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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 01, 2015 |
| Title |
Day 3 LPS stimulated B cells, B220+, Syndecan1-, Blimp1-GFP- (LPS blasts) rep1 |
| Sample type |
SRA |
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| Source name |
Spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
stimulus: Lipopolysaccharide
time: 72 hours
cell type: LPS B cell blasts
markers: B220+, Syndecan1-, Blimp1-GFP-
culture: In vitro
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells using Qiagen RNeasy Micro or Mini Kits (based on cell number), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Sample 14
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| Data processing |
Reads were aligned to the GRCm37/mm9 build of the Mus musculus genome with the Subread aligner. Ten 'subreads' were extracted from each read, and at least three consensus 'subreads' were required for a hit to be reported. Hamming distance or mapping-quality score was used to break the tie when more than one best location was found for a read. Only uniquely mapped reads were retained.
Gene-wise counts were obtained with featureCounts. Reads overlapping exons in annotation build 37.2 of the NCBI RefSeq database were included. Genes were filtered from downstream analysis if they did not have a CPM (counts per million mapped fragments) value of at least 1 in at least one library. Immunoglobulin genes were excluded from expression analysis when we compared B cell populations with ASC populations, because of the large difference in the fraction of immunoglobulin reads between them. Expression analysis for immunoglobulin genes was done separately.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Empirical Bayes moderated-t P values were computed relative to a fold-change cutoff of 1.5-fold using treat. P values were adjusted to control the global false discovery rate (FDR) across all comparisons with the global option of the limma package. Genes were considered differentially expressed if they had an FDR of 0.05 or less and also had at least 8 FPKMs (fragments per kilobase of exon length per million mapped fragments) in one or both of the two cell types being compared.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include normalized log2-FPKM values for each sample.
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| Submission date |
Aug 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
[email protected]
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| Organization name |
Monash University
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| Street address |
Wellington Rd
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| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE60927 |
Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells |
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| Relations |
| BioSample |
SAMN03013586 |
| SRA |
SRX689952 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1493799_LCD.subread.sam.txt.gz |
215.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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