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Series GSE85278 Query DataSets for GSE85278
Status Public on Aug 28, 2016
Title RNA-seq of dexamethasone-treated mouse primary hepatocytes infected with shControl or shSETDB2 adenovirus
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goal of this study is to identify differentially expressed genes in SETDB2 deficient mouse primary hepatocytes (MPH) treated with dexamethasone when compared to control MPH
Methods: Total RNA from MPH treated with either shControl or shSETDB2 adenovirus (pool of 3 mice per group) was isolated by the TRIzol method (Life Technologies) according to manufacturer’s instructions. Total RNA was DNase-treated and RNA integrity was evaluated by Biolanalyzer (Agilent). RNA sequencing was performed by the SBP Genomics Core Facility in Lake Nona (Orlando, FL) using the Illumina HiSeq platform and the following parameters: paired-end read length: 100 BP; number of output reads: 300m reads. The Tophat+Cufflinks pipeline was used for the RNA-seq analysis as described previously (Haas et al., 2013; Trapnell et al., 2012). Differentially expressed genes in shSETDB2 vs. shControl MPH were determined using a 2-fold cutoff, p-value of less than 0.05, and FPKM (fragments per kilobase of transcript per million mapped reads) cutoff of 1. The shSETDB2 and shControl RNA-seq reads were mapped to the mm10 genome using Tophat (Trapnell et al., 2009). The mapping results were further analyzed by Cufflinks, which outputs the final differential gene list.
Overall design mRNA profiles of shControl and shSETDB2 adenoviral infected mouse primary hepatocyte (n=3 mice) were generated by deep sequencing using Illumina HiSeq platform.
Contributor(s) Ding J, Li X
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Submission date Aug 07, 2016
Last update date May 15, 2019
Contact name Manuel Roqueta-Rivera
Organization name Sanford Burnham Preby Medical Research Institute
Street address 6400 Sanger Rd
City Orlando
State/province FL
ZIP/Postal code 32827
Country USA
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (2)
BioProject PRJNA338065
SRA SRP081050

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Supplementary file Size Download File type/resource
GSE85278_MRRetal_CellMetTable_S3.xlsx 2.8 Mb (ftp)(http) XLSX
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