|
| Status |
Public on Jan 26, 2012 |
| Title |
HapMap DNase Seq GM19171 |
| 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=GM19171
|
| 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 |
SRX091627 |
| BioSample |
SAMN00709167 |
| Named Annotation |
GSM778715_NA19171.qnorm.bed.gz |
