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| Status |
Public on May 27, 2022 |
| Title |
Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Rat] |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: To reveal the differences on epithelial cell composition, functional assignments and pharmacokinetics among mammals intestine, we use single cell sequencing to examine the conserved and divergent features among species, providing a cross-species single-cell transcriptomic atlases of ileal epithelium
Methods:Alive ileum epithelial cells were sorted from three adult rats (3 months old). ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000. Raw reads were aligned to the Rnor_6.0 Rat genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers (UMIs). Raw aligned features were loaded and processed using the Seurat package (v4.0.2). Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes.
Results: After cells with low information content and a high fraction of mitochondrial RNAs were excluded, 3040 cells were analyzed.
Conclusions: Seven cell types were identified in rat ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells and tuft cells.
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| Overall design |
Single cell profiles of ileum epithelial cells from adult rats
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| Contributor(s) |
Chen Y, Li H, Wang X, Wang Y, Zhang M, Hong F, Wang H, Cui A, Zhao J, Ji W |
| Citation(s) |
35511361 |
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| Submission date |
Feb 14, 2022 |
| Last update date |
May 27, 2022 |
| Contact name |
Ye-guang Chen |
| E-mail(s) |
ygchen@mail.tsinghua.edu.cn
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| Organization name |
Tsinghua University
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| Department |
School of life science
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| Lab |
Molcell
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| Street address |
Tsinghua Road, Medical Building
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (1) |
| GPL25947 |
Illumina NovaSeq 6000 (Rattus norvegicus) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE196663 |
Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium |
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| Relations |
| BioProject |
PRJNA806779 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE196660_RAW.tar |
9.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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