Mouse pancreatic islet scRNA-seq integrated atlas encompassing different ages, sexes, chemical stress leading to dedifferentiation, and diabetes models with corresponding treatments.
Two datasets (sub-series) were newly generated for the atlas.
Overall design: The atlas integrates data from nine studies and 56 samples with over 300,000 pancreatic islet cells, including over 100,000 beta cells, across different conditions (sex, age, chemical stress, diabetes status). The atlas object with raw and processed expression, annotations, and integrated embedding is contained in GSE211799_adata_atlas.h5ad.gz. Two datasets newly generated for the atlas are in sub-series.
We mapped an external dataset (GSE137909), not contained in the atlas, on top of the atlas and provide the integrated latent embedding in GSE211799_adata_referenceMapping_GSE137909.
More...Mouse pancreatic islet scRNA-seq integrated atlas encompassing different ages, sexes, chemical stress leading to dedifferentiation, and diabetes models with corresponding treatments.
Two datasets (sub-series) were newly generated for the atlas.
Overall design: The atlas integrates data from nine studies and 56 samples with over 300,000 pancreatic islet cells, including over 100,000 beta cells, across different conditions (sex, age, chemical stress, diabetes status). The atlas object with raw and processed expression, annotations, and integrated embedding is contained in GSE211799_adata_atlas.h5ad.gz. Two datasets newly generated for the atlas are in sub-series.
We mapped an external dataset (GSE137909), not contained in the atlas, on top of the atlas and provide the integrated latent embedding in GSE211799_adata_referenceMapping_GSE137909.h5ad.gz
In both anndata integration objects we describe individual anndata fields under uns key field_descriptions.
Code associated with the manuscript: https://github.com/theislab/mm_pancreas_atlas_rep
cellxgene portal entry: https://cellxgene.cziscience.com/collections/296237e2-393d-4e31-b590-b03f74ac5070
Less...| Accession | PRJNA872143; GEO: GSE211799 |
| Type | Umbrella project |
| Submission | Registration date: 22-Aug-2022
Theis lab, Institute of Computational Biology, Helmholtz Munich |
| Relevance | Superseries |
Project Data:
| Resource Name | Number
of Links |
|---|
| Sequence data |
| SRA Experiments | 7 |
| Other datasets |
| BioSample | 7 |
| GEO DataSets | 3 |
Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes encompasses the following 2 sub-projects:
| Project Type | Number of Projects |
| Transcriptome or Gene expression | 2 |
BioProject
accession | Organism | Title |
|---|
| PRJNA872136 | Mus musculus | scRNA-seq of pancreatic islets from male and female aged mice with Fltp-reporter sorting (Theis lab, Institute of Computational...) | | PRJNA872138 | Mus musculus | scRNA-seq of pancreatic islets from adult male mice with Fltp-reporter sorting and pancreatic head-tail separation (Theis lab, Institute of Computational...) |
|