PUBLICATION

Transcriptomic profile of early zebrafish PGCs by single cell sequencing

Authors
Zhang, X., Li, X., Li, R., Zhang, Y., Li, Y., Li, S.
ID
ZDB-PUB-190815-6
Date
2019
Source
PLoS One   14: e0220364 (Journal)
Registered Authors
Keywords
none
Datasets
GEO:GSE122208
MeSH Terms
  • Animals
  • Embryo, Nonmammalian
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Germ Cells/metabolism*
  • Single-Cell Analysis
  • Transcriptome*
  • Zebrafish/genetics*
  • Zebrafish/metabolism
  • Zebrafish Proteins/genetics*
  • Zebrafish Proteins/metabolism
(all 11)
PubMed
31412047 Full text @ PLoS One
Abstract
Single cell RNA-seq is a powerful and sensitive way to capture the genome-wide gene expression. Here, single cell RNA-seq was utilized to study the transcriptomic profile of early zebrafish PGCs (primordial germ cells) at three different developmental stages. The three stages were 6, 11 and 24 hpf (hours post fertilization). For each developmental stage, three zebrafish PGCs from one embryo were collected, and 9 samples in total were used in this experiment. Single cell RNA-seq results showed that 5099-7376 genes were detected among the 9 samples, and the number of expressed genes decreased as development progressed. Based on the gene expression pattern, samples from 6 and 11 hpf clustered closely, while samples from 24 hpf were more dispersed. By WGCNA (weighted gene co-expression network analysis), the two biggest modules that had inverse gene expression patterns were found to be related to PGC formation or migration. Functional enrichment analysis for these two modules showed that PGCs mainly conducted migration and cell division in early development (6/11 hpf) and translation activity became active in late development (24 hpf). Differentially expressed gene analyses showed that more genes were downregulated than upregulated between two adjacent stages, and genes related to PGC formation or migration reported by previous studies decreased significantly from 11 to 24 hpf. Our results provide base knowledge about zebrafish PGC development at the single cell level and can be further studied by other researchers interested in biological development.
Genes / Markers
Marker Marker Type Name
actb2GENEactin, beta 2
atp5poGENEATP synthase peripheral stalk subunit OSCP
aurkaGENEaurora kinase A
cbx3aGENEchromobox homolog 3a (HP1 gamma homolog, Drosophila)
ccnb1GENEcyclin B1
cct4GENEchaperonin containing TCP1, subunit 4 (delta)
cdca8GENEcell division cycle associated 8
coq9GENEcoenzyme Q9 homolog (S. cerevisiae)
cxcr4bGENEchemokine (C-X-C motif), receptor 4b
ddx39aaGENEDEAD (Asp-Glu-Ala-Asp) box polypeptide 39Aa
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Figures
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Expression
Phenotype
No data available
Mutations / Transgenics
Allele Construct Type Affected Genomic Region
ihb14TgTransgenic Insertion
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    Human Disease / Model
    No data available
    Sequence Targeting Reagents
    No data available
    Fish
    Fish
    ihb14Tg (AB)
    1 - 1 of 1
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    Antibodies
    Name Type Antigen Genes Isotypes Host Organism
    Ab4-ddx4polyclonalIgGRabbit
    1 - 1 of 1
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    Orthology
    No data available
    Engineered Foreign Genes
    Marker Marker Type Name
    EGFPEFGEGFP
    1 - 1 of 1
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    Mapping
    No data available
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    Citation
    Zhang, X., Li, X., Li, R., Zhang, Y., Li, Y., Li, S. (2019) Transcriptomic profile of early zebrafish PGCs by single cell sequencing. PLoS One. 14:e0220364.