|
| Status |
Public on Nov 15, 2010 |
| Title |
NA18507: HapMap DNase Seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
NA18507
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphoblastoid cell line
origin: Yoruba from Ibadan, Nigeria (YRI)
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA18507
|
| Growth protocol |
37o in RPMI
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase seq protocol (Boyle et al. 2008) (see attached supplementary file: Duke_DNase_protocol.pdf)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Reads for one lane of Illumina GA flowcell for individual NA18507
|
| Data processing |
Read mapping: We used the raw sequencing reads, trimmed them to 20 bp (see DNase protocol), and mapped them on the human reference genome (hg18) using BWA (using the default settings). Then we filtered out the reads with quality score < 10 or that mapped to more than one location in the genome. For reads obtained using the DNase-seq protocol, since their length is limited to 20bp, we further removed all reads that contained an insertion/deletion or that had more than one mismatch with respect to hg18. The aligned reads of multiple experimental replicates on the same cell-line type were combined into a single file for analysis.
|
| |
|
| Submission date |
Nov 15, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Jacob F Degner |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE25341 |
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data |
|
| Relations |
| SRA |
SRX031172 |
| BioSample |
SAMN00120333 |
