|
| Status |
Public on Oct 04, 2022 |
| Title |
XY_iPSC_p17_2 |
| Sample type |
SRA |
| |
|
| Source name |
hIPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hIPSC
chromosome composition: XY
|
| Growth protocol |
hiPSCs were grown on Geltrex in mTeSR media.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the PureLink RNA Minit Kit (Thermo Fisher).
3'mRNA hiPSC libraries were prepared using the Quant-seq 3’ mRNA Library Prep Kit FWD (Lexogen).
For the hiPSCs, 75bp single-end reads were sequenced on the NextSeq500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
3' polyA RNA
d154
|
| Data processing |
Adapters were trimmed using cutadapt v2.7
Reads were aligned to the human genome (hg38) using hisat v2.2.1
Reads were quantified against GENCODE version 36 using featureCounts v2.0 from the Rsubread package.
Assembly: hg38
Supplementary files format and content: raw counts for each gene for each sample of hiPSCs and TBLs
|
| |
|
| Submission date |
Jun 28, 2022 |
| Last update date |
Oct 04, 2022 |
| Contact name |
Stefan F Pinter |
| E-mail(s) |
spinter@uchc.edu
|
| Organization name |
University of Connecticut, UConn Health
|
| Department |
Genetics and Genome Sciences
|
| Lab |
Pinter lab
|
| Street address |
263 Farmington Avenue
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-6403 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE207109 |
Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta [RNA-seq] |
| GSE207114 |
Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta |
|
| Relations |
| BioSample |
SAMN29402565 |
| SRA |
SRX15929764 |
