|
| Status |
Public on Nov 17, 2016 |
| Title |
NA19098 |
| Sample type |
SRA |
| |
|
| Source name |
Induced pluripotent stem cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Induced pluripotent stem cell
|
| Growth protocol |
iPSC cultures were grown using 0.01mg/cm2 (1:100) hESC-grade Matrigel and Essential 8 (E8) media.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from from frozen cell pellets using the Zymo ZR-Duet DNA/RNA MiniPrep kit, per manufacture specifications.
Libraries were prepared using Illumina TruSeq library preperation per manufacutre specifications.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The reads were mapped to hg19 using STAR with option --outSAMstrandField intronMotif
The alignment were filtered to remove mapped reads with quality less than 10 using samtools -q 10
We used the WASP alignment strategy to filter read that may be mismapped owing to the human genome reference allele bias (pmid26366987)
We also used WASP to remove cofounding effect from sample-specific GC biases and read count differences to allow comparison between samples.
We standardize the values by genes (row) and qqnorm by individuals (column) to get our final quantitative measurements
Genome_build: hg19
Supplementary_files_format_and_content: Each column represnets and individual and each row represnets a gene. Counts are processed and normalized as described above.
|
| |
|
| Submission date |
Nov 15, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
| GSE107654 |
Impact of regulatory variation across human iPSCs and differentiated cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN06020666 |
| SRA |
SRX3452586 |
