|
| Status |
Public on Oct 27, 2013 |
| Title |
pre3_NC |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblasts (MEFs)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: OG2 transgenic mouse embryonic fibroblasts (MEFs)
passage: P10
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
medium: vitamin C (vc)
treatment: control siRNA
|
| 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 MiSeq |
| |
|
| Description |
extracting total RNA 48h later after transfecting Control siRNA(including 36h Vc treatment)
|
| 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.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9
Supplementary_files_format_and_content: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.
|
| |
|
| Submission date |
Jun 21, 2013 |
| 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 |
GPL16417 |
| Series (1) |
| GSE48206 |
Gene Expression Profile for knocking down Tet1 in pre-iPSCs culturing in Vc medium. |
|
| Relations |
| BioSample |
SAMN02211829 |
| SRA |
SRX313015 |
