Analysis of transcriptomes of germinal center (GC) B cells derived from miR-155-sufficient and -deficient mice
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 × cMyc-GFP+ LZ GC-B cells, WT vs 5 × cMyc-GFP+ LZ GC-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.
- Paper
- Epi-microRNA mediated metabolic reprogramming counteracts hypoxia to preserve affinity maturationNature communications · 2024
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 GSE231649_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 PRJNA967244 and SRA study SRP435938. 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.
- GSM7295209 cMyc-GFP+ LZ GC-B cells, WT1 cMyc-GFP+ LZ GC-B cells…
- GSM7295210 cMyc-GFP+ LZ GC-B cells, WT2 cMyc-GFP+ LZ GC-B cells…
- GSM7295211 cMyc-GFP+ LZ GC-B cells, WT3 cMyc-GFP+ LZ GC-B cells…
- GSM7295212 cMyc-GFP+ LZ GC-B cells, WT4 cMyc-GFP+ LZ GC-B cells…
- GSM7295213 cMyc-GFP+ LZ GC-B cells, WT5 cMyc-GFP+ LZ GC-B cells…
- GSM7295214 cMyc-GFP+ LZ GC-B cells, KO1 cMyc-GFP+ LZ GC-B cells…
- GSM7295215 cMyc-GFP+ LZ GC-B cells, KO2 cMyc-GFP+ LZ GC-B cells…
- GSM7295216 cMyc-GFP+ LZ GC-B cells, KO3 cMyc-GFP+ LZ GC-B cells…
- GSM7295217 cMyc-GFP+ LZ GC-B cells, KO4 cMyc-GFP+ LZ GC-B cells…
- GSM7295218 cMyc-GFP+ LZ GC-B cells, KO5 cMyc-GFP+ LZ GC-B cells…
- GSE316392 Lymphocyte-derived cholinergic circuits modulate germinal center output and B cell activation 16 samples shares germinal, derived, 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 germinal, derived, center
- GSE230527 Genome-wide profiling of Kdm2a binding and H3K36me2 of hypoxia-cultured B cells derived from miR-155-sufficient and -deficient mice [ChIP-seq] 18 samples shares mir-155-sufficient, deficient, derived
- GSE278742 Comprehensive transcriptome characterization deciphers mechanisms underpinning the positive selection of B cells in germinal centers. [mouse; short-read] 20 samples shares germinal, center
- GSE237128 Myc transcriptional bursts promote B cell positive selection by T cells in germinal centers 16 samples shares germinal, center
- GSE274693 Lung germinal center like B-cells 14 samples shares germinal, center
- GSE189297 RNA sequencing of wild type or calcineurin-deficient mouse bone marrow-derived dendritic cells stimulated with or without lipoarabinomannan (LAM) from Mycobacterium tuberculosis Aoyama-B 10 samples shares deficient, derived
- 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
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.