|
| Status |
Public on Apr 17, 2019 |
| Title |
TSCendo-B6#1_RNA-seq_re-analyzed |
| Sample type |
SRA |
| |
|
| Source name |
endogenous trophoblast stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: endogenous trophoblast stem cells
|
| Treatment protocol |
For samples in reprogramming, cells were harvested at day 3.
|
| Growth protocol |
TSCs and iTSCs were cultured under TX medium condition as decribed in PMID:24527396. mESCs were cultured in 2i medium and MEFs with DMEM supplemenated with 10% FBS medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were homogenized and RNA was harvested using the RNeasy kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Single-end RNA-seq
This re-analyzed sample is associated with two raw data files which represent technical duplicates.
[processed data files:]
FPKM.txt
FPKM.bed.gz
|
| Data processing |
RNA-seq: Reads were mapped using TopHat to the mouse genome (mm9), and expression levels were calculated using cufflinks (with default parameters).
genome build: mm9
processed data files format and content: RNA-seq: Processed files include a tab-separated text file with FPKM values for each gene/condition, as well as a .bed version visualizing expression levels. Replicates were combined for a single value per cell type. FPKM values are available on the series record.
|
| |
|
| Submission date |
Apr 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tommy Kaplan |
| E-mail(s) |
[email protected]
|
| Organization name |
Hebrew University
|
| Department |
School of Computer Science and Engineering
|
| Street address |
Givat Ram Campus
|
| City |
Jerusalem |
| ZIP/Postal code |
91904 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE98124 |
Direct Induction of the Three Pre-Implantation Blastocyst Cell Types from Fibroblasts |
|
| Relations |
| Reanalysis of |
GSM1576855 |
| BioSample |
SAMN06826923 |
| SRA |
SRX2755485 |
