|
| Status |
Public on Dec 06, 2013 |
| Title |
2-HPC-iPSC-16 rep2 RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
HPC-iPSC_RNAseq
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129-M2rtTA
cell type: HPC-derived induced pluripotent stem cells
passage: 10-12
|
| Growth protocol |
ES cells and iPS cells were maintained in ES cell media containing 15% FBS and 1,000 Uml-1 of LIF.MEF and APCs were cultured in DMEM supplemented with 10% FBS and penicillin/streptomycin. HPCs was freshly isolated from bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cell pellets using TRIZOL regent (Invitrogen) according to the manufacture’s instructions. RNA integrity was confirmed using the 2100 Bioanalyzer (Agilent Technologies) with a minimum RNA integrity number (RIN) of 8. mRNA was enriched by using the oligo(dT) magnetic beads and interrupted to short frangments about 200bp. cDNA was synthesized by random hexamer-primer and purified with PCR product extraction kit (Qiagen). Finally, sequencing primers linked cDNA fragments approximately 200bp were isolated by gel electrophoresis and enriched through PCR amplification to construct the library. And Illumina HiSeqTM 2000 was used for sequencing analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The RNAseq reads were mapped to mouse genome using Tophat (v1.3.3) software and the Ensembl genome annotation (Mus_musculus.NCBIM37.64.gtf), the expression level (FPKM, Fragments Per Kilobase of exon per Million fragments mapped) was estimated by cufflink (v1.2.0) software
Genome Build:
RNA_16_rep2.fpkm: mm9
|
| |
|
| Submission date |
Mar 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tao Cai |
| E-mail(s) |
caitao@nibs.ac.cn
|
| Organization name |
National Institute Of Biological Sciences, Beijing (NIBS)
|
| Lab |
Sequencing Facility
|
| Street address |
No. 7 Science Park Road, Zhongguancun Life Science Park
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE36290 |
High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [RNA-seq] |
| GSE36294 |
High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells |
|
| Relations |
| SRA |
SRX127325 |
| BioSample |
SAMN00808763 |
