|
| Status |
Public on Oct 07, 2014 |
| Title |
OSKM_Cdk9-DN_D5_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Reprogramming intermediates
|
| Organism |
Mus musculus |
| Characteristics |
cell stage: Reprogramming intermediates (Day5 after infection)
strain: OG2/129SV
transduced: Cdk9-DN
|
| Treatment protocol |
Mouse embryonic fibroblasts were transduced with exogenous factors Oct4, Sox2, Klf4, c-Myc together with a control vector or Cdk9-DN
|
| Growth protocol |
Cells were cultured in ESC medium (DMEM with 15% FBS [Gibco], GlutaMax, nonessential amino acids, sodium pyruvate, 0.1 mM β-mercaptoethanol and 1,000 U ml-1 LIF [Millipore])
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was isolated using TRIzol following the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped)
|
| Data processing |
Base calling was performed using CASAVA version 1.8.2 (illumina)
RNA-seq reads were trimmed for adaptor sequence and mapped to mouse genome using Tophat (v2.0.10) and Ensembl genome annotation file(Mus_musculus.NCBIM37.67.gtf)
Cufflinks (v2.2.1) was used to estimated gene expression abundance(FPKM, numbers of fragment per kilobase of each gene per million mapped reads)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each gene were generated by Cufflinks
|
| |
|
| Submission date |
Jul 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Minghui He |
| E-mail(s) |
hemh@genomics.cn
|
| Organization name |
BGI-Shenzhen
|
| Department |
Cancer Research Department
|
| Street address |
Beishan Industrial Zone, Yantian District
|
| City |
ShenZhen |
| State/province |
GuangDong |
| ZIP/Postal code |
518083 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE59813 |
Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (RNA-seq) |
| GSE59833 |
Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming |
|
| Relations |
| BioSample |
SAMN02943023 |
| SRA |
SRX663227 |
