|
| Status |
Public on Sep 25, 2018 |
| Title |
C3Lu |
| Sample type |
SRA |
| |
|
| Source name |
post mortem frozen tissue
|
| Organism |
Pan troglodytes |
| Characteristics |
individual: 4x0516
tissue: lung
Sex: female
|
| Treatment protocol |
Tissues were received postmortem.
|
| Growth protocol |
Tissues were received postmortem.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted RNA from each tissue sample using TRIzol (Invitrogen, as described in Blekhman et al. 2010).
Samples were pooled together in 2 pools for RNA-seq library generation (as described in Blekhman et al. 2010). 50 bp single-end RNA-seq libraries were sequenced on 26 lanes on 4 different flow-cells on an Illumina HiSeq 2500 sequencer in the Gilad lab or at the University of Chicago Genomics Facility, following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Subspecies/admixture- hybrid between Central and Western
|
| Data processing |
50 bp single-end RNA-seq reads from each species were trimmed and mapped to the appropriate genome (hg19, panTro3, rheMac2) using Tophat2 (version 2.0.11) (Kim et al. 2013). We kept only reads that mapped uniquely.
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac2 (Blekhman et al. 2010) was determined using featureCounts within SubRead (version 1.4.4) (Liao et al. 2014).
Genome_build: hg19, panTro3, rheMac2
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals
|
| |
|
| Submission date |
Mar 26, 2018 |
| Last update date |
Sep 25, 2018 |
| Contact name |
Lauren Elizabeth Blake |
| E-mail(s) |
leblake@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Yoav Gilad
|
| Street address |
920 E. 58th Street, CLSC 317
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL19148 |
| Series (1) |
| GSE112356 |
A genomic study of the contribution of DNA methylation to regulatory evolution in primates |
|
| Relations |
| BioSample |
SAMN08797915 |
| SRA |
SRX3849737 |
