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Series GSE95630 Query DataSets for GSE95630
Status Public on Apr 05, 2018
Title Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis [fetal tissues]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design Single cell transcriptome profiles of four main human organs (esophagus, stomach, small and large intestine) from 6 week to 25 week gestation of digestion system were generated by next generation sequencing using Illumina HiSeq X Ten
 
Contributor(s) Gao S, Yan L, Wang R, Li J
Citation(s) 29802404
Submission date Mar 02, 2017
Last update date May 15, 2019
Contact name Rui WANG
E-mail(s) fish_cat_wr@sina.cn
Phone 15801166445
Organization name Peking University
Department Biodynamics Optical Imaging Center (BIOPIC)
Lab Fuchou Tang
Street address No.5 Yiheyuan Road, Haidian District
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (445)
GSM2519485 esophagus_EM2_6w_1-90
GSM2519486 stomach_EM2_6w_1-90
GSM2519487 SI_EM2_6w_1-90
This SubSeries is part of SuperSeries:
GSE103239 Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis
Relations
BioProject PRJNA377736
SRA SRP101290

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95630_Digestion_TPM_new.txt.gz 74.6 Mb (ftp)(http) TXT
GSE95630_README_barcodes.xlsx 96.9 Kb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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