|
| Status |
Public on Jan 18, 2016 |
| Title |
Xbp1 Knock-out (Xbp1KO) rep1, batch 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow, plasma cells, Xbp1 knockout
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Xbp1-/-
tissue: bone marrow
cell type: plasma cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from ex-vivo sorted Blimp1-GFP+CD138+ plasma cells using the Qiagen RNeasy Micro kit.
Libraries were generated using the Illumina TruSeq RNA sample preparation kit following manufacturer instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Xbp1KO_rep1_batch2
|
| Data processing |
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped reads were retained.
Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Ig genes were excluded from the gene-level expression analysis. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 1 in at least one library.
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.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files include normalized log2-FPKM values for each library. EntrezIDs represent NCBI Entrez Gene IDs.
Supplementary_files_format_and_content: GEO_suppl_raw_counts.txt': Includes raw read counts for each gene in each library. The raw read count is the number of mapped reads (or read pairs for paired-end libraries) assigned to each gene. EntrezIDs represent NCBI Entrez Gene IDs.
|
| |
|
| Submission date |
Jul 15, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
[email protected]
|
| Organization name |
Monash University
|
| Street address |
Wellington Rd
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE70981 |
Blimp1 controls plasma cell physiology and function |
|
| Relations |
| SRA |
SRX1098364 |
| BioSample |
SAMN03863204 |
