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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Rattus norvegicus Sus scrofa Macaca mulatta

PROVIDER: GSE196663 | GEO | 2022/05/27

REPOSITORIES: GEO

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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 [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

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 [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

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

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

| PRJNA806779 | ENA

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 Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells.

Project description:The mammalian brain is characterized by distinct classes of cells that differ in morphology, structure, signaling, and function. Dysregulation of gene expression in these cell populations leads to various neurological disorders. Neural cells often need to be acutely purified from animal brains for research, which requires complicated procedure and specific expertise. Primary culture of these cells in vitro is a viable alternative, but the differences in gene expression of cells grown in vitro and in vivo remain unclear. Here, we cultured three major neural cell classes of rat brain (ie, neurons, astrocytes, and oligodendrocyte precursor cells [OPCs]) obtained from commercial sources. We measured transcript abundance of these cell types by RNA sequencing (RNA-seq) and compared with their counterparts acutely purified from mouse brains. Cross-species RNA-seq data analysis revealed hundreds of genes that are differentially expressed between the cultured and acutely purified cells. Astrocytes have more such genes compared to neurons and OPCs, indicating that signaling pathways are greatly perturbed in cultured astrocytes. This dataset provides a powerful resource to demonstrate the similarities and differences of biological processes in mammalian neural cells grown in vitro and in vivo at the molecular level.

| S-EPMC4662426 | biostudies-literature

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