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Regulated and adaptive in vivo insulin secretion from islets only containing β-cells

GSE226479 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2024/07/19 Platform GPL21103
At a glance

RNA-seq (gene expression) · mouse · 22 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
22 samples: 6 × 8-hour fasting, beta-cells, DT-treated mouse vs 6 × 2-hour refed, beta-cells, DT-treated mouse vs 5 × 8-hour fasting, beta-cells, control mouse vs 5 × 2-hour refed, beta-cells, control mouseGroups 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
Regulated and adaptive in vivo insulin secretion from islets only containing β-cellsNature metabolism · 2024
Summary (written by the submitters)
The activity of pancreatic islets’ insulin-producing β-cells is closely regulated by systemic cues and, locally, by adjacent islet hormone-producing “non-β-cells” (namely α-, δ- and γ-cells). Still, it is unclear whether the presence of the non-β-cells is a requirement for accurate insulin secretion. Here, we generated and studied a mouse model in which adult islets are exclusively composed of β-cells, and human pseudoislets containing only primary β-cells.
Read the full summary ↓
Mice lacking non-β-cells had optimal blood glucose regulation. They exhibited enhanced glucose tolerance, insulin sensitivity and restricted body weight gain under high-fat diet. The insulin secretion dynamics in islets composed of only β-cells was like in intact islets, both in homeostatic conditions and upon extreme insulin demand. Similarly, human β-cell pseudoislets retained the glucose-regulated mitochondrial respiration, insulin secretion and exendin-4 responses of human islets comprising all four cell types. Together, the findings indicate that non-β-cells are dispensable for blood glucose homeostasis and β-cell function. This is particularly relevant in diabetes, where non-β-cells become dysfunctional and worsen the disease’s pathophysiology. These results support efforts aimed at developing diabetes treatments by generating β-like cell clusters devoid of non-β-cells, as for example from human embryonic stem cells and/or by in situ conversion of non-β-cells into insulin producers.
Published in
Regulated and adaptive in vivo insulin secretion from islets only containing β-cells
Perez-Frances M, Bru-Tari E, Cohrs C et al. · Nature metabolism 2024 · PMID 39169271 · doi:10.1038/s42255-024-01114-8
This dataset
Open GSE226479 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 GSE226479_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 PRJNA940415 and SRA study SRP425355. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39169271) ↗
Study design
6 × 8-hour fasting, beta-cells, DT-treated mouse vs 6 × 2-hour refed, beta-cells, DT-treated mouse vs 5 × 8-hour fasting, beta-cells, control mouse vs 5 × 2-hour refed, beta-cells, control mouse

Supports a case/control comparison: 12 samples read as cases, 10 as controls.

How we read this: 4 replicated groups read from 22 sample titles; they account for 22 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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