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Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Rat]

ABSTRACT: Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Rat]

PROVIDER: PRJNA806779 | ENA |

REPOSITORIES: ENA

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Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Macaque]

Project description: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 two cynomolgus monkeys (14 years 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 Mmul_10 Macaque 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, 886 cells were analyzed. Conclusions: Eight cell types were identified in macaque ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells, CA7+ cells and tuft cells.

2022-05-27 | GSE196658 | GEO

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Mouse]

Project description: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 mice (10 weeks). 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 GRCm38/mm10 Mouse 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, 1060 cells were analyzed. Conclusions: Eight cell types were identified in mouse ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, Paneth cells, enteroendorcine cells and tuft cells.

2022-05-27 | GSE196662 | GEO

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Rat]

Project description: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.

2022-05-27 | GSE196660 | GEO

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Pig]

Project description: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 pigs (6 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 Sscrofa11.1 Pig 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, 730 cells were analyzed. Conclusions: Eight cell types were identified in pig ileum based on reported markers, including enterocytes, transient-amplifying (TA) cells, goblet cells, goblet progenitor cells, stem cells, enteroendorcine cells, CA7+ cells and tuft cells.

2022-05-27 | GSE196659 | GEO

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium

Project description:Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium

| PRJNA806773 | ENA

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-05-27 | GSE196663 | GEO

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Mouse]

Project description:Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Mouse]

| PRJNA806778 | ENA

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Macaque]

Project description:Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Macaque]

| PRJNA806771 | ENA

Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Pig]

Project description:Cross-species single-cell transcriptomic analysis reveals divergence of cell composition and functions in mammalian ileum epithelium [scRNA-seq_Pig]

| PRJNA806770 | ENA

Ileum and colon goblet cell proteome

Project description:This study is a comparative proteomics study of FACS sorted Muc2 expressing and non expressing cells in mouse ileum and colon.

2021-04-19 | PXD011527 | Pride

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