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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| 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.
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| Contributor(s) |
Dong J, Hu Y, Fan X, Wu X, Tang F |
| Citation(s) |
29540203, 30787436 |
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| Submission date |
Sep 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ji Dong |
| E-mail(s) |
dongji5211314@126.com
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| Organization name |
Peking University
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| Street address |
Yiheyuan 5#
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (32)
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| Relations |
| BioProject |
PRJNA343327 |
| SRA |
SRP090067 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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