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Sample GSM2750793 Query DataSets for GSM2750793
Status Public on Apr 02, 2018
Title RNAseq_Setdb1 cKO iMEFs_siDnmt1_1
Sample type SRA
 
Source name iMEF
Organism Mus musculus
Characteristics cell type: iMEF (Setdb1 cKO iMEF)
treatments: Transfected with Dnmt1 siRNA
Treatment protocol For knockdown, siRNAs targeting Dnmt1 or control siRNA was transfected into Setdb1 cKO iMEFs using RNAiMAX. Transfected cells were passaged 24 h after transfection. A second transfection was conducted with the same reagents on the following day. Cells were harvested at day 6 and RNA was isolated. 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 Aug 22, 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 SAMN07535874
SRA SRX3110376

Supplementary file Size Download File type/resource
GSM2750793_sample3_genes.fpkm_tracking.txt.gz 918.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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