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Series GSE106587 Query DataSets for GSE106587
Status Public on Apr 27, 2018
Title Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
Organism Danio rerio
Experiment type Expression profiling by high throughput sequencing
Summary During embryogenesis, cells acquire distinct fates by transitioning through transcriptional states. To uncover these transcriptional trajectories during zebrafish embryogenesis, we sequenced 38,731 cells and developed URD, a simulated diffusion-based computational reconstruction method. URD identified the trajectories of 25 cell types through early somitogenesis, gene expression along them, and their spatial origin in the blastula. Analysis of Nodal signaling mutants revealed that their transcriptomes were canalized into a subset of wild-type transcriptional trajectories. Some wild-type developmental branchpoints contained cells expressing genes characteristic of multiple fates. These cells appeared to trans-specify from one fate to another. These findings reconstruct the transcriptional trajectories of a vertebrate embryo, highlight the concurrent canalization and plasticity of embryonic specification, and provide a framework to reconstruct complex developmental trees from single-cell transcriptomes.
This SuperSeries is composed of the SubSeries listed below.
 
Overall design Drop-seq analysis of wild-type embryos (38,731 cells, 12 timepoints, 28 samples total, 20-40 embryos per sample), SMART-seq2 analysis of wild-type and MZoep mutant embryos (52 wild-type and 364 MZoep cells from 50% epiboly stage), and 10X single-cell sequencing analysis of WT and MZoep mutant embryos (3,000 WT and 2,200 MZoep cells from 6-somites stage).
 
Citation(s) 29700225
Submission date Nov 06, 2017
Last update date May 15, 2019
Contact name Jeffrey Allen Farrell
E-mail(s) jeffrey.farrell@nih.gov
Organization name National Institute of Child Health and Human Development
Department Division of Developmental Biology
Lab Farrell Lab
Street address 6 Center Drive (6A/1A06)
City Bethesda
State/province MD
ZIP/Postal code 20814
Country USA
 
Platforms (2)
GPL18413 Illumina HiSeq 2500 (Danio rerio)
GPL20828 Illumina NextSeq 500 (Danio rerio)
Samples (446)
GSM2838045 oep_p0_S10
GSM2838046 oep_p0_S11
GSM2838047 oep_p0_S12
This SuperSeries is composed of the following SubSeries:
GSE106466 Single-cell RNAseq (SMART-seq2) of wild-type (TLAB) and MZoep (tz57) zebrafish embryos at 50% epiboly stage
GSE106474 Drop-seq analysis of wild-type (TLAB) zebrafish embryos from high to 6-somite stage (12 timepoints)
GSE112824 10x analysis of wild-type (TLAB) and MZoep zebrafish embryos at 6-somite stage
Relations
BioProject PRJNA417291

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Supplementary file Size Download File type/resource
GSE106587_RAW.tar 34.4 Mb (http)(custom) TAR (of MTX, TSV)
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