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Series GSE87038 Query DataSets for GSE87038
Status Public on Feb 26, 2018
Title Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Background:
Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive.
Results:
We perform single-cell RNA sequencing analysis of 1,916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed.
Conclusions:
We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene- regulatory networks governing mammalian organogenesis.

 
Overall design Here, we performed single-cell RNA sequencing (RNA-Seq) analysis of 1,916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, including the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine.
 
Contributor(s) Dong J, Hu Y, Fan X, Wu X, Tang F
Citation(s) 29540203, 30787436
Submission date Sep 16, 2016
Last update date May 15, 2019
Contact name Ji Dong
E-mail(s) dongji5211314@126.com
Organization name Peking University
Street address Yiheyuan 5#
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (32)
GSM2319557 forebrain_E9.5_embryo1
GSM2319558 heart_E9.5_embryo1
GSM2319559 intestine_E9.5_embryo1
Relations
BioProject PRJNA343327
SRA SRP090067

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
GSE87038_Cell_Information_and_Barcode_Information.xlsx 121.0 Kb (ftp)(http) XLSX
GSE87038_Mouse_Organogenesis_UMI_counts_matrix.xlsx 152.8 Mb (ftp)(http) XLSX
GSE87038_Mouse_Organogenesis_expression_matrix_log2_based_TPM_divided_by_10.xlsx 221.6 Mb (ftp)(http) XLSX
GSE87038_RAW.tar 34.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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