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| Status |
Public on Dec 23, 2022 |
| Title |
Mouse pancreatic islet scRNA-seq atlas across sexes, ages, and stress conditions including diabetes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| 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
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| Contributor(s) |
Hrovatin K, Bastidas-Ponce A, Zappia L, Bakhti M, Büttner M, Sallino C, Sterr M, Böttcher A, Migliorini A, Lickert H, Theis FJ |
| Citation |
Karin Hrovatin, Aimee Bastidas-Ponce, Mostafa Bakhti, Luke Zappia, Maren Buttner, Ciro Sallino, Michael Sterr, Anika Bottcher, Adriana Migliorini, Heiko Lickert, and Fabian J Theis. Delineating mouse beta-cell identity during lifetime and in diabetes with a single cell atlas. bioRxiv 2022.12.22.521557; doi:10.1101/2022.12.22.521557
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| Submission date |
Aug 22, 2022 |
| Last update date |
Feb 23, 2023 |
| Contact name |
Karin Hrovatin |
| Organization name |
Helmholtz Munich
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| Department |
Institute of Computational Biology
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| Lab |
Theis lab
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| Street address |
Ingolstädter Landstraße 1
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| City |
Munich |
| ZIP/Postal code |
D-85764 |
| Country |
Germany |
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| Platforms (2) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (7)
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| This SuperSeries is composed of the following SubSeries: |
| GSE211795 |
scRNA-seq of pancreatic islets from male and female aged mice with Fltp-reporter sorting |
| GSE211796 |
scRNA-seq of pancreatic islets from adult male mice with Fltp-reporter sorting and pancreatic head-tail separation |
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| Relations |
| BioProject |
PRJNA872143 |
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