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Sample GSM3029762 Query DataSets for GSM3029762
Status Public on Apr 02, 2018
Title RNAseq_Setdb1 cKO iMEFs_PD_2
Sample type SRA
 
Source name iMEF
Organism Mus musculus
Characteristics cell type: iMEF (Setdb1 cKO iMEF)
treatment: PD0325091 treatment
Treatment protocol For TSA treatment, Setdb1 cKO iMEFs were treated with 150 nM TSA for 24 hrs. For PD0325091 treatment, 1 µM MEK inhibitor PD0325901 for last 24 hr. For simultaneous KO of Setdb1, 4OHT was added at day 0.
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).
RNA libraries were prepared for sequencing using Illumina TruSeq RNA Sample Prep Kit protocols
 
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 the exception of “-g 1”.
Mm9 Refseq gtf file was downloaded from UCSC (http://genome.ucsc.edu) in Oct 22, 2014 and applied as gene annotation file.
After obtaining the aligned bam files, the Cufflinks algorithm was used to calculate FPKM with the Refseq gtf file.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Mar 02, 2018
Last update date Apr 03, 2018
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 SAMN08631348
SRA SRX3758503

Supplementary file Size Download File type/resource
GSM3029762_P343_08_genes.fpkm_tracking.txt.gz 734.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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