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The Transcriptional Cofactor SKI Regulates Medullary Thymic Epithelial Cell Differentiation and Peripheral T Cell Responses

GSE220665 Mus musculus (mouse) RNA-seq (gene expression) 42 samples Submitted 2024/06/26 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 42 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
42 samples
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
SKI Regulates Medullary Thymic Epithelial Cell Differentiation to Control Peripheral T Cell Responses in MiceJournal of immunology (Baltimore, Md. : 1950) · 2024
Summary (written by the submitters)
The thymus is an important site for the establishment and maintenance of an appropriate immune response through positive and negative selection of developing T cells. During selection, developing T cells interact with cortical and medullary thymic epithelial cells (TECs), termed cTECs and mTECs respectively. Our lab found that TEC-specific deletion of Ski decreased the mTEC compartment in the thymus and that tissue restricted antigen (TRA) expression in mTECs was also altered.
Read the full summary ↓
Interestingly, these mice were significantly protected from developing experimental autoimmune encephalomyelitis (EAE) disease compared to the control mice and naïve CD4 T cells purified from Ski-deleted mice showed a defect in proliferation in vitro after global T cell receptor (TCR) stimulation. Overall, our findings suggest that SKI signaling in the thymus regulates mTEC differentiation and function as well as downstream peripheral T cell responses and provide evidence for targeting SKI in T cell driven autoimmune diseases such as multiple sclerosis.
Published in
SKI Regulates Medullary Thymic Epithelial Cell Differentiation to Control Peripheral T Cell Responses in Mice
Chiu H, Weinstein KN, Spath S et al. · Journal of immunology (Baltimore, Md. : 1950) 2024 · PMID 38767415 · doi:10.4049/jimmunol.2300262
This dataset
Open GSE220665 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 GSE220665_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 PRJNA910943 and SRA study SRP412401. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38767415) ↗
Study design
A cohort of 42 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run lib78027 … lib78068 and carry no group information.

Samples in this study

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.