|
| Status |
Public on May 29, 2020 |
| Title |
529 |
| Sample type |
SRA |
| |
|
| Source name |
post-mortem heart tissue
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: post-mortem heart
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
DNA and RNA were extracted from frozen tissues using Trizol extraction according to manufacturer's instructions (QIAGEN Cat No./ID: 79306).
Illumina TruSeq RNA Library Prep kit v2 according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
For chimpanzee/human comparisons RNASeq reads were trimmed to 75bp single-end reads to match published human datasets for comparison using fastx_toolkit.
Reads aligned with STAR aligner v2.6.1b (Dobin et al. 2015) with default settings to the respective genome (GRCh38.p13 or Pan_tro_3.0 from Ensembl release 95).
Gene counts were obtained with subread featureCounts (Liao et al. 2014) using a previously described annotation file of human-chimpanzee orthologous exons (Pavlovic et al. 2018).
For chimpanzee eQTL mapping, RNASeq reads were kept as 100bp single-end reads and aligned with START aligner v2.6.1b (Dobin et al. 2015) with the {--quantMode GeneCounts} parameter to compile a gene expression matrix.
Genes were filtered to require at least 8 read counts in 75% of samples, leaving 13545 genes for further analysis. The resulting read count matrix was converted to log(CPM), standardized across individuals, and quantile normalized to a normal distribution across genes as previously described (Degner et al. 2012).
Genome_build: Pan_tro_3.0 (Ensembl release 95)
Supplementary_files_format_and_content: ChimpanzeesRawGeneCount_eQTL_Mapping.tsv: RNA-seq counts for all genes for all chimpanzee individuals analyzed in this study. Reformatted output of {STAR --quantMode GeneCounts}.
Supplementary_files_format_and_content: ChimpanzeesQQNorm_eQTL_Mapping.tsv: Standardized and quantile normalized CPM expression for all chimpanzee individuals (minus MD_And) for eQTL mapping.
Supplementary_files_format_and_content: OrthologousExonRawGeneCounts_Human.tsv: RNA-seq counts for all human/chimpanzee orthologous genes for all human individuals analyzed in this study. Reformatted output of subRead.
Supplementary_files_format_and_content: OrthologousExonRawGeneCounts_Chimpanzee.tsv: RNA-seq counts for all human/chimpanzee orthologous genes for all chimpanzee individuals analyzed in this study. Reformatted output of subRead.
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
May 29, 2020 |
| Contact name |
Benjamin Jung Fair |
| E-mail(s) |
bjf79@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Section of Genetic Medicine
|
| Lab |
Yoav Gilad
|
| Street address |
920 E. 58th Street, CLSC 317
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platform ID |
GPL23423 |
| Series (1) |
| GSE151397 |
Gene expression variability in human and chimpanzee populations share common determinants |
|
| Relations |
| BioSample |
SAMN15048772 |
| SRA |
SRX8419123 |
