|
| Status |
Public on Jan 01, 2013 |
| Title |
SI3-d23 |
| Sample type |
SRA |
| |
|
| Source name |
secondary reprogramming cells
|
| Organism |
Mus musculus |
| Characteristics |
day of dox treatment: 21
days cultured without doxycycline: 2
cell type: secondary reprogramming cells
|
| Treatment protocol |
Secondary MEFs were treated with doxycycline for 14, 21, 22, 23 or 27 days
|
| Growth protocol |
Secondary MEFs were isolated and treated with doxycycline to induce reprogramming
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA was purified using Qiagen RNAeasy kit with on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina CASAVA 1.8 was used to perform basecalling
The first 15 bases of each read were trimmed
Top-Hat 1.3 was used to align to mm9 genome
Reads mapped to multiple location in the genome were dicarded
RPKM were calculated for protein coding gene using exon union model.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file of RPKM
|
| |
|
| Submission date |
Nov 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yu Liu |
| Organization name |
University of Toronto
|
| Department |
Molecular Genetics
|
| Lab |
Jeff Wrana
|
| Street address |
600 University Ave
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G1X5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE42100 |
Stabilization competency signature |
|
| Relations |
| SRA |
SRX203171 |
| BioSample |
SAMN01803660 |
