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The histone demethylase KDM5C regulates IRF transcriptional programming impacting dendritic cell population heterogeneity and function (RNA-seq)

GSE262866 Mus musculus (mouse) RNA-seq (gene expression) 55 samples Submitted 2024/09/25 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 55 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
55 samples: 10 conditions, mostly with about 6 replicates eachGroups 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
Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and functionCell reports · 2024
Summary (written by the submitters)
Functional and phenotypic heterogeneity of dendritic cells (DCs) plays a crucial role in facilitating the development of diverse immune responses essential for host protection. We found that KDM5C, a histone lysine demethylase, regulates conventional DC (cDC) and plasmacytoid DC (pDC) population heterogeneity and function. Mice deficient in KDM5C in DCs, have increased proportions of cDC2Bs and cDC1s, which was partly dependent on type I interferon and pDCs.
Read the full summary ↓
Loss of KDM5C resulted in an increase in Ly6C- pDCs, which, compared to Ly6C+ pDCs, have limited ability to produce type I interferon and can more efficiently stimulate antigen-specific CD8 T cells. KDM5C-deficient DCs have increased expression of inflammatory genes, altered expression of lineage-specific genes, and reduced function. In response to Listeria infection, KDM5C-deficient mice mounted reduced CD8 responses due to decreased antigen presentation by cDC1s. Thus, KDM5C is a key regulator of DC heterogeneity and a critical driver functional properties of DCs.
Published in
Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function
Guak H, Weiland M, Ark AV et al. · Cell reports 2024 · PMID 39052479 · doi:10.1016/j.celrep.2024.114506
This dataset
Open GSE262866 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 GSE262866_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 PRJNA1094398 and SRA study SRP498806. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39052479) ↗
Study design
10 conditions, mostly with about 6 replicates each
KO_pDC_Ly6c_pos ×6 KO_pDC_Ly6c_neg ×6 KO_cDC1 ×6 KO_cDC2B ×6 WT_pDC_Ly6c_pos ×6 WT_cDC1 ×6 WT_cDC2A ×6 WT_cDC2B ×6 +2 more

Supports a between-group comparison across 55 samples.

How we read this: 10 replicated groups read from 55 sample titles; they account for 55 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

+ 15 more — browse all 55 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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