NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM778721 Query DataSets for GSM778721
Status Public on Jan 26, 2012
Title HapMap DNase Seq GM19203
Sample type SRA
 
Source name lymphoblastoid cell line
Organism Homo sapiens
Characteristics cell type: lymphoblastoid cell line
population: YRI
ethnicity: YORUBA
country of origin: NIGERIA
Biomaterial provider http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM19203
Growth protocol 37o in RPMI
Extracted molecule genomic DNA
Extraction protocol Dnase seq protocol (provided as supplementary file linked to GSE31388)
 
Library strategy DNase-Hypersensitivity
Library source genomic
Library selection DNAse
Instrument model Illumina Genome Analyzer II
 
Description DNase-Seq
Data processing Raw data from GAII are provided for each individual. We also provide BED file format data for each individual for the top 5% of the genome in terms of total sensitivity. This data was mapped to hg18 using a custom read-mapping algorithm which we describe in detail in the associated publication. Measures of DNase sensitivity were quantile normalized within each individual to a standard normal distribution. Each individual was corrected for GC bias and the top 4 principle components were removed from the data (See manuscript).
 
Submission date Aug 15, 2011
Last update date May 28, 2018
Contact name Jacob F Degner
E-mail(s) jdegner@uchicago.edu
Organization name University of Chicago
Department Human Genetics
Lab Pritchard
Street address 920 E. 58th St
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
 
Platform ID GPL9115
Series (1)
GSE31388 Variation in chromatin accessibility is a key determinant of heritable variation in gene expression
Relations
SRA SRX091633
BioSample SAMN00709173
Named Annotation GSM778721_NA19203.qnorm.bed.gz

Supplementary file Size Download File type/resource
GSM778721_NA19203.qnorm.bed.gz 20.8 Mb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap