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

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE103239 | 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

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

Project description: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.

2018-04-05 | GSE103154 | GEO

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

Project description:Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis

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The Spatial and Temporal Transcriptomic Landscapes of Ginseng, Panax ginseng C. A. Meyer.

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Dissecting dynamic expression of autophagy-related genes during human fetal digestive tract development via single-cell RNA sequencing.

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Single cell transcriptomic and spatial landscapes of the developing human pancreas - spatial transcriptomics

Project description:The progress made in directed differentiation of stem cells has shown that understanding human pancreas development can provide cues for generating unlimited amounts of insulin-producing beta cells for transplantation therapy in diabetes. However, current differentiation protocols have not been successful in reproducibly generating functional human beta cells in vitro, partly due to incomplete understanding of human pancreas development. Here, we present detailed transcriptomic analysis of the various cell types of the developing human pancreas, including their spatial gene patterns. We integrated single cell RNA sequencing with spatial transcriptomics at multiple developmental timepoints and revealed distinct temporal-spatial gene cascades in the developing human pancreas.

2022-12-21 | GSE197317 | GEO

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The human gastrointestinal tract through space and time- Fetal Spatial transcriptomics

Project description:Single-cell RNAseq (scRNAseq) and paired VDJ analysis and spatial transcriptomics, we create the first comprehensive cell atlas of the healthy developing, paediatric and adult human gut, including 347,980 cells from up to 10 distinct anatomical sites. We use this data to trace the cellular composition of the gut throughout life, define novel cell markers and cell-cell interactions. We find four neuronal cell populations in the developing enteric nervous system, with expression patterns indicative of irritable bowel syndrome and Hirschsprung’s disease, and identify key cell players and communication networks initiating lymphoid structure formation in early human development.

2021-04-30 | E-MTAB-10386 | biostudies-arrayexpress

Single cell transcriptomic and spatial landscapes of the developing human pancreas

2022-12-21 | GSE197064 | GEO

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