NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM886460 Query DataSets for GSM886460
Status Public on Dec 06, 2013
Title 3-APC-iPSC-3 rep1 RNAseq
Sample type SRA
 
Source name APC-iPSC_RNAseq
Organism Mus musculus
Characteristics strain: 129-M2rtTA
cell type: APC-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_3_rep1.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 SRX127326
BioSample SAMN00808764

Supplementary file Size Download File type/resource
GSM886460_RNA_3_rep1.fpkm.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap