Project description:We report the application of Whole Genome Bisulfite Sequencing to identify differentially methylated regions (DMR) in two RNAi transgenic lines, with dowregulated expression of the demeter-like gene PtaDML10, in comparisson to wild-type plants of Populus tremula x Populus alba plants.
Project description:Purpose: we performed comparative RNA-seq analyses to identify differentially expressed genes between KD transgenic lines and Wild Type
Project description:Cotton (Gossypium hirsutum) is the major contributor of feedstock for the fabric industry and thus building genomic resources in cotton such as this study are a way to understand the cotton plant's biology. Cotton cultivars that suppress PHYA1D (PhyA1 homeolog on the D genome of a tetraploid) exhibit early-flowering, increased fiber length and increased seed yield. In our proposed study, flower buds (also called squares) samples were collected from control (Croker 312 wildtype line) and RNAi lines carrying the PhyA1D suppression. RNA samples from the two lines including three biological replicates were subjected to RNA-seq sequencing to elucidate the transcriptome profile.
Project description:Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage. Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. RNA-seq reads obtained from the replicate were further filtered and aligned against the whole tomato genome. Differential expressed genes between samples were defined by DESeq software using two separate models, based on PPEE > 0.05 and false discovery rate (FDR)<0.001. Quantitative RT–PCR was performed using SYBR Green assays. Results: A total of 1728 differentially expressed genes were identified in the SlDof1 RNAi fruit compared with the wild type and among them were a number of ripening-relate genes.
Project description:Protein interactions of the tau protein are of interest in efforts to decipher the mechanisms of cell death in Alzheimer Disease (AD), a subset of frontotemporal dementias (FTD) and other tauopathies. We recently reported on extensive interactions of tau with the ribonucleoproteome and chaperones. A confounder of this prior work was that it probed steady-state interactions of plasmid-encoded four-repeat (4R) tau in dividing cells. Since then, we genome-edited a genomic safe harbor locus in two human neuronal cell lines, namely IMR-32 and ReNcell VM, creating inducible EGFP tagged wild-type and P301L tau models. We expressed balanced levels of 3R- and 4R-tau and interrogated tau protein interactions at specific times following its induction. In addition to its association with the ribonucleoproteome, tau was observed to interact in these models with proteins that escaped prior investigations.
Project description:The soybean msh1 RNAi transgenic line show various growth phenotype. We use microarray analysis to characterize gene expression pattern for two of the phenotypes - variegation and stunted growth.