Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression effects of morpholino directed spRunt-1 knockdown on hatched blastula stage embryos

ABSTRACT: Runt domain (Runx) transcription factors constitute a metazoan family of sequence specific DNA binding proteins that are essential for animal development. The sea urchin Runx gene SpRunt-1, which is expressed globally during early embryogenesis, is required for blastula stage cell proliferation and subsequently for cell survival. To obtain a comprehensive list of SpRunt-1 regulatory targets we screened a custom microarray representing the blastula stage transcriptome of Strongylocentrotus purpuratus, comparing relative hybridization signals generated by labeled RNA from 18 hr control versus SpRunt-1 morphant embryos. For an 8x15k chip the 8 arrays were 4 biological replicates and a dye swap of the same 4. Biological Replicates - Four separate embryo cultures, each from a different mating pair were initiated and divided into a control group and a treatment group. All of the embryos in the treatment group were micoinjected with a splice-blocking morpholino antisense oligonucleotide (MASO) targeted to SpRunt-1. All control and sample embryos were developed to hatched blastula stage (18 hours post-fertilization) in filtered seawater at 15Â°C. Total RNA was extracted from each of the four separate samples (3,600 embryos in each sample) with an RNA yield near 5 micro grams per sample. Total RNA was also extracted from the untreated embryos of each separate culture pooled together (about 14,400) with an RNA yield near 20 micro grams. Technical (dye swap) Replicates - Control derived Cy3 (green) labeled aRNA was mixed with sample derived Cy5 (red) labeled aRNA in one biological replicate set of 4 samples and using half of the extracted RNA amount. The other half of the RNA was reciprocally labeled with control derived aRNA Cy5 labeled and sample derived aRNA Cy3 labeled.

ORGANISM(S): Strongylocentrotus purpuratus

SUBMITTER: Anthony Robertson

PROVIDER: E-GEOD-19751 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Dimorphic fungi have the ability to change morphology during their lifecycle, a crucial feature for the establishment of infection and fungal growth and development in planta. Life cycle of the dimorphic sugarcane smut fungi, Sporisorium scitamineum, involves recognition and mating of compatible saprophytic yeast-like haploid sporidia (MAT-1 and MAT-2) that upon fusion, develop into infective dikaryotic mycelia. Although the dimorphic transition is intrinsically linked with the pathogenicity and virulence of S. scitamineum, it has never been studied using a proteomics approach. In the present study, an iTRAQ-based comparative proteomic analysis of three distinct stages covering the dimorphic transition period - haploid sporidial stage (MAT-1 and MAT-2) to the transition phase (24 hours post co-culturing (hpc)) and dikaryotic mycelial stage (48 hpc) was carried out. Functional categorization showed that the most altered biological processes were energy production, primary metabolism especially carbohydrate, amino acid, fatty acid, followed by translation, post-translation and protein turnover. The identified proteins could be grouped into 8 distinct clusters with different trends in abundance. Enrichment analysis of the clusters showed that biological processes related to energy production through oxidative phosphorylation, citrate cycle, and β-oxidation, transcription, translation and redox homeostasis were specifically altered. In addition, an overall downregulation of carbohydrate metabolism and reprogrammed amino acid metabolism were observed. Several differentially abundant proteins (DAPs), especially in the dikaryotic mycelial stage were predicted as effectors. Taken together, key molecular mechanisms underpinning the dimorphic transition in S. scitamineum at the proteome level were highlighted. A catalogue of stage-specific and dimorphic transition-associated -proteins and potential effectors identified herein are potential candidates for defective mutant screening to elucidate their functional role in the dimorphic transition and pathogenicity in S. scitamineum.

Dataset Information

Gene expression effects of morpholino directed spRunt-1 knockdown on hatched blastula stage embryos

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets