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Intragraft memory-like CD127hiCD4+Foxp3+ regulatory T cells maintain transplant tolerance

GSE220447 Mus musculus (mouse) RNA-seq (gene expression) 33 samples Submitted 2024/03/22 Platform GPL19057Platform GPL16417
At a glance

RNA-seq (gene expression) · mouse · 33 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
33 samples: 11 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
Intragraft memory-like CD127hiCD4+Foxp3+ Tregs maintain transplant toleranceJCI insight · 2024
Summary (written by the submitters)
CD4+Foxp3+ regulatory T cells (Tregs) play an essential role in suppressing transplant rejection but their role within the graft, is poorly understood. To address this, we compared phenotypic and transcriptomic characteristics of Treg populations within lymphoid-organs and grafts in an islet xenotransplant model of tolerance induced by co-stimulation blockade.
Read the full summary ↓
In this study, Tregs were essential for tolerance induction and their numbers increased over time. Tregs demonstrated phenotypic and transcriptional heterogeneity within the graft, and lymphoid organs of tolerant mice. A sub-population of CD127highTreg with memory-like and suppressive features were present in high proportions within long surviving islet-grafts of tolerant mice and had a transcriptomic profile consistent with tissue-Tregs. Importantly these CD127highTregs were better able to prevent rejection by effector T cells, after adoptive transfer into secondary Rag-/- hosts, than naïve Tregs, or unselected Tregs isolated from tolerant mice. We propose that after initial development within the draining lymph node they undergo further genetic reprogramming within the graft towards a phenotype that has shared characteristics with other tissue or tumour Tregs. These findings provide a new focus for engineering such cells either in vivo or for adoptive transfer for inducing tolerance.
Published in
Intragraft memory-like CD127hiCD4+Foxp3+ Tregs maintain transplant tolerance
Zhao Y, Nicholson L, Wang H et al. · JCI insight 2024 · PMID 38516885 · doi:10.1172/jci.insight.169119
This dataset
Open GSE220447 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 GSE220447_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 PRJNA909782 and SRA study SRP411857. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38516885) ↗
Study design
11 conditions, mostly in triplicate
SP/NaiveCD45+CD4 ×3 SP/Tolerant-CD45+CD4 ×3 SP/Naïve-CD4+ ×3 SP/Tolerant-CD4+ ×3 SP/Naïve-Treg ×3 SP/CD127-Tregs ×3 SP/CD127highTregs ×3 Graft-Tregs ×3 +3 more

Supports a between-group comparison across 33 samples.

How we read this: 11 replicated groups read from 33 sample titles; they account for 33 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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