|
| Status |
Public on Jan 01, 2018 |
| Title |
GFP-D3 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA at D3 after GFP transfection for 2 days
|
| Organism |
Mus musculus |
| Characteristics |
cell type: OG2 transgenic mouse embryonic fibroblasts (MEFs)
passage: P2
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Extracting total RNA at D3 after GFP transfection for 2 days
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), the reference genome using mm10, then put all the samples results together and normalized by EDAseq(1.99.1), genes expression fold change were calculated using normalized raw reads.
Genome_build: mm10
Supplementary_files_format_and_content: Each files contain Rsem output, including TPM and FPKM.
|
| |
|
| Submission date |
May 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lihui Lin |
| E-mail(s) |
lin_lihui@gibh.ac.cn
|
| Phone |
020-32015291
|
| Organization name |
Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science
|
| Department |
Stem cell
|
| Lab |
Pei Duanqing
|
| Street address |
No.190, Kaiyuan Street
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
GD20 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE57546 |
A Direct and Accelerated Platform for Analyzing Reprogramming by Defined factors |
|
| Relations |
| BioSample |
SAMN02769520 |
| SRA |
SRX540184 |
