NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2336784 Query DataSets for GSM2336784
Status Public on Dec 30, 2017
Title E14_rep1_RNAseq
Sample type SRA
 
Source name E14
Organism Mus musculus
Characteristics cell line: E14TG2
cell state: ground state
culture condition: 2i /LIF conditions
Growth protocol To maintain ESCs in ground state or naïve state, mouse ESC lines (E14TG2a) were cultured in 2i /LIF conditions as described (Ying et al., 2008).
Extracted molecule total RNA
Extraction protocol Total RNA was prepared with TRIzol reagents (Life Technologies).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq3000 system (lllumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description ES_rep1_0
Data processing Illumina Casava software used for basecalling.
We trimmed and mapped reads to the mouse mm10 reference assembly (GRCm38) by the Tophat2 software (Kim et al., 2013). We used default parameters expect that we reduced maximum insertion and deletion length to 2 bp, and kept only uniquely mapped, “no mixed” and “no discordant” reads.
We calculated FPKM for GENCODE M7 gene models using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each replicate.
 
Submission date Oct 05, 2016
Last update date May 15, 2019
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Department Institutes of Biomedical Sciences
Street address 130 DongAn Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21493
Series (1)
GSE87632 RNAseq of ground state mouse embryonic stem cells.
Relations
BioSample SAMN05863702
SRA SRX2212080

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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