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Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells (RNA-seq of SMC3 KO FL-BMDC differentiation and activation)

GSE270816 Mus musculus (mouse) RNA-seq (gene expression) 26 samples Submitted 2026/01/13 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 26 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
26 samples: 10 conditions, mostly in triplicateGroups 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
Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cellsScience immunology · 2026
Summary (written by the submitters)
The cohesin protein complex extrudes chromatin between CTCF binding sites and organizes it into topologically associated domains (TADs), yet the biological implications of this regulatory mechanism are poorly understood. We show that the cohesin subunit Smc3 is required for the postmitotic differentiation and function of antigen-presenting dendritic cells (DCs).
Read the full summary ↓
In particular, Smc3 deletion impaired antigen cross-presentation and IL-12 secretion by type 1 conventional DCs (cDC1s), thereby crippling antimicrobial and antitumor immune responses. The chromatin profile of DCs was shaped by the interplay of cohesin and the cDC1-specifying transcription factor IRF8. Conversely, optimal expression of IRF8 itself required CTCF/cohesin-binding elements demarcating the Irf8 gene. Cohesin-mediated chromatin remodeling facilitated chromatin priming at activation-inducible genes; accordingly, deletion of CTCF/cohesin-binding sites flanking the Il12b gene reduced basal and activation-induced IL-12 production by cDC1s. Our data reveal an essential role for cohesin-mediated chromatin regulation in the differentiation and function of a key immune cell type.
Published in
Cohesin-mediated chromatin organization controls the differentiation and function of dendritic cells
Adams NM, Galitsyna A, Tiniakou I et al. · Science immunology 2026 · PMID 41650249 · doi:10.1126/sciimmunol.adx4622
This dataset
Open GSE270816 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 GSE270816_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 PRJNA1128567 and SRA study SRP516237. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41650249) ↗
Study design
10 conditions, mostly in triplicate
RNA_WT_pDC_unstim ×3 RNA_WT_cDC1_unstim ×3 RNA_WT_cDC2_unstim ×3 RNA_SMC3KO_pDC_unstim ×3 RNA_SMC3KO_cDC1_unstim ×3 RNA_SMC3KO_cDC2_unstim ×3 RNA_WT_cDC1_CpGAB ×2 RNA_WT_cDC2_CpGAB ×2 +2 more

Supports a between-group comparison across 26 samples.

How we read this: 10 replicated groups read from 26 sample titles; they account for 26 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
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