|
| Status |
Public on Oct 17, 2013 |
| Title |
AG18359 |
| Sample type |
SRA |
| |
|
| Source name |
AG18359
|
| Organism |
Pan troglodytes |
| Characteristics |
cell type: lymphoblastoid cell line
gender: Female
|
| Growth protocol |
Cells were cultured in RPMI-1640 media supplemented with 15% FBS, 2mM L-glutamine, 100 IU/mL penicillin and 100ug/mL streptomycin. Cells were incubated at 37°C with 5% CO2 . Cells were split every 2-3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Mini kit. Libraries were constucted with the Illumina TruSeq kit. Libraries were subsequently sequenced on a Hi-Seq 2000 by standard protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the genome using BWA v0.5.9.
Reads not mapping to the genome, mapping ambiguously, or mapping with a quality score less than 10 were filtered out with SAMtools v0.1.18.
The number of reads overlapping a single exon from a defined set of orthologous exons (available at http://gilad.uchicago.edu/orthoExon) were counted.
The read counts were used to calculate the reads per kilobase per million mapped reads (RPKM).
To facilitate comparisons with mass spec. data, the RPKM measures for an internal reference cell line (GM19238) were used to calculate a log2-ratio of expression measurements.
Genome_build: hg19, panTro3 and rheMac2
Supplementary_files_format_and_content: .txt files: Each line represents a gene. Column 1 contains the Ensembl gene ID. Column 2 contains the RPKM measure for that gene in that individual.
|
| |
|
| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Darren A. Cusanovich |
| E-mail(s) |
darrenc@arizona.edu
|
| Organization name |
University of Arizona
|
| Department |
Cellular and Molecular Medicine
|
| Street address |
1230 N Cherry Avenue, BSRL 421
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85721 |
| Country |
USA |
| |
|
| Platform ID |
GPL16809 |
| Series (1) |
| GSE49682 |
Primate transcript and protein expression levels evolve under compensatory selection pressures |
|
| Relations |
| BioSample |
SAMN02314105 |
| SRA |
SRX333021 |
