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| Status |
Public on Aug 14, 2014 |
| Title |
cKO.2_RNAseq |
| Sample type |
SRA |
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| Source name |
Splenic B cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: LPS stimulated B cells
genotype/variation: cKO
passage: 8-12
strain: C57BL/6
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| 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.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using RNeasy (Qiagen)
NEBNext Ultra RNA Library Prep Kit for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| 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.
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| Submission date |
May 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Takashi MaruYama |
| E-mail(s) |
ta-maru@umin.ac.jp
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| Organization name |
Gifu University
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| Street address |
1-1 Yanagido
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| City |
Gifu |
| ZIP/Postal code |
501-1193 |
| Country |
Japan |
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| Platform ID |
GPL11002 |
| Series (1) |
| GSE57837 |
Genome wide analysis of gene expression in LPS stimulated splenic B cell. |
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| Relations |
| BioSample |
SAMN02795951 |
| SRA |
SRX547502 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1394794_cKO.2_RNAseq.list.txt.gz |
249.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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