NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2610269 Query DataSets for GSM2610269
Status Public on May 01, 2020
Title SC3
Sample type SRA
 
Source name Control iPS-3
Organism Mus musculus
Characteristics tissue: normal induced pluripotent stem cell
Growth protocol MEF were maintained in 90% DMEM + 10% FBS. Mouse ES and iPSCs were maintained in M15 medium, which is composed of Dulbecco’s modified Eagle’s medium (DMEM; Gibco Invitrogen, Carlsbad, CA)supplemented with 15% FBS (Gibco), 100 μM -mercaptoethanol (Sigma-Aldrich, St. Louis, MO), 2 mM non-essential amino acids(Gibco), 2 mM L-glutamine(Gibco), 1 mM sodium pyruvate (Gibco),and 10 ng/ml leukemia inhibitory factor (LIF; Chemicon, Temecula, CA) on feeder cells composed of mitomycin C-treated primary mouse embryonic fibroblast (MEF) cells.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells by RNAiso Plus (Takara, Dalian, China).
Libraries were prepared from 100-1000ng total RNA using the VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China) according to the manufacturer’s protocol. Libraries were validated by the 2100 BioAnalyzer (Agilent, Beijing, China), normalized, and pooled for sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing base calling were performed with Illumina CASAVA-1.8.2
This yielded about 10M usable reads per sample. Short read sequences were mapped to a UCSC mm10 reference sequences
Differential gene expression analysis, statistical testing and annotation were performed using the number of uniquely mapped reads per kilobase transcriptome per million mapppable reads (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited xls files include RPKM values and Coverage for each Sample
 
Submission date May 09, 2017
Last update date May 01, 2020
Contact name Zhaoyu lin
E-mail(s) linzy@nju.edu.cn
Organization name Nanjing University
Street address 12 Xuefu Road
City Nanjing
State/province Jiangsu
ZIP/Postal code 210061
Country China
 
Platform ID GPL21273
Series (1)
GSE85272 Comparison of the transcription of palmitoylcarnitine induced pluripotent stem cells, normal induced pluripotent stem cells and embryonic stem cells through RNA-seq
Relations
BioSample SAMN06920734
SRA SRX2792694

Supplementary file Size Download File type/resource
GSM2610269_SC3.Gene.rpkm.txt.gz 307.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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