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Sample GSM1172739 Query DataSets for GSM1172739
Status Public on Oct 27, 2013
Title pre3_siTet1
Sample type SRA
 
Source name mouse embryonic fibroblasts (MEFs)
Organism Mus musculus
Characteristics cell type: OG2 transgenic mouse embryonic fibroblasts (MEFs)
passage: P10
strain: 1/2 129SVJ+3/8 C57B6+1/8 CBA
medium: vitamin C (vc)
treatment: Tet siRNA
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description extracting total RNA 48h later after transfecting Tet1 siRNA(including 36h Vc treatment)
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Transcripts per million(TPM) were calculated using RSEM(1.1.21) with parameters(-p 8 --estimated-rspd --no-bam-output).
Genome_build: mm9
Supplementary_files_format_and_content: TXT files including tau values for each RNA-seq samples, and TPM values are generated for all the samples.
 
Submission date Jun 21, 2013
Last update date May 15, 2019
Contact name Lihui Lin
E-mail(s) lin_lihui@gibh.ac.cn
Phone 020-32015291
Organization name Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science
Department Stem cell
Lab Pei Duanqing
Street address No.190, Kaiyuan Street
City Guangzhou
State/province Guangdong
ZIP/Postal code GD20
Country China
 
Platform ID GPL16417
Series (1)
GSE48206 Gene Expression Profile for knocking down Tet1 in pre-iPSCs culturing in Vc medium.
Relations
BioSample SAMN02211828
SRA SRX313016

Supplementary file Size Download File type/resource
GSM1172739_pre3_siTet1.genes.results.txt.gz 323.5 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

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