RNA-seq analysis of germinal center-derived splenic IgG1 or IgM plasma cells
RNA-seq (gene expression) · mouse · 10 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 5 × IgM plasma cells vs 5 × IgG1 plasma cellsGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE312596_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1374270 and SRA study SRP651544. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 10 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9349886 IgM plasma cells-1 IgM plasma cells
- GSM9349887 IgM plasma cells-2 IgM plasma cells
- GSM9349888 IgM plasma cells-3 IgM plasma cells
- GSM9349889 IgM plasma cells-4 IgM plasma cells
- GSM9349890 IgM plasma cells-5 IgM plasma cells
- GSM9349891 IgG1 plasma cells-1 IgG1 plasma cells
- GSM9349892 IgG1 plasma cells-2 IgG1 plasma cells
- GSM9349893 IgG1 plasma cells-3 IgG1 plasma cells
- GSM9349894 IgG1 plasma cells-4 IgG1 plasma cells
- GSM9349895 IgG1 plasma cells-5 IgG1 plasma cells
- GSE284622 Antigen-selected gut IgA is generated from IgG1 germinal center B cells 54 samples shares igg1, germinal
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares rna-seq, plasma
- GSE302124 Plasmacytoid dendritic cells are dispensable or detrimental in murine systemic or respiratory viral infections [RNA-Seq 1] 18 samples shares rna-seq, plasma
- GSE330911 Spleen and brain T cells in Toxoplasma gondii infection- scRNA-seq, CITE-seq and TCRab 30 samples shares rna-seq, plasma
- GSE264164 RNA-seq and ATAC-seq of follicular B cells and germinal center B cells with a conditional deletion of Brwd1 23 samples shares germinal, rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares rna-seq
- GSE227108 Integrated single-cell analysis defines the epigenetic basis of castration-resistant prostate luminal cells (scRNA-seq) 18 samples shares rna-seq
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.