GEO series

Temporal Single-Cell Transcriptional Dynamics of Murine Pancreatic Islet Remodeling During Hyperglycaemia Progression

GSE329967 Mus musculus (mouse) Single-cell RNA-seq 33 samples Submitted 2026/05/25 Platform GPL21103Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 33 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 33 samples: 33 samples, each with a distinct title — no replicated groupsGroups 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)

Pancreatic islets undergo coordinated cellular remodeling during obesity-induced insulin resistance. However, longitudinal changes across endocrine and non-endocrine compartments remain largely unexplored. We present a comprehensive high-resolution atlas using longitudinal single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) on islets from C57BL/6 mice subjected to high-fat diet (HFD) feeding for 8, 16, and 24 weeks, along with age-matched controls on regular chow (RC).

Read the full summary ↓

We mapped dynamic changes in islet cell composition and transcriptional states. Trajectory inference indicated diversification of beta-cell programs into adaptive and inflammatory states under HFD. Progression of insulin resistance induced shrinkage and transcriptional remodeling of glucagon-secreting alpha-cells, marked by upregulation of genes related to intracellular transport and oxidative stress, accompanied by the emergence of a polyhormonal alpha-cell subpopulation. Similarly, we identified delta-cell subpopulations exhibiting beta-like transcriptional signatures and polyhormonal identity under nutritional stress, suggesting adaptive delta-cell plasticity that may partially compensate for beta-cell loss during insulin resistance. The islet microenvironment exhibited robust expansion of proinflammatory M1 macrophages, reaching a plateau by 16 weeks of HFD, indicating niche saturation. Cell-cell communication analyses revealed disruption of key signaling pathways within endocrine and between endocrine and non-endocrine cells under HFD conditions. Notably, CCL27a–chemokine receptor signaling between beta-cells and M1 macrophages was significantly reduced in HFD islets, likely driven by reduced Ccl27a expression and chromatin accessibility in a distinct beta cell subpopulation, which we further validated using INS-1 cells exposed to HFD-like conditions. Comparative analysis with scRNA seq of human islets confirmed conserved stress signatures. Furthermore, genetic variants at the CCL27 locus were associated with increased T2D risk and HOMA-IR in human populations, establishing a novel link between beta-cell stress and systemic inflammation. This resource provides a hierarchical framework for understanding islet failure and identifies potential therapeutic nodes for type 2 diabetes.

This dataset

Open GSE329967 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE329967_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1462288 and SRA study SRP697673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

33 samples, each with a distinct title — no replicated groups

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

How we read this: Read from 33 sample titles: 33 distinct titles with little repetition. 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

GSM9714162 Regular Chow 8 Weeks 1R scRNA
GSM9714163 Regular Chow 8 Weeks 2R scRNA
GSM9714164 Regular Chow 8 Weeks 3R scRNA
GSM9714165 Regular Chow 14 Weeks 1R scRNA
GSM9714166 Regular Chow 14 Weeks 2R scRNA
GSM9714167 Regular Chow 14 Weeks 3R scRNA
GSM9714168 Regular Chow 22 Weeks 1R scRNA
GSM9714169 Regular Chow 22 Weeks 2R scRNA
GSM9714170 Regular Chow 22 Weeks 3R scRNA
GSM9714171 Regular Chow 30 Weeks 1R scRNA
GSM9714172 Regular Chow 30 Weeks 2R scRNA
GSM9714173 Regular Chow 30 Weeks 3R scRNA
GSM9714174 High Fat Diet 8 Weeks 1R scRNA
GSM9714175 High Fat Diet 8 Weeks 2R scRNA
GSM9714176 High Fat Diet 8 Weeks 3R scRNA
GSM9714177 High Fat Diet 16 Weeks 1R scRNA
GSM9714178 High Fat Diet 16 Weeks 2R scRNA
GSM9714179 High Fat Diet 16 Weeks 3R scRNA
GSM9714180 High Fat Diet 24 Weeks 1R scRNA
GSM9714181 High Fat Diet 24 Weeks 2R scRNA
GSM9714182 High Fat Diet 24 Weeks 3R scRNA
GSM9714183 Regular Chow 8 Weeks 1 scATAC
GSM9714184 Regular Chow 8 Weeks 2 scATAC
GSM9714185 Regular Chow 8 Weeks 3 scATAC
GSM9714186 Regular Chow 14 Weeks 1 scATAC
GSM9714187 Regular Chow 14 Weeks 2 scATAC
GSM9714188 Regular Chow 30 Weeks 1 scATAC
GSM9714189 Regular Chow 30 Weeks 2 scATAC
GSM9714190 High Fat Diet 8 Weeks 1 scATAC
GSM9714191 High Fat Diet 8 Weeks 2 scATAC
GSM9714192 High Fat Diet 24 Weeks 1 scATAC
GSM9714193 High Fat Diet 24 Weeks 2 scATAC
GSM9714194 High Fat Diet 24 Weeks 3 scATAC

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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.