Project description:We identified a GATA-like gene named fuchi nashi (fuchi) as a gene required for establishing a germ disc in the early embryo of the spider Parasteatoda tepidariorum. fuchi transcript is initially expressed in cells at both polar regions of the embryo and later in endodermal and extraembryonic cells. To genome-widely identify genes whose expressions are regulated by fuchi, we conducted RNA-sequencing of whole embryos at three different early stages (stages 2 and 3 and early stage 5) that were untreated (control) or treated for fuchi parental RNA interference (pRNAi).
Project description:We identified a lineage-specific GATA-like gene named fuchi nashi (fuchi) as a gene required for establishing a germ disc in the early embryo of the common house spider Parasteatoda tepidariorum. To investigate possible involvement of the early fuchi activity in regulation of chromatin accessibility, we used an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Whole embryos at stage 3 that were untreated (wild-type) or treated for fuchi or hedgehog (hh) parental RNAi (pRNAi), as well as wild-type whole embryos at stages 1 and 2, were analyzed by ATAC-seq. We found that chromatin accesibilities were specifically altered by fuchi pRNAi at many regions of the genome, whereas chromatin accessibilities were little affected by Pt-hh pRNAi, which served as negative control.
2022-06-10 | GSE193870 | GEO
Project description:Bacterial microbiome in S. nashi and adjacent plant environments
Project description:This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. In other experiments, we have shown that Mago is required for correct splicing of the MAP kinase gene and its depletion causes a large reduction in MAP kinase mRNA levels. MAP kinase is a large gene in heterochromatin. In this study, we find that heterochromatic genes are disproportionately down-regulated in Mago-depleted cells, and those with large introns are particularly likely to be affected. SRA accession number: SRP003001.1
Project description:This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. In other experiments, we have shown that Mago is required for correct splicing of the MAP kinase gene and its depletion causes a large reduction in MAP kinase mRNA levels. MAP kinase is a large gene in heterochromatin. In this study, we find that heterochromatic genes are disproportionately down-regulated in Mago-depleted cells, and those with large introns are particularly likely to be affected. SRA accession number: SRP003001.1 Sequencing of poly(A)+ RNA from S2R+ cells treated with either lacZ (control) or mago (experimental) dsRNA
Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized