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

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

PROVIDER: PRJNA400600 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5309850_1.fastq.gz	Fastqsanger.gz
	SRR5309850_2.fastq.gz	Fastqsanger.gz
	SRR5309860_1.fastq.gz	Fastqsanger.gz
	SRR5309860_2.fastq.gz	Fastqsanger.gz
	SRR5309870_1.fastq.gz	Fastqsanger.gz

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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

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

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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.

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