|
| Status |
Public on Dec 23, 2017 |
| Title |
NA18856_ATAC_iPSC |
| Sample type |
SRA |
| |
|
| Source name |
Induced pluripotent stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Induced pluripotent stem cell
derived from cell line: NA18856
|
| Biomaterial provider |
parental cell line from Coriell
|
| Growth protocol |
iPSC cultures were grown using 0.01mg/cm2 (1:100) hESC-grade Matrigel and Essential 8 (E8) media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared using the ATAC-seq protocol
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Paired end ATAC-seq reads were mapped using bowtie2 allowing for two mismatches per read. After mitochondrial reads were removed, we once again re-mapped all nuclear reads using the WASP to remove reads that map with allelic bias. We then removed all duplicate fragments (duplicates of both read pairs) and reads with a mapping quality (MAPQ) less than 10.
Genome_build: hg19
Supplementary_files_format_and_content: Each column represents an individual and each row represents an accessibility window. Counts are raw counts of transposition events.
|
| |
|
| Submission date |
Dec 22, 2017 |
| Last update date |
Dec 26, 2017 |
| Contact name |
Nicholas E Banovich |
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Gilad
|
| Street address |
920 E. 58th Street, CLSC 317
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60453 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE89895 |
Impact of regulatory variation across human iPSCs and differentiated cells |
| GSE108458 |
Impact of regulatory variation across human iPSCs and differentiated cells [ATAC-seq iPSC] |
|
| Relations |
| BioSample |
SAMN08226904 |
| SRA |
SRX3505442 |
