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Sample GSM2739369 Query DataSets for GSM2739369
Status Public on Apr 02, 2018
Title RNAseq_Setdb1 cKO iMEFs_WT_1
Sample type SRA
 
Source name iMEF
Organism Mus musculus
Characteristics cell type: iMEF (Setdb1 cKO iMEF)
time point: no treatment
Treatment protocol For KO 4OHT was treated for first 4days then cells were harvested at day 5
Growth protocol Cells were cultured in DMEM (Nacalai: 08458-45) with MEM non-essential amino acids (Gibco: 11140-035), 2-mercaptoethanol (used at 0.1 mM, Nacalai), 10% FBS. Cells were split every three days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with RNeasy mini kit (QIAGEN: 74134).
rRNA was removed using epicentre's Ribo-Zero rRNA Removal kit. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing We aligned reads to the reference genome (UCSC mm9) using TopHat (version 2.0.12 and 2.1.1) with "-g 1" parameter.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file, and two comparisons were done (WT vs cKO, WT vs cKO long culture)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Aug 10, 2017
Last update date May 15, 2019
Contact name Masaki Kato
E-mail(s) mkato@riken.jp
Organization name RIKEN
Lab Cellular Memory Laboratory
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 3510198
Country Japan
 
Platform ID GPL18480
Series (2)
GSE102486 A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing [RNA-Seq]
GSE102490 A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing
Relations
BioSample SAMN07503273
SRA SRX3091714

Supplementary file Size Download File type/resource
GSM2739369_Sample1_genes.fpkm_tracking.txt.gz 749.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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