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Sample GSM1394793 Query DataSets for GSM1394793
Status Public on Aug 14, 2014
Title cKO.1_RNAseq
Sample type SRA
Source name Splenic B cells
Organism Mus musculus
Characteristics cell type: LPS stimulated B cells
genotype/variation: cKO
passage: 8-12
strain: C57BL/6
Growth protocol Purified splenic B cells cultured under LPS (20 mg/ml) stimulation for 72 h in RPMI 1640 medium supplemented with 10% heat-inactivated FCS, 100 U/mL penicillin, 100 mg/mL streptomycin, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, and 50 mM 2-mercaptoethanol at 37degree in 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by using RNeasy (Qiagen)
NEBNext Ultra RNA Library Prep Kit for Illumina
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Basecalls performed using CASAVA version 1.8.
38bp reads aligned to genome using bowtie program with default settings on TopHat 2.0, filtered with low Phred score(< 25), converted to BED files using SamTools, filtered rRNAs and tRNAs annotations using IntersectBed command in BEDtools.
Gene annotations were found using RegionMiner on Genomatix Genome Analyzer, inputting BED files, processed across 2 replicates for identification of differentially expressed genes between cKO and Ctrl
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include NE values for each Sample. A normalized expression value (NE-value) calculated based on the following formula: NE =10^7 * the number of reads in transcripts / the number of total reads mapped * length of the transcripts.
Submission date May 20, 2014
Last update date May 15, 2019
Contact name Takashi MaruYama
Organization name Gifu University
Street address 1-1 Yanagido
City Gifu
ZIP/Postal code 501-1193
Country Japan
Platform ID GPL11002
Series (1)
GSE57837 Genome wide analysis of gene expression in LPS stimulated splenic B cell.
BioSample SAMN02795950
SRA SRX547501

Supplementary file Size Download File type/resource
GSM1394793_cKO.1_RNAseq.list.txt.gz 250.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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