|
Status |
Public on Jan 26, 2012 |
Title |
HapMap DNase Seq GM19144 |
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=GM19144
|
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 |
SRX091621 |
BioSample |
SAMN00709161 |
Named Annotation |
GSM778709_NA19144.qnorm.bed.gz |