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Differential chromatin accessability in follicular B cells, marginal zone B cells and newly formed plasma cells. [ATAC-Seq]

GSE335246 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2026/07/08 Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
12 samples: 4 × marginal zone B cell, biol vs 4 × LPS immunized, day 4, Blimp1+ plasma cell, biol vs 3 × follicular B cell, biolGroups 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)
Marginal zozne B cells are poised to rapidly differentiate into plasma cells through biochemical pathways activated by Notch2 signaling. We sought to determine differences in chromatin accessability at plasma cell program-relevant loci between these cells and follicular B cells also located within the spleen but less receptive to Notch signaling. To ths end, we prepared ATAC-seq libriaries from steady state marginal zone and follicular B cells as well as newly formed plasma cells generated in Blimp1GFP/+ reporter mice 4 days post immunization with LPS.
This dataset
Open GSE335246 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE335246_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1477796 and SRA study SRP709081. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × marginal zone B cell, biol vs 4 × LPS immunized, day 4, Blimp1+ plasma cell, biol vs 3 × follicular B cell, biol

Supports a between-group comparison across 11 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 11 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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