|
| Status |
Public on Feb 10, 2024 |
| Title |
Rep2-2TS22C |
| Sample type |
SRA |
| |
|
| Source name |
Tet-Off Sox2 mESCs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Tet-Off Sox2 mESCs
genotype: wild-type
treatment: N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol® reagent according to the manufacturer's protocol. 2µg total RNA was used for library construction.
RNA libraries were constructed by GENEWIZ. Briefly, libraries were enriched for mRNA via poly(A) selection. Then, cDNA was generated from the RNA and adapters ligated to the cDNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The raw 150 bp paired-end RNA-seq reads obtained were aligned to the mm10 reference transcriptome using RSEM and bowtie 2.0.
Gene level alignment results for each sample were then merged and annotated with glbase3.
RSEM was used to calculate the read counts per gene (Li and Dewey, 2011); and EDAseq (Risso et al., 2011) was used to normalize said read counts for GC content.
The final read count table was generated by filtering for genes with read counts with at least 20 counts in at least two samples.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains normalized RNA expression gene counts. The first column denotes the Ensembl gene ID (ensg); the second column denotes the official gene name (name); and the third column onwards denotes the normalized RNA expression gene counts for each RNA sample.
|
| |
|
| Submission date |
Feb 05, 2024 |
| Last update date |
Feb 10, 2024 |
| Contact name |
Sik Yin Ho |
| E-mail(s) |
jessiehsy3590@gmail.com
|
| Organization name |
The University of Hong Kong
|
| Street address |
Laboratory Block, 21 Sassoon Block
|
| City |
Hong Kong |
| ZIP/Postal code |
00000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE255055 |
Removing an acid residue is necessary and sufficient to turn SOX17 into a pluripotency factor |
|
| Relations |
| BioSample |
SAMN39830047 |
| SRA |
SRX23533899 |
