Project description:We examined the role of HES1 in high salt response as a novel regulator of NFAT5. We analyzed gene expression of HeLa cells under isoosmotic and high salt condition.
Project description:Transcriptional profiling related cytokines and chemokines of mouse kidneys comparing the kidneys of WNK4 D561A/+ mice fed an 8% high-salt diet with those of WNK4+/+ littermates with a normal diet. Goal was to determine the effects of a high-salt condition on the immune system in kidney.
Project description:The goal of this study are to compare the transcriptome profiling (RNA-seq) of human cervical cells (HeLa) transcriptome profiling (RNA-seq) under the condition of inhibition of respiratory chain by antimycin A or hypoxia.
Project description:Study of gene expression under no salt condition from total leaf RNA and gene expression after five days of salt stress in 150mM NaCl from total leaf RNA of PcINO1 and OsINO1 introgressed IR-64 transgenic rice lines.
Project description:Soil salinity is a major production constrain for agricultural crops, especially in Oryza sativa (rice). Analyzing physiological effect and molecular mechanism under salt stress is key for developing stress-tolerant plants. Roots system has a major role in coping with the osmotic change impacted by salinity and few salt-stress-related transcriptome studies in rice have been previously reported. However, transcriptome data sets using rice roots grown in soil condition are more relevant for further applications, but have not yet been available. The present work analyzed rice root and shoot physiological characteristics in response to salt stress using 250 mM NaCl for different timepoints. Subsequently, we identified that 5 day treatment is critical timepoint for stress response in the specific experimental design. We then generated RNA-Seq-based transcriptome data set with rice roots treated with 250 mM NaCl for 5 days along with untreated controls in soil condition using rice japonica cultivar Chilbo. We identified 447 upregulated genes under salt stress with more than fourfold changes (p value < 0.05, FDR < 0.05) and used qRT-PCR for six genes to confirm their salt-dependent induction patterns. GO-enrichment analysis indicated that carbohydrate and amino-acid metabolic process are significantly affected by the salt stress. MapMan overview analysis indicated that secondary metabolite-related genes are induced under salt stress. Metabolites profiling analysis confirmed that phenolics and flavonoids accumulate in root under salt stress. We further constructed a functional network consisting of regulatory genes based on predicted protein–protein interactions, suggesting useful regulatory molecular network for future applications.
Project description:Purpose: Genome-wide expression analysis for introgression line 9L136 and indica variety 93-11 under salt reatment and control to identify specifically differentially expressed in 9L136 under salt stress. Methods: Roots of two-half leaf seedlings of 9L136 and 93-11 were sequenced using an Illumina HiSeq2500 Sequencer; high-quality paired-end reads were mapped to the Nipponbare reference genome (MSU Rice Genome Annotation Project Release 7) using the spliced read mapper TopHat version 2.0.12, and Significant differentially expressed genes (DEGs) were determined based on a threshold of 2-fold expression change and false discovery rate (FDR) < 0.05 using Cuffdiff, one module of Cufflinks. qRT-PCR analysis were performed using SYBR Green Master Mix on CFX96 Real Time System. Results: 1388 genes which specifically differentilly expressed in 9L136 under salt stress were identified, and expression profile of 18 genes randomely selected was confirmed by qRT-PCR.
Project description:Nucleosomes that contain the histone variant H2A.Z are enriched around transcriptional start sites in many organisms. A single octameric nucleosome can contain two H2A.Z histones (homotypic) or one H2A.Z and one canonical H2A (heterotype). We generated high-resolution maps of homotypic and heterotypic Drosophila H2A.Z (H2Av) nucleosomes. Although homotypic and heterotypic H2Av nucleosomes map throughout most of the genome, homotypic nucleosomes are enriched and heterotypic nucleosomes are depleted downstream of active promoters and intron/exon boundaries. The distribution of homotypic H2A.Z nucleosomes resembles that of salt-soluble nucleosomes and shows evidence of displacement during transcriptional elongation. Homotypic nucleosomes are also depleted downstream of paused polymerases, where salt-soluble nucleosomes are conspicuously depleted. Our results suggest a model whereby H2A.Z enrichment patterns result from different structural interactions within the core of heterotypic and homotypic nucleosomes following disruption during transcriptional elongation. We analyzed two replicates for input, heterotypic and homotypic purifications. We sequenced one library for each of the single H2Av pulldown and 80mM salt soluble samples.
