5 male flies were lysed in 200 ul TRIzol reagent and total RNA was extracted according to the manufacturer's instructions, followed by an extra round of ethanol precipitation.
Libraries were prepared using Illumina TruSeq Stranded mRNA v2, with the following changes from the manufacturer’s protocol: starting samples were 250ng total RNA; fragmentation was performed for 10 minutes at 94°; no spike-ins were used; and 14 cycles of PCR were used to enrich libraries. Libraries were sequenced on an Illumina NextSeq 500 using v1 chemistry.

tag: genotype

value: 5-10 days posteclosion


title: mouse cells with scramble shRNA control AO227_5

description:
total RNA > 200 nt
mRNA isolated from mouse cells treated with scramble shRNA

source_name: splenic B220+ GFP+ lymphocytes_scramble shRNA


title: 25.Mef2.IR

description: Mef2 knockdown replicate 5


title: mouse cells with scramble shRNA control AO227_4


title: 22.Mef2.IR

description: Mef2 knockdown replicate 2


title: 5.Ctrl

description: control replicate 5


title: mouse cells with scramble shRNA control AO227_3


title: 21.Mef2.IR

description: Mef2 knockdown replicate 1


title: md901_11027_2_input

description: input DNA for H3K27Ac ChIPseq in MD901 with shCREBBP.11027_2


title: mouse cells with scramble shRNA control AO227_2


title: GM12878_FACS_sorted_G2_1

city: Palo Alto

first: Xingqi

last: Chen

address: 269 Campus Drive

institute: Stanford University

data_processing:
Library strategy: ATAC-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie, duplicate fragments were then removed using Picard. Peaks were called using the ZINBA algorithm, which was first applied to each dataset independently, using the following parameters: a 300bp window, 50bp offset, background and enriched components were modeled using the intercept, while the zero-inflated component was modeled using alignability, a posterior probability of 0.99 was used to select the set of significant regions. The peak sets from the same cell-type and number of cells were merged.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, arbitrary score (1000), strand

source_name: ATCC cell line GM12878

growth_protocol: ATCC cell lines (GM12878, HT1080) were purchesed from ATCC and maintained in standerd protocol according to the instruction, and sorted with FACS.

extract_protocol:
50K cells were used for ATAC-seq lib in every group of FACS sorted cells
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit and using custom-made Tn5 transposase ( where Atto-590 labled adaptor)

treatment_protocol: cells were fixed and sorted based on DAPI staining and ATAC-see color intensity

value: FACS sorted G2 group


title: GM12878_FACS_sorted_G2_2


title: polyA mRNA RNA-seq from A549 (ENCLB555AUL)

description:
https://www.encodeproject.org/experiments/ENCSR000CON/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line A549. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size.
experiment encode accession: ENCSR000CON
assay title: polyA mRNA RNA-seq
assembly: GRCh38, hg19
encode release date: 2011-10-17
lab: Thomas Gingeras, CSHL
library encode accession: ENCLB555AUL
size range: >200
spikeins used: /references/ENCSR402QNO/

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

source_name: Homo sapiens A549 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/8900792d-af50-4ee5-bb33-0afc8879eddf/@@download/attachment/LID8963.pdf

value: immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: 58 year

tag: dev stage

value: adult

tag: lab

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS444ENC at ENCODE; https://www.encodeproject.org/ENCBS444ENC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ENCODE dbxrefs A549; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=A549

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-185.aspx


title: Sample_181_4_K27Ac

description: H3K27Ac ChIP in mouse cells with shCrebbp 181_4

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: mouse mm10 build
Supplementary_files_format_and_content: bigwig and bigbed formats

source_name: splenic B220+ lymphocytes

tag: cell type

value: lymphoma cells

value: Crebbp knock-down

value: H3K27Ac (ab4729, Rabbit, 2 ug)


title: Sample_181_4_Input

description: input DNA for H3K27Ac ChIP in mouse cells with shCrebbp 181_4


title: GM12878_FACS_sorted_S_1

value: FACS sorted S group


title: 4.Ctrl

description: control replicate 4


title: GM12878_FACS_sorted_S_2