Project description:We identified genome-wide sites of occupancy for the intestine-specific transcription factor ELT-2 in L3-staged N2 worm by performing ELT-2 ChIP-seq on whole worms; we performed RNA-seq on L3-staged N2 whole worms
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
Project description:ChIP-seq and input sequence data used in the development and evaluation of the BEADS normalization method. Examination of ChIP and input sequence reads across the worm genome
Project description:The goal of RNA-seq is to identify the differential expressed genes in the wild-type worm and nmad-1 mutant worm at 20°C and 25°C respectively. 100 pairs of germlines were extracted and collected from worm tips. Two biological replicates were assigned for each group and the RNA profiles were generated by deep sequencing, using NEXTseq 500 Illumina. We mapped about 20 - 30 million reads per sample to C. elegans genome (build ce10) with bowtie2 workflow. Differential expression genes were identified through EBSeq in RSEM pipeline with 0.05 p value and 1.2 fold change. Our results showed elevated number of misregulated genes in the nmad-1 mutant groups at 25°C.
Project description:We have developed a single-worm RNA-seq method to effectively profile gene expression in individual C. elegans and applied this method to study C. elegans responses to pathogen infection.
Project description:Spirobranchus kraussii (Annelida: Serpulidae) was recognized as being widely distributed both in the Pacific and Atlantic Oceans. However, the sampling records far from its type locality (South Africa) have been questioned. Actually, recent molecular phylogenetic studies showed that S. kraussii contains genetically distinct species. In this study, we performed molecular phylogenetic analyses of S. cf. kraussii collected from Japan using the nucleotide sequences of a mitochondrial gene and two nuclear genes. Three lineages were recovered within Spirobranchus kraussii-complex in Japan, and one (Spirobranchus sp. 6) showed moderate genetic difference (approximately 4%) in the mitochondrial cytb gene sequence from Spirobranchus sp. 1, an undescribed sequenced species from Honshu Island, Japan. However, the nucleotide sequences of the 18S rRNA gene and ITS2 region were nearly indistinguishable. The other lineage was clearly distinct from the other previously sequenced species and is thus considered to be another distinct species of this species complex (Spirobranchus sp. 5). Although detailed morphological assessment of these lineages is necessary to define their taxonomic status, the present study provided further implications for the species diversity within the S. kraussii-complex.