|
| Status |
Public on May 12, 2016 |
| Title |
Activated Id3 Knockout rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
cell type: B cell
genotype/variation: Id3 knockout
protocol: activated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
2014.RG5
|
| Data processing |
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries.
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. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and had an expression change of two folds or greater. The called differentially expressed genes must also have 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: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file "Samples_Raw_Counts.txt" includes raw read counts for genes in each library.
|
| |
|
| Submission date |
Sep 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
[email protected]
|
| Organization name |
Olivia Newton John Cancer Research Institute
|
| Department |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE72831 |
Dynamic changes in E protein activity orchestrate germinal center and plasma cell development [RNA-Seq] |
| GSE72832 |
Dynamic changes in E protein activity orchestrate germinal center and plasma cell development |
|
| Relations |
| BioSample |
SAMN04043999 |
| SRA |
SRX1212565 |
