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Sample GSM1637971 Query DataSets for GSM1637971
Status Public on Jan 15, 2016
Title Lentivirus treated, replicate 3
Sample type SRA
 
Source name transformed COS-1 cell line
Organism Chlorocebus sabaeus
Characteristics cell line: COS-1
treatment: Lentivirus treated
Treatment protocol Cells were serum-starved for 14 h, and then treated with 2ng/ml of epidermal growth factor (EGF) for 90 min.
Growth protocol Cells were grown in DMEM with 10% FBS at 37oC, 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using BioRad Total RNA isolation Kits and PureZOL according to the manufacturer’s instruction. The RNA quality was examined using Agilent Bioanalyzer.
Library was constructed in UT Southwestern genomics core using illumina’s mRNA-Seq sample preparation kits to generate full sequence from any poly-A tailed RNA to generate library with single-read, paired-end or multiplexing sequencing on all illumina sequencing systems (Genome Analyzer or HiSeq). The service included mRNA isolation, cDNA synthesize, fragmentation, adding adaptors, size selection, amplification and QC.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava software used for basecalling.
Reads were mapped to the Chlorocebus sabaeus genome version ChiSab1.0 using Tophat2 v2.0.10 with the multithreading option -p 5 and the remaining parameters as the default allowing for two mismatches. Tophat2 was using bowtie2 v2.1.0.0 as the underlying mapper.
Mapped reads were assembled into transcripts with cufflinks v2.1.1 using the multithreading option -p 5 and the remaining options as the defaults. The gtf used for transcript construction was the Chlorocebus.sabaeus.Chlsabe.0.pre.gtf downloaded from the Ensembl pre release site ftp://ftp.ensembl.org/pub/pre/gtf/chlorocebus_sabaeus/
Aligned reads were used as inputs for cuffdiff2 to determine gene expression levels (FPKM) and differential expression between conditions using the multithreading option -p 8 and the minimum alignment count of 7 (--min-alignment-count 7). All other parameters were set to the defaults.
Differential expression was tested for LV treatment by comparing the combined alignments of samples 4, 5 and 6 (LV) to the combined alignments of samples 1,2 and 3 using cuffdiff2.
Genome_build: ChiSab1.0 GCA 000409795.1
Supplementary_files_format_and_content: Genes_FPKMValues.txt is a tab-delimited text file containing the gene ID, locus, and FPKM values for each gene assembled using cufflinks. gene_exp.diff is the resulting differential expression results for Lentivirus treated vs. NT. This file is output by cuffdiff. A q-value cutoff of 0.05 was used to determine differentially expressed genes.
 
Submission date Mar 19, 2015
Last update date May 15, 2019
Contact name Eric Christian Rouchka
E-mail(s) eric.rouchka@louisville.edu
Organization name University of Louisville
Department Biochemistry and Molecular Genetics
Lab KY INBRE Bioinformatics Core
Street address 522 East Gray Street
City Louisville
State/province Kentucky
ZIP/Postal code 40292
Country USA
 
Platform ID GPL18769
Series (1)
GSE67063 Understanding the role of Shoc2 protein in spatio-temporal regulation of extracellular signal-regulated kinase (ERK1/2) cascade
Relations
BioSample SAMN03433696
SRA SRX959610

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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