Project description:The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR. Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype.
Project description:The goal of this study is to compare the transcriptome stability of DN1wt versus DN1gl/gl and DN1CD2-Ostm1gl/glTR Methods: DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were generated by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: TopHat and Cufflinks. qRTâ??PCR validation was performed using SYBR Green assays Results: DN1 gl/gl showed a distinctive transcriptome signature in comparison to DN1 wt and DN1 gl/glTR with respectivelly 146 and 205 differentially expressed genes and 205. Migration genes were significantly affected in DN1 gl/gl samples and RAC1 and S1PR1 gene expressions were confirmed using RT-qPCR. Conclusions: RNA seq allowed us to identify the enhanced expression of migration genes (RAC1 and S1PR1) in DN1gl/gl, that were both normalized in the DN1 cells from transgenic gl/glTR mice, which suggests defective T cell migration associated to the osteopetrotic thymus phenotype. DN1 thymocytes mRNA profiles of 19-day-old wild-type (WT), osteopetrotic grey-lethal (gl/gl) and transgenic CD2-Ostm1 gl/gl mice were compared by deep sequencing,DN1 cells from 2-3 mice per genotype were pooled, no technical replicates, using Illumina HiSeq 2000.
Project description:Priestia endophytica FH5, which was isolated from healthy tomato rhizosphere soil, had biological activity against a variety of plant diseases, including R. solani. We isolated the chemicals generated by strain FH5 to better understand the interaction between strain FH5 and R. solani. A transcriptome study of strain FH5 with and without R. solani exposure was also performed. In response to the fungal pathogen R. solani, strain FH5 changed genes linked to amino acid transport, carbohydrate transport, energy generation and conversion, and inorganic ion transport and metabolism, according to our findings.
