|
| Status |
Public on Nov 29, 2021 |
| Title |
C1C1e-1 |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cells
|
| Organism |
Pan troglodytes |
| Characteristics |
cell type: induced pluripotent stem cells
cell line: C1C1e
|
| Treatment protocol |
iPSCs were collected using accutase and flash frozen for storage at -80C.
|
| Growth protocol |
iPSC lines were grown in mTeSR1 or mTeSR Plus (StemCell Technologies).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using the Direct-Zol RNA Miniprep kit (Zymo Research, cat #R2051) or by Genewiz.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep (Illumina) or by Genewiz and sequenced on a HiSeq 4000 (2x150bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
diploid-and-auto-tetraploid_gene_counts.txt
|
| Data processing |
Sequencing reads were trimmed for adapter sequences using cutadapt v1.8.1 and read quality was confirmed using fastqc v0.11.9.
Reads were aligned using STAR v2.7.1a with two-pass mapping to a concatenated human-chimpanzee genome (hg38 and pt6).
The number of uniquely-mapped reads (MAPQ = 255) that overlap each gene was counted with featurecounts from the subread v1.6.0 package using a curated annotation (hg38.pt6.gtf). To generate the annotations, GRCh38.94 human exon annotations from Ensembl were mapped from hg38 to pt6 using pslMap. After removing mappings where the number of bases that map is less than half of the query exon size, we retained only exons that uniquely mapped from humans to chimpanzees. We then removed genes for which exons map to opposite DNA strands, different scaffolded chromosomes, or where consecutive exons map more than 800kb apart. We further filtered out exons where more than 10% of reads from diploid or auto-tetraploid lines map to the incorrect species when mapped to the composite genome.
Genome_build: hg38 and pt6
Supplementary_files_format_and_content: Gene counts for each species are represented with the human ensembl ID in the processed files. For allo-tetraploid lines, each sample is represented twice in the associated processed file, once as human allele counts ("Hs" prefix) and once as chimpanzee allele counts ("Pt" prefix).
|
| |
|
| Submission date |
Sep 24, 2021 |
| Last update date |
Nov 29, 2021 |
| Contact name |
Janet Song |
| Organization name |
Boston Children's Hospital
|
| Lab |
Walsh
|
| Street address |
3 Blackfan St
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL23423 |
| Series (1) |
| GSE184768 |
Genetic studies of human-chimpanzee divergence using stem cell fusions |
|
| Relations |
| BioSample |
SAMN21618579 |
| SRA |
SRX12346078 |
