title: microRNA-seq from fibroblast of arm (ENCLB561XOB)

description:
https://www.encodeproject.org/experiments/ENCSR697KHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human fibroblast of arm
experiment encode accession: ENCSR697KHQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB561XOB
size range: <30

value: fibroblast of arm

value: primary cell

tag: description

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: microRNA-seq from fibroblast of arm (ENCLB242OXW)

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/ENCSR697KHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human fibroblast of arm
experiment encode accession: ENCSR697KHQ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB242OXW
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: biosample encode accession

tag: age

tag: dev stage

tag: Sex

tag: lab

tag: link

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


title: ChIP-seq from limb (ENCLB121DTO)

description:
https://www.encodeproject.org/experiments/ENCSR242PHH/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR242PHH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB121DTO
size range: 300-500

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (10.5 days)

tag: antibody

value: limb

value: tissue

value: Limb from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/

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


title: ChIP-seq from limb (ENCLB967FXK)

description:
https://www.encodeproject.org/experiments/ENCSR242PHH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR242PHH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB967FXK
size range: 300-500

value: Limb from 51 embryonic 10.5 day mice

tag: health state

value: healthy

value: ENCBS892NXC at ENCODE; https://www.encodeproject.org/ENCBS892NXC/


title: ChIP-seq from Karpas-422 (ENCLB622GCR)

description:
https://www.encodeproject.org/experiments/ENCSR910XKX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR910XKX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622GCR
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens Karpas-422 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

tag: line

value: immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: adult

value: female

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

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 OCI-LY7 (ENCLB362DZN)

description:
https://www.encodeproject.org/experiments/ENCSR752KQT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR752KQT
assay title: ChIP-seq
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB362DZN
size range: 200-600
nucleic acid starting quantity: 17.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY7 immortalized cell line

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: 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: male

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 limb (ENCLB144FDT)

description:
https://www.encodeproject.org/experiments/ENCSR238SGC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 10.5 day mouse limb
experiment encode accession: ENCSR238SGC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR687ALB
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB144FDT
size range: 300-500

value: limb

value: tissue

value: Limb from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS844FSC at ENCODE; https://www.encodeproject.org/ENCBS844FSC/

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


title: ChIP-seq from OCI-LY1 (ENCLB563BJY)

description:
https://www.encodeproject.org/experiments/ENCSR597UDW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR597UDW
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB563BJY
size range: 200-600
nucleic acid starting quantity: 9.675
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY1 immortalized cell line

value: 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: Bradley Bernstein, Broad

value: ENCBS945KYE at ENCODE; https://www.encodeproject.org/ENCBS945KYE/

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 (ENCLB419KER)

description:
https://www.encodeproject.org/experiments/ENCSR587FCM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR587FCM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB419KER
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens SUDHL6 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: male

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

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 OCI-LY1 (ENCLB367EFH)

description:
https://www.encodeproject.org/experiments/ENCSR569IIN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR569IIN
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB367EFH
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/dc2b7414-3879-49b3-b862-349fadbc5d8d/@@download/attachment/ChIP_Protocol_For_Fresh_or%20Frozen_Cells_v09.3.pdf

value: Control

value: B cell lymphoma

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/


title: ChIP-seq from SUDHL6 (ENCLB466WSR)

description:
https://www.encodeproject.org/experiments/ENCSR511OIE/
***************
biological replicate number: 2
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: ENCLB466WSR
size range: 200-600

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: immortalized cell line

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


title: ChIP-seq from fibroblast of arm (ENCLB078QTQ)

description:
https://www.encodeproject.org/experiments/ENCSR906NGD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR906NGD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB078QTQ
size range: 200-600
nucleic acid starting quantity: 97.75
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: 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: ChIP-seq from fibroblast of arm (ENCLB503MGA)

description:
https://www.encodeproject.org/experiments/ENCSR906NGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906NGD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503MGA
size range: 200-600
nucleic acid starting quantity: 122.75
nucleic acid starting quantity units: ng

value: adult

value: male

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


title: ChIP-seq from hindbrain (ENCLB130ETG)

description:
https://www.encodeproject.org/experiments/ENCSR191XBS/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR191XBS
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB130ETG
size range: 300-500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (10.5 days)

value: Control

value: hindbrain

value: tissue

value: Hindbrain from 51 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS723QMZ at ENCODE; https://www.encodeproject.org/ENCBS723QMZ/

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


title: ChIP-seq from hindbrain (ENCLB653KTR)

description:
https://www.encodeproject.org/experiments/ENCSR191XBS/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on embryonic 10.5 day mouse hindbrain
experiment encode accession: ENCSR191XBS
assay title: ChIP-seq
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB653KTR
size range: 300-500

value: Hindbrain from 69 embryonic 10.5 day mice

value: ENCBS626UIA at ENCODE; https://www.encodeproject.org/ENCBS626UIA/


title: ChIP-seq from SUDHL6 (ENCLB450ABL)

description:
https://www.encodeproject.org/experiments/ENCSR511OIE/
***************
biological replicate number: 2
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: ENCLB450ABL
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a47aaf7e-38f5-4326-914a-98991f61345a/@@download/attachment/Alon%27s%20SCN%20revised.pdf

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: Bradley Bernstein, Broad

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

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 MCF-7 (ENCLB115TEN)

description:
https://www.encodeproject.org/experiments/ENCSR493NBY/
***************
biological replicate number: 1
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: ENCLB115TEN
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 immortalized cell line

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

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

tag: passage number

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/

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 embryonic facial prominence (ENCLB315PHC)

description:
https://www.encodeproject.org/experiments/ENCSR151APL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 10.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR151APL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR682UEM
encode release date: 2016-07-19
lab: Bing Ren, UCSD
library encode accession: ENCLB315PHC
size range: 300-500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (10.5 days)

value: embryonic facial prominence

value: tissue

value: Craniofacial prominence from 69 embryonic 10.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS938XWJ at ENCODE; https://www.encodeproject.org/ENCBS938XWJ/

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


title: ChIP-seq from Karpas-422 (ENCLB425UAC)

description:
https://www.encodeproject.org/experiments/ENCSR978BQI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR978BQI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB425UAC
size range: 200-600

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: 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 Karpas-422 (ENCLB612QFL)

description:
https://www.encodeproject.org/experiments/ENCSR963HAR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR963HAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB612QFL
size range: 200-600

value: adult

value: female


title: ChIP-seq from DOHH2 (ENCLB156GXN)

description:
https://www.encodeproject.org/experiments/ENCSR460SEN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR460SEN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB156GXN
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens DOHH2 immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: male

value: ENCBS662OGM at ENCODE; https://www.encodeproject.org/ENCBS662OGM/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from SUDHL6 (ENCLB954NXW)

description:
https://www.encodeproject.org/experiments/ENCSR494LJG/
***************
biological replicate number: 2
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: ENCLB954NXW
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: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

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 OCI-LY1 (ENCLB790URK)

description:
https://www.encodeproject.org/experiments/ENCSR859JNA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR859JNA
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790URK
size range: 200-600

value: 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: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

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: R3_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.

organism: Macaca mulatta

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

tag: cell line

value: lymphoblastoid cell line (LCL)

tag: ip antibody

value: none (input)


title: ChIP-seq from fibroblast of arm (ENCLB779ELE)

description:
https://www.encodeproject.org/experiments/ENCSR479HKJ/
***************
biological replicate number: 1
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: ENCLB779ELE
size range: 200-600
nucleic acid starting quantity: 133
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: 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: ChIP-seq from DOHH2 (ENCLB593ZGZ)

description:
https://www.encodeproject.org/experiments/ENCSR784AQY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR784AQY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB593ZGZ
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: Bradley Bernstein, Broad

value: ENCBS662OGM at ENCODE; https://www.encodeproject.org/ENCBS662OGM/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: R2_input

value: lymphoblastoid cell line (LCL)

value: none (input)


title: R3_IP

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


title: ChIP-seq from DOHH2 (ENCLB541DJK)

description:
https://www.encodeproject.org/experiments/ENCSR784AQY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR784AQY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB541DJK
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: adult

value: refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/


title: ChIP-seq from SK-N-SH (ENCLB056AOW)

description:
https://www.encodeproject.org/experiments/ENCSR914QOK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR914QOK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB056AOW
size range: 200-600

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

value: SK-N-SH

value: 4 year

value: child

value: female

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: ChIP-seq from MCF-7 (ENCLB953JFG)

description:
https://www.encodeproject.org/experiments/ENCSR768LHG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR768LHG
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB953JFG
size range: 200-600

extract_protocol: not provided

value: Control

value: immortalized cell line

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

value: 69 year

value: breast cancer (adenocarcinoma)

value: Bradley Bernstein, Broad

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/

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: R2_IP

value: lymphoblastoid cell line (LCL)

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


title: ChIP-seq from MCF-7 (ENCLB479DDJ)

description:
https://www.encodeproject.org/experiments/ENCSR768LHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR768LHG
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB479DDJ
size range: 200-600

value: adult


title: C2_input

organism: Pan troglodytes

value: none (input)


title: C2_IP


title: ChIP-seq from SK-N-SH (ENCLB891ZOW)

description:
https://www.encodeproject.org/experiments/ENCSR914QOK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR914QOK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB891ZOW
size range: 200-600

value: SK-N-SH

value: 4 year

value: child

value: female

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


title: ChIP-seq from DOHH2 (ENCLB404CPG)

description:
https://www.encodeproject.org/experiments/ENCSR741STU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR741STU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB404CPG
size range: 200-600

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: male

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from DOHH2 (ENCLB658ING)

description:
https://www.encodeproject.org/experiments/ENCSR741STU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR741STU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB658ING
size range: 200-600

value: refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma

value: Bradley Bernstein, Broad

value: ENCBS662OGM at ENCODE; https://www.encodeproject.org/ENCBS662OGM/


title: ChIP-seq from SUDHL6 (ENCLB239XCW)

description:
https://www.encodeproject.org/experiments/ENCSR694PMV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR694PMV
assay title: ChIP-seq
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB239XCW
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: adult

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

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 Karpas-422 (ENCLB058TFM)

description:
https://www.encodeproject.org/experiments/ENCSR660IQS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR660IQS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB058TFM
size range: 200-600

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: female

value: human B cell non-Hodgkin's lymphoma

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

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 Karpas-422 (ENCLB269URX)

description:
https://www.encodeproject.org/experiments/ENCSR910XKX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR910XKX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269URX
size range: 200-600

value: immortalized cell line

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


title: microRNA-seq from HCT116 (ENCLB221LTL)

description:
https://www.encodeproject.org/experiments/ENCSR650SEP/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human HCT116
experiment encode accession: ENCSR650SEP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB221LTL
size range: <30

source_name: Homo sapiens HCT116 immortalized cell line

value: colorectal carcinoma (PMID:7214343)

value: unknown

value: male

value: colorectal carcinoma

value: Barbara Wold, Caltech

value: ENCBS004UZY at ENCODE; https://www.encodeproject.org/ENCBS004UZY/

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-LY1 (ENCLB499ZHY)

description:
https://www.encodeproject.org/experiments/ENCSR422JNY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR422JNY
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB499ZHY
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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: Bradley Bernstein, Broad

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

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 DOHH2 (ENCLB980RFK)

description:
https://www.encodeproject.org/experiments/ENCSR627TNG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR627TNG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB980RFK
size range: 200-600

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: ENCBS652PBR at ENCODE; https://www.encodeproject.org/ENCBS652PBR/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: microRNA-seq from HCT116 (ENCLB215EDP)

description:
https://www.encodeproject.org/experiments/ENCSR650SEP/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human HCT116
experiment encode accession: ENCSR650SEP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB215EDP
size range: <30

value: colorectal carcinoma (PMID:7214343)

value: unknown

value: male

value: colorectal carcinoma

value: Barbara Wold, Caltech

value: ENCBS009DQE at ENCODE; https://www.encodeproject.org/ENCBS009DQE/

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: WGBS from GM12878 (ENCLB794YYH)

description:
https://www.encodeproject.org/experiments/ENCSR890UQO/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing GM12878
experiment encode accession: ENCSR890UQO
assay title: WGBS
assembly: GRCh38
encode release date: 2016-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB794YYH

source_name: Homo sapiens GM12878 immortalized cell line

value: GM12878, B-lymphocyte, lymphoblastoid

value: adult

value: female

value: Richard Myers, HAIB

value: ENCBS057BBL at ENCODE; https://www.encodeproject.org/ENCBS057BBL/

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; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from OCI-LY1 (ENCLB299AAB)

description:
https://www.encodeproject.org/experiments/ENCSR569IIN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR569IIN
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB299AAB
size range: 300-800

value: Control

value: 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: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS945KYE at ENCODE; https://www.encodeproject.org/ENCBS945KYE/

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: WGBS from HepG2 (ENCLB223EJM)

description:
https://www.encodeproject.org/experiments/ENCSR881XOU/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HepG2
experiment encode accession: ENCSR881XOU
assay title: WGBS
assembly: GRCh38
encode release date: 2015-10-13
lab: Richard Myers, HAIB
library encode accession: ENCLB223EJM

source_name: Homo sapiens HepG2 immortalized cell line

value: HepG2, hepatocellular carcinoma

value: 15 year

value: child

value: male

value: hepatocellular carcinoma

value: ENCBS778JAH at ENCODE; https://www.encodeproject.org/ENCBS778JAH/

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


title: ChIP-seq from OCI-LY1 (ENCLB543MQZ)

description:
https://www.encodeproject.org/experiments/ENCSR597UDW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR597UDW
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB543MQZ
size range: 200-600

value: immortalized cell line

value: adult

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/


title: WGBS from HepG2 (ENCLB569VMN)

description:
https://www.encodeproject.org/experiments/ENCSR881XOU/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing HepG2
experiment encode accession: ENCSR881XOU
assay title: WGBS
assembly: GRCh38
encode release date: 2015-10-13
lab: Richard Myers, HAIB
library encode accession: ENCLB569VMN

value: Richard Myers, HAIB

value: ENCBS612GBT at ENCODE; https://www.encodeproject.org/ENCBS612GBT/


title: ChIP-seq from DOHH2 (ENCLB603FQD)

description:
https://www.encodeproject.org/experiments/ENCSR627TNG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR627TNG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB603FQD
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: Bradley Bernstein, Broad

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from SUDHL6 (ENCLB035XAR)

description:
https://www.encodeproject.org/experiments/ENCSR316KHQ/
***************
biological replicate number: 1
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: ENCLB035XAR
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: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

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 OCI-LY3 (ENCLB791ERU)

description:
https://www.encodeproject.org/experiments/ENCSR867TPP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR867TPP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB791ERU
size range: 200-600

source_name: Homo sapiens OCI-LY3 immortalized cell line

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

value: B cell lymphoma

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 OCI-LY3 (ENCLB190ZSO)

description:
https://www.encodeproject.org/experiments/ENCSR867TPP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR867TPP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB190ZSO
size range: 300-600

value: adult

value: Bradley Bernstein, Broad

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


title: ChIP-seq from fibroblast of arm (ENCLB670CHL)

description:
https://www.encodeproject.org/experiments/ENCSR866KFY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR866KFY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670CHL
size range: 200-600
nucleic acid starting quantity: 21.88
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: 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: ChIP-seq from OCI-LY7 (ENCLB942TTE)

description:
https://www.encodeproject.org/experiments/ENCSR243AIS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR243AIS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB942TTE
size range: 200-600
nucleic acid starting quantity: 272.5
nucleic acid starting quantity units: ng

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: male

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 HCT116 (ENCLB149OYB)

description:
https://www.encodeproject.org/experiments/ENCSR198WIH/
***************
biological replicate number: 1
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: ENCLB149OYB
size range: 200-600

value: Control

value: cells obtained from ATCC

value: unknown

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

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 SK-N-SH (ENCLB431MHE)

description:
https://www.encodeproject.org/experiments/ENCSR185OHN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR185OHN
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB431MHE
size range: 200-600

value: SK-N-SH

value: 4 year

value: child

value: female

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 HCT116 (ENCLB969JXW)

description:
https://www.encodeproject.org/experiments/ENCSR810BDB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR810BDB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB969JXW
size range: 200-600

value: immortalized cell line

value: male

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


title: ChIP-seq from OCI-LY1 (ENCLB223HEF)

description:
https://www.encodeproject.org/experiments/ENCSR184QUS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR184QUS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB223HEF
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: adult

value: B cell lymphoma

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

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 Karpas-422 (ENCLB224YGM)

description:
https://www.encodeproject.org/experiments/ENCSR963HAR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR963HAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB224YGM
size range: 200-600

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: WGBS from K562 (ENCLB742NWU)

description:
https://www.encodeproject.org/experiments/ENCSR765JPC/
***************
biological replicate number: 1
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing K562
experiment encode accession: ENCSR765JPC
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB742NWU
size range: 100-300

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: K562, myelogenous leukemia

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/

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 ES-E14 (ENCLB112GPU)

description:
https://www.encodeproject.org/experiments/ENCSR095IPH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on E0 mouse ES-E14
experiment encode accession: ENCSR095IPH
assay title: ChIP-seq
encode release date: 2014-10-23
lab: Bing Ren, UCSD
library encode accession: ENCLB112GPU

source_name: Mus musculus strain 129/Ola ES-E14 stem cell male

value: Control

value: stem cell

value: mouse embryonic stem cell line E14

value: unknown

value: male

value: Bing Ren, UCSD

value: ENCBS054SMP at ENCODE; https://www.encodeproject.org/ENCBS054SMP/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: ChIP-seq from OCI-LY1 (ENCLB371EZY)

description:
https://www.encodeproject.org/experiments/ENCSR449AYM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR449AYM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB371EZY
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: 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: Bradley Bernstein, Broad

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

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 fibroblast of arm (ENCLB305UEH)

description:
https://www.encodeproject.org/experiments/ENCSR922FLS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR922FLS
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB305UEH
size range: 200-600

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

value: Control

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: 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: ChIP-seq from OCI-LY1 (ENCLB380HWY)

description:
https://www.encodeproject.org/experiments/ENCSR449AYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR449AYM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB380HWY
size range: 200-600
nucleic acid starting quantity: 252.5
nucleic acid starting quantity units: ng

value: 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: male

value: ENCBS945KYE at ENCODE; https://www.encodeproject.org/ENCBS945KYE/


title: ChIP-seq from DOHH2 (ENCLB234AXH)

description:
https://www.encodeproject.org/experiments/ENCSR460SEN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR460SEN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB234AXH
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: adult

value: Bradley Bernstein, Broad

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from OCI-LY7 (ENCLB868KJZ)

description:
https://www.encodeproject.org/experiments/ENCSR447ZGY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR447ZGY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB868KJZ
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: B cell lymphoma

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: WGBS from K562 (ENCLB542OXH)

description:
https://www.encodeproject.org/experiments/ENCSR765JPC/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing K562
experiment encode accession: ENCSR765JPC
assay title: WGBS
assembly: GRCh38
encode release date: 2016-03-22
lab: Richard Myers, HAIB
library encode accession: ENCLB542OXH

value: immortalized cell line

value: K562, myelogenous leukemia

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS577JGM at ENCODE; https://www.encodeproject.org/ENCBS577JGM/

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: C1_input

value: lymphoblastoid cell line (LCL)

value: none (input)


title: C2C12 polyA RNA-seq siKlf5 DMd3

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

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

molecule: polyA RNA

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: RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA. RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA). Libraries were paired-ended sequenced on a HiSeq2500 sequencer (Illumina, San Diego, CA). Reads were aligned to mm9 genome using default parameter for RNA-star. Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.

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.

tag: cell type

value: C2C12 myoblast

tag: differentiation stage


title: C1_IP

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


title: ChIP-seq from OCI-LY7 (ENCLB195ELU)

description:
https://www.encodeproject.org/experiments/ENCSR447ZGY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR447ZGY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB195ELU
size range: 200-600
nucleic acid starting quantity: 2.85
nucleic acid starting quantity units: ng
instrument models: Illumina HiSeq 2000,Illumina NextSeq 500

source_name: Homo sapiens OCI-LY7 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: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

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


title: ChIP-seq from OCI-LY7 (ENCLB342BAX)

description:
https://www.encodeproject.org/experiments/ENCSR063AUO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR063AUO
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB342BAX
size range: 200-600

value: Control

value: immortalized cell line

value: ENCBS121JKZ at ENCODE; https://www.encodeproject.org/ENCBS121JKZ/

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: C2C12 polyA RNA-seq siKlf5 DMd2


title: ChIP-seq from OCI-LY1 (ENCLB681SUP)

description:
https://www.encodeproject.org/experiments/ENCSR422JNY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR422JNY
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB681SUP
size range: 200-600
nucleic acid starting quantity: 19.05
nucleic acid starting quantity units: ng

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: ENCBS945KYE at ENCODE; https://www.encodeproject.org/ENCBS945KYE/

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 polyA RNA-seq siKlf5 DMd1

value: C2C12 myoblast


title: ChIP-seq from Karpas-422 (ENCLB415MTR)

description:
https://www.encodeproject.org/experiments/ENCSR660IQS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR660IQS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB415MTR
size range: 200-600

source_name: Homo sapiens Karpas-422 immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: female

value: human B cell non-Hodgkin's lymphoma

value: ENCBS171YVY at ENCODE; https://www.encodeproject.org/ENCBS171YVY/

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 Karpas-422 (ENCLB386GMR)

description:
https://www.encodeproject.org/experiments/ENCSR910XKX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR910XKX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB386GMR
size range: 200-600

value: immortalized cell line

value: adult

value: Bradley Bernstein, Broad

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


title: ChIP-seq from OCI-LY7 (ENCLB440CWP)

description:
https://www.encodeproject.org/experiments/ENCSR752KQT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR752KQT
assay title: ChIP-seq
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB440CWP
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: male

value: B cell lymphoma

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: ChIP-seq from Karpas-422 (ENCLB960FNO)

description:
https://www.encodeproject.org/experiments/ENCSR367UDO/
***************
biological replicate number: 2
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: ENCLB960FNO
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: Control

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/


title: ChIP-seq from OCI-LY3 (ENCLB770PIT)

description:
https://www.encodeproject.org/experiments/ENCSR638FRE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR638FRE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB770PIT
size range: 200-600

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

value: 52 year

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 OCI-LY7 (ENCLB449QWH)

description:
https://www.encodeproject.org/experiments/ENCSR063AUO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR063AUO
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB449QWH
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eaafee87-23f3-4bb4-adb1-585af01db120/@@download/attachment/ChIP%20New%20General%20ChIP%20Protocol%20041510%20v05.pdf

value: immortalized cell line

value: adult

value: Bradley Bernstein, Broad

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


title: WGBS from GM12878 (ENCLB898WPW)

description:
https://www.encodeproject.org/experiments/ENCSR890UQO/
***************
biological replicate number: 2
technical replicate number: 1
description: HAIB Whole Genome Bisulfite Sequencing GM12878
experiment encode accession: ENCSR890UQO
assay title: WGBS
assembly: GRCh38
encode release date: 2016-02-23
lab: Richard Myers, HAIB
library encode accession: ENCLB898WPW

value: A standard Myers lab growth of GM12878, B-lymphocyte, lymphoblastoid

value: unknown

value: female

value: Richard Myers, HAIB

value: ENCBS232JAP at ENCODE; https://www.encodeproject.org/ENCBS232JAP/

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; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from OCI-LY3 (ENCLB238IOK)

description:
https://www.encodeproject.org/experiments/ENCSR604JFH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR604JFH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB238IOK
size range: 200-600

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

value: male

value: B cell lymphoma


title: ChIP-seq from fibroblast of arm (ENCLB974HCB)

description:
https://www.encodeproject.org/experiments/ENCSR914AWT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR914AWT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB974HCB
size range: 200-600
nucleic acid starting quantity: 151.5
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: 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: microRNA-seq from MCF-7 (ENCLB235RRZ)

description:
https://www.encodeproject.org/experiments/ENCSR343HIX/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human MCF-7
experiment encode accession: ENCSR343HIX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB235RRZ
size range: <30

value: immortalized cell line

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

value: Barbara Wold, Caltech

value: ENCBS254AYH at ENCODE; https://www.encodeproject.org/ENCBS254AYH/

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: ENCODE dbxrefs MCF-7; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MCF-7


title: C2C12 polyA RNA-seq siCtrl DMd1

value: C2C12 myoblast


title: ChIP-seq from OCI-LY3 (ENCLB542IVG)

description:
https://www.encodeproject.org/experiments/ENCSR638FRE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR638FRE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB542IVG
size range: 300-600

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

value: 52 year

value: male

value: B cell lymphoma

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 Karpas-422 (ENCLB235TND)

description:
https://www.encodeproject.org/experiments/ENCSR867UKC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR867UKC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB235TND
size range: 200-600

value: immortalized cell line

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: microRNA-seq from MCF-7 (ENCLB357SJI)

description:
https://www.encodeproject.org/experiments/ENCSR343HIX/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human MCF-7
experiment encode accession: ENCSR343HIX
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB357SJI
size range: <30

value: mammary gland, adenocarcinoma. (PMID:4357757), newly promoted to tier 2:not in 2011 analysis

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: Barbara Wold, Caltech

value: ENCBS155VQC at ENCODE; https://www.encodeproject.org/ENCBS155VQC/

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: ENCODE dbxrefs MCF-7; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=MCF-7


title: C2C12 polyA RNA-seq siCtrl DMd2

value: C2C12 myoblast


title: ChIP-seq from fibroblast of arm (ENCLB866EZN)

description:
https://www.encodeproject.org/experiments/ENCSR866KFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR866KFY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB866EZN
size range: 200-600
nucleic acid starting quantity: 19
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: 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-LY7 (ENCLB769IJW)

description:
https://www.encodeproject.org/experiments/ENCSR243AIS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR243AIS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB769IJW
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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: 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 Karpas-422 (ENCLB352ZHN)

description:
https://www.encodeproject.org/experiments/ENCSR306VSH/
***************
biological replicate number: 1
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: ENCLB352ZHN
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: female

value: human B cell non-Hodgkin's lymphoma

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

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 SUDHL6 (ENCLB906CZN)

description:
https://www.encodeproject.org/experiments/ENCSR587FCM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR587FCM
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB906CZN
size range: 200-600

source_name: Homo sapiens SUDHL6 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: male

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

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: DNase-seq from fibroblast of arm (ENCLB544CVI)

description:
https://www.encodeproject.org/experiments/ENCSR217TAW/
***************
biological replicate number: 1
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: ENCLB544CVI
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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: 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: ChIP-seq from OCI-LY3 (ENCLB083CCE)

description:
https://www.encodeproject.org/experiments/ENCSR857GMX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR857GMX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB083CCE
size range: 300-600

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

value: B cell lymphoma

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 OCI-LY3 (ENCLB627TJR)

description:
https://www.encodeproject.org/experiments/ENCSR857GMX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR857GMX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB627TJR
size range: 200-600

value: male

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


title: ChIP-seq from OCI-LY7 (ENCLB390FDV)

description:
https://www.encodeproject.org/experiments/ENCSR060WGK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR060WGK
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB390FDV
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: 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 ES-E14 (ENCLB642JSS)

description:
https://www.encodeproject.org/experiments/ENCSR095IPH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on E0 mouse ES-E14
experiment encode accession: ENCSR095IPH
assay title: ChIP-seq
encode release date: 2014-10-23
lab: Bing Ren, UCSD
library encode accession: ENCLB642JSS

value: Control

value: stem cell

value: mouse embryonic stem cell line E14

value: unknown

value: Bing Ren, UCSD

value: ENCBS042ENC at ENCODE; https://www.encodeproject.org/ENCBS042ENC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_C320; http://web.expasy.org/cellosaurus/CVCL_C320

value: ENCODE dbxrefs ES-E14; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=ES-E14


title: ChIP-seq from OCI-LY1 (ENCLB592ZSK)

description:
https://www.encodeproject.org/experiments/ENCSR184QUS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR184QUS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592ZSK
size range: 200-600
nucleic acid starting quantity: 23
nucleic acid starting quantity units: ng

value: 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: Bradley Bernstein, Broad

value: ENCBS945KYE at ENCODE; https://www.encodeproject.org/ENCBS945KYE/

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 (ENCLB189TIB)

description:
https://www.encodeproject.org/experiments/ENCSR179YLS/
***************
biological replicate number: 1
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: ENCLB189TIB
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: Control

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: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

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 SUDHL6 (ENCLB288YZC)

description:
https://www.encodeproject.org/experiments/ENCSR694PMV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR694PMV
assay title: ChIP-seq
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB288YZC
size range: 200-600

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

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


title: ChIP-seq from SK-N-SH (ENCLB555ACS)

description:
https://www.encodeproject.org/experiments/ENCSR000FCV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCV
assay title: ChIP-seq
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACS
size range: 200-500

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

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 OCI-LY7 (ENCLB990HZB)

description:
https://www.encodeproject.org/experiments/ENCSR063AUO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR063AUO
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB990HZB
size range: 200-600

value: Control

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: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS121JKZ at ENCODE; https://www.encodeproject.org/ENCBS121JKZ/

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 OCI-LY3 (ENCLB139DMK)

description:
https://www.encodeproject.org/experiments/ENCSR581LZU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR581LZU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB139DMK
size range: 200-600

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

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 OCI-LY7 (ENCLB331CZI)

description:
https://www.encodeproject.org/experiments/ENCSR063AUO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR063AUO
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB331CZI
size range: 200-600

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


title: PS1M_HYY_banana1_TGACCA_L001_R1_001

city: Haikou

first: XIn

last: Chen

address: 4th College Road

country: China

institute: catas

description: small RNA

data_processing:
Raw RNA-Seq reads with low quality were firstly discarded. Sequencing adaptors were trimmed using an in-house method that recursively searches for the longest substring of the adaptor appearing within a sequence read. If a raw sequence read did not have a substring of the adaptor longer than 6nt, it was considered as having no adaptor.
The adaptor-trimmed sequences with no ambiguous reads, which were referred to as qualified reads, were then mapped to the genome sequences of banana genome using Bowtie 0.12.7 allowing no more than one mismatch.
Reads Number Per Million (CPM) were calculated for each miRNA
Raw number of reads were also normalized using upper-quatertile normalization method for differential expression analysis
Genome_build: banana A genome database (http://banana-genome.cirad.fr/)
Supplementary_files_format_and_content: excel file with raw and normalized read count of known and novel miRNAs.

organism: Musa acuminata AAA Group

source_name: leaf and root_susceptible

growth_protocol: normal condition (NC) of 24°C in MS medium with 8 h light/16 h dark

extract_protocol:
Total RNA was extracted and purified from plant samples using RNApure Plant Kit. Then, total RNA (amount >20 μg; concentration≥200 ng/μl) was sent to Illumina Sequencing Platform of Yikong Genomics for sequencing.
Total RNA was size-fractionated and isolated to obtain 10-30 nt sRNAs. Subsequently, 5' and 3' primers were ligated to sRNAs to synthesize double-stranded nucleic acids by RT-PCR. PCR products were sequenced by sequencing-by-synthesis (SBS) technique.

tag: cultivar

value: Brasilian banana

tag: genotype

value: AAA

tag: tissue

value: leaf and root

tag: harvest time

value: five full-spread leaves and one tip

tag: fusarium wilt susceptibility

value: fusarium wilt-susceptible


title: C2C12 polyA RNA-seq siKlf5 DMd0

value: C2C12 myoblast


title: ChIP-seq from OCI-LY3 (ENCLB530DKZ)

description:
https://www.encodeproject.org/experiments/ENCSR548PZS/
***************
biological replicate number: 1
technical replicate number: 3
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: ENCLB530DKZ
size range: 300-600
nucleic acid starting quantity: 28.322
nucleic acid starting quantity units: ng

tag: description

tag: biosample encode accession

tag: age

tag: dev stage

value: adult

value: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

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


title: ChIP-seq from OCI-LY7 (ENCLB365DHJ)

description:
https://www.encodeproject.org/experiments/ENCSR063AUO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR063AUO
assay title: ChIP-seq
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB365DHJ
size range: 300-800

tag: antibody

value: Control

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

tag: Sex

tag: lab

tag: link

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: C2C12 polyA RNA-seq siCtrl DMd3


title: ChIP-seq from SK-N-SH (ENCLB555ACO)

description:
https://www.encodeproject.org/experiments/ENCSR000FCT/
***************
biological replicate number: 1
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: ENCLB555ACO
size range: 200-500

tag: line

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: 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 OCI-LY7 (ENCLB662SQM)

description:
https://www.encodeproject.org/experiments/ENCSR060WGK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR060WGK
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB662SQM
size range: 200-600
nucleic acid starting quantity: 23.775
nucleic acid starting quantity units: ng

value: immortalized cell line

value: adult

value: male

tag: health state

value: B cell lymphoma

value: Bradley Bernstein, Broad


title: C2C12 polyA RNA-seq siCtrl DMd0

tag: cell type

value: C2C12 myoblast


title: ChIP-seq from OCI-LY3 (ENCLB662WPC)

description:
https://www.encodeproject.org/experiments/ENCSR604JFH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR604JFH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB662WPC
size range: 300-600

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

value: 52 year

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 OCI-LY3 (ENCLB452TCW)

description:
https://www.encodeproject.org/experiments/ENCSR548PZS/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB452TCW
size range: 300-600
nucleic acid starting quantity: 176.12
nucleic acid starting quantity units: ng


title: ChIP-seq from OCI-LY3 (ENCLB936QCA)

description:
https://www.encodeproject.org/experiments/ENCSR581LZU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR581LZU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB936QCA
size range: 300-600


title: PS1M_HYY_superbanana2_TTAGGC_L001_R1_001

description: small RNA

organism: Musa AAB Group

source_name: leaf and root_resistant

value: Plantain Banana

value: AAB

value: leaf and root

value: five full-spread leaves and one tip

value: fusarium wilt-resistant


title: ChIP-seq from SK-N-SH (ENCLB555ACR)

description:
https://www.encodeproject.org/experiments/ENCSR000FCU/
***************
biological replicate number: 2
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: ENCLB555ACR
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: female

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: ChIP-seq from SK-N-SH (ENCLB555ACK)

description:
https://www.encodeproject.org/experiments/ENCSR000FCR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACK
size range: 200-500

value: immortalized cell line

value: ENCBS489AAA at ENCODE; https://www.encodeproject.org/ENCBS489AAA/


title: ChIP-seq from SK-N-SH (ENCLB555ACL)

description:
https://www.encodeproject.org/experiments/ENCSR000FCR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACL
size range: 200-500

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


title: ChIP-seq from SK-N-SH (ENCLB555ACT)

description:
https://www.encodeproject.org/experiments/ENCSR000FCV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 SK-N-SH ChIP-Seq
experiment encode accession: ENCSR000FCV
assay title: ChIP-seq
possible controls: ENCSR000FDA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACT
size range: 200-500


title: ChIP-seq from OCI-LY3 (ENCLB553KPF)

description:
https://www.encodeproject.org/experiments/ENCSR548PZS/
***************
biological replicate number: 1
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: ENCLB553KPF
size range: 300-600

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: B cell lymphoma

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: DNase-seq from Karpas-422 (ENCLB613MEH)

description:
https://www.encodeproject.org/experiments/ENCSR019JDO/
***************
biological replicate number: 1
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: ENCLB613MEH

value: 73 year

value: female

value: human B cell non-Hodgkin's lymphoma

value: John Stamatoyannopoulos, UW

value: ENCBS530UDH at ENCODE; https://www.encodeproject.org/ENCBS530UDH/

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

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