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| Status |
Public on Sep 24, 2021 |
| Title |
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo |
| Organism |
Lytechinus variegatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 hours of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to "stitch" together developmental timepoints. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by sixth cleavage, though a small percentage of ectoderm cells briefly co-expressed endoderm markers indicating an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells originated at 6th cleavage also and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. 79 of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate.
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| Overall design |
19 scRNA-seq samples, with 1 replicate capturing 18 time points over 24 hours of sea urchin development
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| Contributor(s) |
Massri AJ, Greenstreet L, Afanassiev A, Berrio A, Wray GA, Schiebinger G, McClay DR |
| Citation(s) |
34463740 |
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| Submission date |
Sep 21, 2021 |
| Last update date |
Dec 31, 2021 |
| Contact name |
David R McClay |
| Organization name |
Duke University
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| Department |
Biology
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| Street address |
124 Science Drive room 4115
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| City |
Durham |
| ZIP/Postal code |
27707 |
| Country |
USA |
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| Platforms (1) |
| GPL30656 |
Illumina NovaSeq 6000 (Lytechinus variegatus) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA765003 |
| SRA |
SRP338083 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE184538_RAW.tar |
183.3 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE184538_lv_aggregate.cloupe.gz |
186.3 Mb |
(ftp)(http) |
CLOUPE |
| GSE184538_lv_umap.rds.gz |
1.8 Gb |
(ftp)(http) |
RDS |
| GSE184538_lv_umap_markers.csv.gz |
792.2 Kb |
(ftp)(http) |
CSV |
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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