Unknown,Transcriptomics,Genomics,Proteomics

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Single-cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish

ABSTRACT: TgBAC(gata5:EGFP) transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6, 8, 10, 13 hours post fertilization (hpf) and morpholinos injected Gata5/6 know-down (KD) embryos at 13 hpf were pre-screened for GFP signal and dissociated into single-cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting (FACS). Single-cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform (Rapid Run Model). Note that the 10h single-cell library was sequenced twice (Named as cDNA10h_1* and cDNA10h_2* separately).

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Danio rerio

SUBMITTER: Michael Wilson

PROVIDER: E-MTAB-9193 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Congenital malformations are a prevalent cause of infant mortality in the United States and their induction has been linked to a variety of factors, including exposure to teratogens. However, the molecular mechanisms of teratogenicity are not fully understood. MicroRNAs are an important group of small, non-coding RNAs that regulate mRNA expression. MicroRNA roles in early embryonic development are well established, and their disruption during development can cause abnormalities. We hypothesized that developmental exposure to teratogens such as valproic acid alters microRNA expression profiles in developing embryos. Valproic acid is an anticonvulsant and mood-stabilizing drug used to treat epilepsy, bipolar disorder and migraines. To examine the effects of valproic acid on microRNA expression during development, we used zebrafish embryos as a model vertebrate developmental system. Zebrafish embryos were continuously exposed to valproic acid (1 mM) or vehicle control (ethanol) starting from 4 hours post-fertilization (hpf) and sampled at 48 and 96 hpf to determine the miRNA expression profiles prior to and after the onset of developmental defects. At 96 hpf, 95% of the larvae showed skeletal deformities, abnormal swimming behavior, and pericardial effusion. Microarray expression profiling was done using Agilent zebrafish miRNA microarrays. Microarray results revealed changes in miRNA expression at both the time points. Thirteen miRNAs were differentially expressed at 48 hpf and 22 miRNAs were altered at 96 hpf. Among them, six miRNAs (miR-16a, 18c, 122, 132, 457b, and 724) were common to both time points. Bioinformatic target prediction and examination of published literature revealed that these miRNAs target several genes involved in the normal functioning of the central nervous system. These results suggest that the teratogenic effects of valproic acid could involve altered miRNA expression. Small RNA profiles were deteremined in valproic acid exposed zebrafish embryos using Agilent miRNA microarrays

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Single-cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish

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