Project description:The metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be up-regulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity. Branch tips from three adult colonies of Acropora millepora were sampled at midday and midnight
Project description:We induced specific deletion of miR-17-92 in Sertoli cells at the time of Amh expression in mouse embryos. We analyzed the effect of this deletion in the long term in adult testis. The transcriptome of mutant testis was consistently altered but do not produce a phenotype due to the testis homeostasis.
Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase. Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.
Project description:We compared the effect of acute (Moya et al 2012) and chronic exposure to elevated pCO2 on gene expression in primary polyps of Acropora millepora Examination of transcriptome in Acropora millepora primary polyps at 380 and 750 ppm CO2 (air) after 9 days exposure
Project description:We created a mutator protein, Evolugene with very fast in vivo mutation rate and gene specificity in E. coli. To comprehensively analyze the specificity and mutagenicity, we sequenced ~3.3 kb DNA around the target gene from cells taken at cycle 27 by Illumina sequencing.
Project description:This experiment analyses the expression data of the wild type P. syringae pv. tomato DC3000 grown in the absence and in the presence of phloretin and naringenin.
Project description:We created a mutator protein, eMutaT7[transition] with targeted in vivo hypermutation in E. coli. To investigate the gene-specific mutagenesis, we sequenced ~3.3 kb DNA around the target gene from cells taken at cycle 0 (n = 1) and cycle 20 (n = 3) by Illumina sequencing.
Project description:We used the Illumina RNAseq approach to study the effects of acute exposure to elevated CO2 on gene expression in primary polyps of Acropora millepora Examination of transcriptome in Acropora millepora primary polyps at 380, 750 and 1000 ppm CO2 after 3 days exposure
Project description:Agilent CpG microarray in combination with enriched methylated DNA by a MBD protein were carried out in each pool of genomic DNA from primary breast tumor and matched adjacent normal tissues. 1.Common reference vs enriched methylated DNA in tumor 2. Common reference vs enriched methylated DNA in adjacent normal 3. Then compare two data indirectly