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Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis [adult tissues]

ABSTRACT: Here, using a modified STRT-seq protocol, we analyzed the large intestine (LI) from two adults.In detail, the total 1891 single cells were picked from two adults LI. After the same rigorous filtration as fetal, 1463 individual cells were used for subsequent analysis. We identified 18 cell types including all main cell types existed in intestine such as enterocyte, goblet cell, enteroendocrine, Paneth cell, stem cell and immune cell. Take advantage of single cell RNA sequencing, we found that there were subtypes existed in some cell types. Subsequently, combined with our previous fetal data, we investigate the transcriptomic similarity and difference between human from fetal to adult. The transcriptome feature and development process from fetal to adult were revealed for the first time at single-cell resolution.

ORGANISM(S): Homo sapiens

PROVIDER: GSE103154 | GEO | 2018/04/05

REPOSITORIES: GEO

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Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis [fetal tissues]

Project description:The development of digestion tract is critical for proper digestion of food and absorbance of nutrient for an individual. It includes the spatial segregation into esophagus, stomach, small and large intestine. The temporal-spatial gene expression profiles of human digestion tract in vivo have never been analyzed at single-cell resolution.Here we analyzed esophagus, stomach, small intestine (SI) and large intestine (LI) from multiple human embryos between 6 and 25 weeks of gestation by single cell RNA-seq analyses.We firstly identified 51 clusters of different types of cells using t- Distributed Stochastic Neighbor Embedding (t-SNE) analysis.Moreover,cell type of each organ were identified according to the known marker genes and new cell types were further analyzed.The dynamic change of each cell type were tracked during the human embryonic digestive tract development.We found HOX family geens paly different roles in the regulation of digestion tract developemnt. In addition, Hedgehog,TGFβ and BMP signaling pathway are essential for SI and LI development in human fetal. The function of nutrient digestion and absorption was increased as the SI development in human fetal.Finally, we demonstrated that the immune system was established at late stage of human fetal and verified the immune-like cells,such as T cell, B cells and macrophage. In summary, by using single cell RNA seq technique, we identified the waves of signaling pathways and critical cell types for the human digestion tract development.

2018-04-05 | GSE95630 | GEO

Distinct human stem cell populations in small and large intestine

Project description:The intestine is composed of an epithelial layer, containing rapidly proliferating cells that mature into two distinct anatomic regions, the small and the large intestine. Although previous studies have identified stem cells as the cell-of-origin for the whole intestine, no studies have compared stem cells derived from the small and large intestine. Here, we report intrinsic differences between these two populations of cells. Primary epithelial cells isolated from human fetal small and large intestine and expanded with Wnt agonist, R-spondin 2, displayed differential expression of stem cell markers and separate hierarchical clustering of gene expression involved in differentiation, proliferation and disease pathways. Using a three-dimensional in vitro differentiation assay, single cells derived from small and large intestine formed distinct organoid architecture with cellular hierarchy similar to that found in primary tissue. Our characterization of human fetal intestinal stem cells defies the classical definition proposed by most where small and large intestine are repopulated by an identical epithelial stem cell and raises the question of the importance of intrinsic and extrinsic cues in the development of intestinal diseases. 12 samples were analyzed. They consisted of human fetal small and large intestine (SI; n=6 and LI; n=6) stem cells, expanded with Wnt agonist and R-spondin 2. Differential expression of genes in epithelial cells from both the large and small intestine were observed.

2015-01-15 | E-GEOD-56525 | biostudies-arrayexpress

Comprehensive transcriptomic profiles of non-small cell lung cancer by single-cell RNA-seq

Project description:Lung cancer has been the leading cause of cancer death seriously threatening human health. The lung cancers display high heterogeneity in terms of pathology and molecular biomarkers. However, previous studies are mainly based on population of cancer cells due to technical limitations, which would conceal important information from rare single cells. Hence, using a modified STRT-seq technique, we profiled transcriptomes of over 9,000 single cells from 20 primary non-small cell lung cancer (NSCLC) patients diagnosed with stage I-IV. We identified major epithelial cell types, stroma cells and immune cells existed in lung, analyzed the differences between normal and tumor tissues and described the heterogeneity of intra- and inter-tumor tissues at single cell level. Furthermore, we analyzed the potential relationship of malignant epithelial cells, stroma cells and immune cells. In summary, our comprehensive analysis provided maps of transcriptomes characteristics of lung cancers and will be helpful for the prognosis and therapy of lung cancers.

2022-07-30 | GSE119911 | GEO

Single-cell RNA sequencing of mouse embryonic cells from the oocyte, 2-cell, 4-cell, 8-cell, blastocyst, and morula stages

Project description:STRT-N is a newly optimized single-cell RNA sequencing method for studies of early genome activation in mammalian preimplantation development. Here, single embryos from the oocyte, 2-cell, 4-cell, 8-cell, blastocyst, and morula stages were sampled for experiments and were sequenced using STRT-N method.

2023-02-16 | E-MTAB-12572 | biostudies-arrayexpress

Single-cell transcriptomic survey of adenomatous polyposis patients with germline APC mutations

Project description:Patients with germline APC mutations are recognized by hundreds of adenoma polyps in colon, which will give rise to adenocarcinoma inevitably. Over 700 germline APC mutations have been reported to be the leading cause of adenomatous polyposis. However, the underlying mechanism of APC mutation triggered colonic cancer remains mysterious. Here, using a modified STRT-seq protocol, we analyzed over 4000 single cells from the four matching adenomatous polyposis, adenocarcinoma, adjacent normal colon tissue and one lymphatic metastasis from four adenomatous polyposis patients with APC mutations. We identified the main cell types existed in human intestine such as B cells, mast cells, T cells, macrophage cells, endothelial cells, stromal cells and epithelial cells. And the proportional changes of various cell types during the development of adenoma were showed. The transcriptomic similarities and differences between adenoma, adenocarcinoma and adjacent normal tissue were comprehensively investigated. For better understanding the tumor progression process, we also take advantage of other genomic signatures, such as SNV and CNV. We found that the gene expression signatures of adenoma and adenocarcinoma were largely similar when compared with adjacent normal tissue. But the mutation accumulation was indeed observed during the progression from adenoma to adenocarcinoma. To summarized, our work will help us accurately investigate the pathogenic mechanism and heterogeneity of APC inactive mutation triggered colonic cancer, which will also help us better understand the non-familial colorectal cancers

2019-10-25 | GSE109308 | GEO

Characterization of the single-cell (ES and MEF) transcriptional landscape by highly multiplex RNA-Seq

Project description:Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constitutent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-Seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data was projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselvesâall without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the complete transcriptomes of 92 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology and disease. 92 single cells (48 mouse ES cells, 44 mouse embryonic fibroblasts and 4 negative controls) were analyzed by single-cell tagged reverse transcription (STRT)

2011-05-24 | E-GEOD-29087 | biostudies-arrayexpress

Project description:fetal intestine

| PRJNA476418 | ENA

Single cell profiling of CD4+ T cells from human fetal intestine

Project description:Single cell profiling of CD4+ T cells from human fetal intestine

| PRJNA506660 | ENA

scRNA-seq of human fetal lung and intestine tissue

Project description:Here, we performed single cell RNA sequencing (scRNA-seq) of 1 (one) human fetal lung tissue specimen (18.9 week) and 2 (two) human fetal intestine specimens (12.1 and 18.9 week) (total of 3 (three) independent biological specimens). The data set is composed of approximately 5,000 lung cells and 7,500 intestine cells. Lineages captured across both tissues include but are not limited to epithelium, stroma, immune, neurons and endothelium.

2020-12-20 | E-MTAB-9363 | biostudies-arrayexpress

Single-cell RNA-seq of mouse cerebral cortex

Project description:We have applied a recently developed, highly accurate and sensitive single-cell RNA-seq method (STRT/C1) to perform a molecular census of two regions of the mouse cerebral cortex: the somatosensory cortex and hippocampus CA1.

2015-02-20 | GSE60361 | GEO

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