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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 09, 2015 |
| Title |
Decoding the regulatory network of early blood development from single-cell gene expression measurements. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Reconstruction of the molecular pathways controlling organ development has been hampered by a lack of methods to resolve embryonic progenitor cells. Here we describe a strategy to address this problem that combines gene expression profiling of large numbers of single cells with data analysis based on diffusion maps for dimensionality reduction and network synthesis from state transition graphs. Applying the approach to hematopoietic development in the mouse embryo, we map the progression of mesoderm toward blood using single-cell gene expression analysis of 3,934 cells with blood-forming potential captured at four time points between E7.0 and E8.5. Transitions between individual cellular states are then used as input to develop a single-cell network synthesis toolkit to generate a computationally executable transcriptional regulatory network model of blood development. Several model predictions concerning the roles of Sox and Hox factors are validated experimentally. Our results demonstrate that single-cell analysis of a developing organ coupled with computational approaches can reveal the transcriptional programs that underpin organogenesis.
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| Overall design |
Transcriptome analysis in populations of 50 cells from each of 5 mouse embryos at primitive streak, neural plate and head fold stages of development
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| Contributor(s) |
Moignard V, Woodhouse S, Haghverdi L, Lilly J, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E, Nishikawa S, Piterman N, Kouskoff V, Theis FJ, Fisher J, Göttgens B |
| Citation(s) |
25664528 |
| Submission date |
Sep 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Evangelia Diamanti |
| E-mail(s) |
ed347@cam.ac.uk
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| Phone |
01223 62317
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| Organization name |
University of Cambridge
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| Department |
Haematology
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| Lab |
Gottgens
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| Street address |
Wellcome Trust / MRC Building, Hills Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0XY |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA261245 |
| SRA |
SRP047176 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE61470_HTSEQ_counts.xls.gz |
1.1 Mb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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