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Effect of mechanical stimulation on immune function of dendritic cells (DCs)

GSE207653 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/04/08 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 6 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
Cell shape sensing licenses dendritic cells for homeostatic migration to lymph nodesNature immunology · 2024
Summary (written by the submitters)
Address the effect of mechanical stimulation by confinement on the status of activation of dendritic cells and the role of cPLA2 in orchestrating this response. We performed gene expression analysis using data obtained from RNA-seq of 3 independent experiment of DCs from WT and KO of cPLA2.
Published in
Cell shape sensing licenses dendritic cells for homeostatic migration to lymph nodes
Alraies Z, Rivera CA, Delgado MG et al. · Nature immunology 2024 · PMID 38834865 · doi:10.1038/s41590-024-01856-3
This dataset
Open GSE207653 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 GSE207653_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 PRJNA856627 and SRA study SRP385281. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38834865) ↗
Study design
6 conditions, mostly in triplicate
immature non-confined DCs, WT control, ×3 immature non-confined DCs, KO control, ×3 LPS-activated non-confined DCs, WT, ×3 LPS-activated non-confined DCs, KO, ×3 immature Confined DCs, WT confined at 3µm, ×3 immature Confined DCs, KO confined at 3µm, ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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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