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Lymph node stromal cells support the maturation of pre-DCs into cDCs via colony stimulating factor 1

GSE184661 Mus musculus (mouse) RNA-seq (gene expression) 27 samples Submitted 2024/09/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 27 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
27 samples: 9 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.
Summary (written by the submitters)
Conventional dendritic cells (cDCs) arise from committed precursor dendritic cells (pre DCs) in the bone marrow that continuously seed the periphery. Pre-DCs and other upstream progenitors proliferate and mature in response to Fms-related receptor tyrosine kinase 3 ligand (FLT3L), which is considered the most important cytokine for cDC development.
Read the full summary ↓
However, other cytokines such as stem cell factor (SCF) and colony stimulating factor 1 (CSF1) were also shown to induce pre-DC maturation into DC-like cells. It is not completely understood which cells contribute to cDC development once pre-DCs arrive in peripheral tissues. Here, we analyzed the impact of lymph node (LN) fibroblastic stromal cells (FSCs) on the maturation of pre-DCs into cDCs. We could demonstrate that ex vivo isolated LN FSCs co-cultured with pre-DCs induce precursor maturation into DC-like cells, which were capable of efficiently promoting the proliferation of naïve CD4+ T cells. Interestingly, FSCs isolated from mesenteric lymph nodes (mLNs) or peripheral LNs (pLNs) induced DC-like cells with highly comparable transcriptomes, showing similarity to both ex vivo isolated DCs and macrophages based on characteristic signature genes. Finally, by performing supplementation and receptor blocking studies we could demonstrate that CSF1 is a driving factor for LN FSC-mediated pre-DC maturation into DC-like cells. In summary, we could identify CSF1 as a novel stromal cell-derived factor that supports the maturation of pre-DCs into cDCs within secondary lymphoid organs.
This dataset
Open GSE184661 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 GSE184661_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 PRJNA765599 and SRA study SRP338407. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in triplicate
preDC_input ×3 pLN_LO ×3 pLN_HI ×3 mLN_LO ×3 mLN_HI ×3 MCSF_LO ×3 MCSF_HI ×3 Flt3L_LO ×3 +1 more

Supports a between-group comparison across 27 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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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