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Sample GSM1526553 Query DataSets for GSM1526553
Status Public on Oct 01, 2015
Title 475 - WT
Sample type SRA
 
Source name mESC
Organism Mus musculus
Characteristics cell type: embryonic stem cells
strain: C57BL/6
Sex: male
day: 5
clone: 1
genotype: Trimfl/fl
Treatment protocol Trim71 conditional ("WT") cells were treated with 500 nM 4-OHT for 2 days to induce Trim71 mutation. Cells were further cultivated before cell harvest for at least 7 days to minimize indirect effects of the drug treatment.
Growth protocol mES cells were cultivated in complete mES medium (FCS+LIF). Before analysis, harvested cells were subjected to SSEA-1 MACS sorting to correct for spontanious differentiation during culture. Two different mES cell clones were used in this study (with each WT and KO condition)
Extracted molecule total RNA
Extraction protocol Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufactures’ protocol
Illumina TruSeq RNA Sample Preparation Kit v2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on April 2014
Normalization using DeSeq2
Genome_build: mm10
 
Submission date Oct 16, 2014
Last update date May 15, 2019
Contact name Joachim Schultze
E-mail(s) j.schultze@uni-bonn.de
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL18480
Series (1)
GSE62398 mRNA sequencing of Trim71 conditional ("WT") and Trim71 KO mES cells
Relations
BioSample SAMN03112809
SRA SRX734165

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

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