Comparative transcriptomic analysis of pre-plasma germinal center B cells in wild type and Kdm6b B knockout models
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 5 × Pre-Plasma germinal center B cells, WT vs 4 × Pre-Plasma germinal center B cells, KOGroups 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.
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 GSE270908_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 PRJNA1128812 and SRA study SRP516363. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 2 replicated groups read from 12 sample titles; they account for 9 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.
- GSM8354732 Pre-Plasma germinal center B cells, 6WT
- GSM8354733 Pre-Plasma germinal center B cells, 7KO
- GSM8354734 Pre-Plasma germinal center B cells, 8KO
- GSM8354735 Pre-Plasma germinal center B cells, KO1 Pre-Plasma germinal cen…
- GSM8354736 Pre-Plasma germinal center B cells, KO2 Pre-Plasma germinal cen…
- GSM8354737 Pre-Plasma germinal center B cells, KO6 Pre-Plasma germinal cen…
- GSM8354738 Pre-Plasma germinal center B cells, KO7 Pre-Plasma germinal cen…
- GSM8354739 Pre-Plasma germinal center B cells, WT1 Pre-Plasma germinal cen…
- GSM8354740 Pre-Plasma germinal center B cells, WT2 Pre-Plasma germinal cen…
- GSM8354741 Pre-Plasma germinal center B cells, WT3 Pre-Plasma germinal cen…
- GSM8354742 Pre-Plasma germinal center B cells, WT4 Pre-Plasma germinal cen…
- GSM8354743 Pre-Plasma germinal center B cells, WT7 Pre-Plasma germinal cen…
- GSE275123 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) III 21 samples shares pre-plasma, germinal, center
- GSE275124 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 4 and Figure 5) 20 samples shares pre-plasma, germinal, center
- GSE275121 Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure2) 1 13 samples shares pre-plasma, germinal, center
- GSE337004 Comparative RNA-seq analysis of PM2.5 responses in wildtype and malignantly transformed mouse mammary epithelial cells cultured as spheroids 8 samples shares comparative, wild, type
- GSE266438 Loss of Sphingosine-1-Phosphate Receptor 4 weakens innate mechanisms leading to defective lymph node hypertrophy and germinal center formation 45 samples shares germinal, center
- GSE309127 Rapid boosting increases germinal center responses to sequential vaccines 33 samples shares germinal, center
- GSE288450 Vaccines combining slow release and follicle targeting of antigens increase germinal center B cell clonal diversity and clonal expansion 33 samples shares germinal, center
- GSE282304 REL deregulation stands as a primary hit for AID-imprinted B-cells along the germinal center competition 30 samples shares germinal, center
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.