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| Status |
Public on Apr 26, 2018 |
| Title |
Systematic mapping of cell state trajectories, cell lineage, and perturbations in the zebrafish embryo using single cell transcriptomics |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
High-throughput mapping of cellular differentiation hierarchies from single-cell data promises to empower systematic interrogations of vertebrate development and disease. Here, we applied single-cell RNA sequencing to >92,000 cells from zebrafish embryos during the first day of development. Using a graph-based approach, we mapped a cell state landscape that describes axis patterning, germ layer formation, and organogenesis. We tested how clonally related cells traverse this landscape by developing a transposon-based barcoding approach (“TracerSeq”) for reconstructing single-cell lineage histories. Clonally related cells were often restricted by the state landscape, including a case in which two independent lineages converge on similar fates. Cell fates remained restricted to this landscape in chordin-deficient embryos. We provide web-based resources for further analysis of the single-cell data.
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| Overall design |
Single-cell mRNA sequencing of zebrafish embryonic cells. Samples1-7: Single cell libraries from untreated embryos (4-24 hours post-fertilization). Samples8-12: Single cell libraries from embryos injected with TracerSeq lineage cassette at the 1-cell stage. Samples13-18: Single cell libraries from embryos injected with sgRNA + Cas9 at the 1-cell stage.
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| Contributor(s) |
Wagner DE, Weinreb C, Collins ZM, Megason SG, Klein AM |
| Citation(s) |
29700229 |
| Submission date |
Mar 23, 2018 |
| Last update date |
May 04, 2020 |
| Contact name |
Daniel E Wagner |
| E-mail(s) |
wagnerde@gmail.com
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| Phone |
8023099497
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| Organization name |
Harvard Medical School
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| Department |
Systems Biology
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| Street address |
200 Longwood Ave, Harvard Medical School, Systems Biology, Warren Alpert 536
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL20828 |
Illumina NextSeq 500 (Danio rerio) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA445487 |
| SRA |
SRP136369 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112294_ClusterNames.csv.gz |
1.7 Kb |
(ftp)(http) |
CSV |
| GSE112294_LibraryName_SRR_readme.txt |
2.1 Kb |
(ftp)(http) |
TXT |
| GSE112294_RAW.tar |
1.6 Gb |
(http)(custom) |
TAR (of CSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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