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Early life B cell memory is archived in the mouse B-1 cell compartment and drives Chronic Lymphocytic Leukemia-like disease [bulkVDJ-seq]

GSE314340 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2026/03/09 Platform GPL16417
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 14 conditions, mostly in duplicateGroups 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)
The adult B cell pool is a developmental mosaic comprising short-lived naïve B cells and long-lived memory. Using genetic time-stamping, we previously showed that early life origin (ELO) B cells contributed substantially to the adult mouse immune system. In this study, we found that ELO B cells share a memory-like signature. Notably, B-1 cells exhibited an enrichment for the PD-L2/CD80 double positive (DP) immunophenotype associated with highly differentiated memory.
Read the full summary ↓
Indeed, microbial antigen exposure in neonates expanded distinct specificities within the DP B-1 cell compartment, identifying the latter as a reservoir of IgM memory. B cell chronic lymphocytic leukemia (CLL) is a disease marked by the accumulation of memory-like B cells. By applying time-stamping to a mouse model for unmutated CLL (U-CLL), we demonstrated that leukemic expansion is driven by B-1 cell clones arising prior to postnatal day 10. Importantly, B-1 cells in mice and man closely mirrored the molecular profile of U-CLL. These results suggest that an age-associated leukemia can originate from ELO B cells.
This dataset
Open GSE314340 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 GSE314340_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: 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 PRJNA1391011 and SRA study SRP656758. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly in duplicate
Day 10 time-stamped WT control mouse 85, FACS… ×2 Day 10 time-stamped WT control mouse 85, FACS… ×2 Day 10 time-stamped TCL-1 mouse 86, FACS sort… ×2 Day 10 time-stamped TCL-1 mouse 86, FACS sort… ×2 Day 19 time-stamped TCL-1 mouse 90, FACS sort… ×2 Day 19 time-stamped TCL-1 mouse 90, FACS sort… ×2 Day 19 time-stamped TCL-1 mouse 91, FACS sort… ×2 Day 19 time-stamped TCL-1 mouse 91, FACS sort… ×2 +8 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 30 sample titles; they account for 28 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
Datasets on a similar topic

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