|
| Status |
Public on Nov 09, 2023 |
| Title |
pMesendoderm_day1_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
PiPSC clone 8
|
| Organism |
Sus scrofa |
| Characteristics |
cell line: PiPSC clone 8
cell type: Pig iPS cells
time: Day 1
differentiation status: PiPSC8 differentiated to primitive streak/mesendoderm with E8A100ch3 at day1
|
| Growth protocol |
Growth or differentiation medium as described in the assocaited study.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA are extracted using QIAGEN Rneasy Plus Mini Kit
The ligation-mediated sequencing protocol was used to prepare and index cDNA libraries (Hou et al 2015)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
ec.tsv, tpm.tsv
|
| Data processing |
Basecalls were performed using illuminas bcl2fastq's version 2.17 for the Hiseq 3000 machine and NextSeq Demultiplex performed with native Dragen 3.8.4
Sequences were filtered and trimmed to remove low quality reads, adaptors, and other sequencing artificats
Sequencing reads were mapped to the Sus Scrofa Assembly Sscrofa11.1 (GCA_000003025.6) with bowtie 1.2.3
Gene expected couts were calculated using RSEM 1.2.3
Assembly: Sus Scrofa Assembly Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: Processed data files are both in tab-seperated value format and contain expected counts (ec.tsv) and transcripts per million (tpm.tsv)
|
| |
|
| Submission date |
Mar 22, 2023 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Li-Fang (Jack) Chu |
| E-mail(s) |
lifangjack.chu@ucalgary.ca
|
| Organization name |
University of Calgary
|
| Lab |
Chu Laboratory
|
| Street address |
2500 University Drive NW
|
| City |
Calgary |
| State/province |
Alberta |
| ZIP/Postal code |
T2N 1N4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24486 |
| Series (1) |
| GSE227985 |
Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in vitro modeling of species-specific developmental timing |
|
| Relations |
| BioSample |
SAMN33864551 |
| SRA |
SRX19751535 |
