GEO Publications
Handout
NAR 2024 (latest)
NAR 2002 (original)
All publications
FAQ
MIAME
Email GEO
NCBI
>
GEO
>
Accession Display
Not logged in |
Login
GEO help:
Mouse over screen elements for information.
Scope:
Self
Platform
Samples
Series
Family
Format:
HTML
SOFT
MINiML
Amount:
Brief
Quick
GEO accession:
Sample GSM736588
Query DataSets for GSM736588
Status
Public on Jun 03, 2011
Title
Stam_MCF-7_2
Sample type
SRA
Source name
MCF-7
Organism
Homo sapiens
Characteristics
biomaterial_type: immortalized cell line
line: MCF-7
cell organism: Human
cell description: mammary gland, adenocarcinoma. (PMID: 4357757)
cell karyotype: cancer
cell sex: F
replicate: 2
Biomaterial provider
ATCC
Growth protocol
Cells were grown according to ENCODE cell culture protocols:
http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:MCF-7_Crawford_protocol.pdf
Yale_TFBS(Farnham):MCF-7_Farnham_protocol.pdf UW_Stam:Stam_15_protocols.pdf
Extracted molecule
genomic DNA
Extraction protocol
For extraction protocol details see:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase
Library strategy
DNase-Hypersensitivity
Library source
genomic
Library selection
DNAse
Instrument model
Illumina Genome Analyzer II
Data processing
For data processing details see:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwDnase
Submission date
Jun 02, 2011
Last update date
May 15, 2019
Contact name
ENCODE DCC
E-mail(s)
encode-help@lists.stanford.edu
Organization name
ENCODE DCC
Street address
300 Pasteur Dr
City
Stanford
State/province
CA
ZIP/Postal code
94305-5120
Country
USA
Platform ID
GPL9115
Series (2)
GSE29692
DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington
GSE51334
DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions
Relations
Reanalyzed by
GSE53962
Reanalyzed by
GSE54296
Reanalyzed by
GSE59016
SRA
SRX069181
BioSample
SAMN00622306
Named Annotation
GSM736588_hg19_wgEncodeUwDnaseMcf7RawRep2.bigWig
Supplementary file
Size
Download
File type/resource
GSM736588_hg19_wgEncodeUwDnaseMcf7AlnRep2.bam
2.3 Gb
(ftp)
(http)
BAM
GSM736588_hg19_wgEncodeUwDnaseMcf7HotspotsRep2.broadPeak.gz
4.1 Mb
(ftp)
(http)
BROADPEAK
GSM736588_hg19_wgEncodeUwDnaseMcf7PkRep2.narrowPeak.gz
2.0 Mb
(ftp)
(http)
NARROWPEAK
GSM736588_hg19_wgEncodeUwDnaseMcf7RawRep2.bigWig
227.7 Mb
(ftp)
(http)
BIGWIG
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file
|
NLM
|
NIH
|
GEO Help
|
Disclaimer
|
Accessibility
|