GEO series

Myc transcriptional bursts promote B cell positive selection by T cells in germinal centers

GSE237128 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2024/10/15 Platform GPL17021

At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 16 samples: 4 × IsoCtrl_4h_LZ vs 4 × AntiCD40_4h_LZ vs 4 × IsoCtrl_4h_DZ vs 4 × AntiCD40_4h_DZGroups 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.

Summary (written by the submitters)

Antibody affinity maturation occurs in secondary lymphoid organs within germinal centers (GCs) where B cells mutate their antibody-encoding genes in the dark zone (DZ) followed by a selection of the high-affinity variants in the light zone (LZ) by T cells. The amount of the T cell-derived selection signals is proportional to the BCR affinity and the magnitude of Myc expression.

Read the full summary ↓

However, since the lifetimes of Myc mRNA and protein are extremely short, it is unclear how high levels of Myc are maintained in the GC B cell to allow positive selection. Here, by measuring Myc transcripts in situ at the single-cell level, we find that T cell help promotes the frequency of Myc transcriptional bursts. T cell help primarily increases the number of Myc-positive cells rather than the amount of Myc per cell. Measurement of Myc intronic and exonic transcripts in situ demonstrates that positive selection is mediated by Myc transcriptional bursts through a rapid increase in the active transcription sites rather than an elevation in transcription rate or gene accessibility. Thus, the amount of Myc transcriptional bursts over time in the LZ, rather than Myc abundance, dictates B cell selection in germinal centers.

This dataset

Open GSE237128 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE237128_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA994027 and SRA study SRP448773. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

4 × IsoCtrl_4h_LZ vs 4 × AntiCD40_4h_LZ vs 4 × IsoCtrl_4h_DZ vs 4 × AntiCD40_4h_DZ

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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.

Samples in this study

GSM7595856 IsoCtrl_4h_LZ_1 IsoCtrl_4h_LZ
GSM7595857 IsoCtrl_4h_LZ_2 IsoCtrl_4h_LZ
GSM7595858 IsoCtrl_4h_LZ_3 IsoCtrl_4h_LZ
GSM7595859 IsoCtrl_4h_LZ_4 IsoCtrl_4h_LZ
GSM7595860 AntiCD40_4h_LZ_1 AntiCD40_4h_LZ
GSM7595861 AntiCD40_4h_LZ_2 AntiCD40_4h_LZ
GSM7595862 AntiCD40_4h_LZ_3 AntiCD40_4h_LZ
GSM7595863 AntiCD40_4h_LZ_4 AntiCD40_4h_LZ
GSM7595864 IsoCtrl_4h_DZ_1 IsoCtrl_4h_DZ
GSM7595865 IsoCtrl_4h_DZ_2 IsoCtrl_4h_DZ
GSM7595866 IsoCtrl_4h_DZ_3 IsoCtrl_4h_DZ
GSM7595867 IsoCtrl_4h_DZ_4 IsoCtrl_4h_DZ
GSM7595868 AntiCD40_4h_DZ_1 AntiCD40_4h_DZ
GSM7595869 AntiCD40_4h_DZ_2 AntiCD40_4h_DZ
GSM7595870 AntiCD40_4h_DZ_3 AntiCD40_4h_DZ
GSM7595871 AntiCD40_4h_DZ_4 AntiCD40_4h_DZ

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