Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:Hence, in order to investigate the gene expression profiles of skeletal muscle, we analyzed the four stages (1 day, 14 days, 28 days, and 2 years old) of breast muscle in White-King pigeon using transcriptome sequencing.
Project description:microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. Here, six small RNA (sRNA) and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, the spatiotemporal variation in the Vv-miRNAs’ regulation on their target genes was systematically analyzed. Totally, 242 known and 132 novel Vv-miRNAs were identified, and 193 target mRNAs including 103 for known and 90 for novel miRNAs were validated in one or more of tissues examined. The interesting finding was that over 50% of novel miRNAs were expressed exclusively in flowers or berries where they had tissue-specific cleavage roles on their target genes, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries were found to response to exogenous gibberellin (GA) and/or ethylene by real time RT-PCR (qRT-PCR) analysis, confirming their regulatory functions during berry development. Other finding was that about 93.6% of the known miRNAs possessed the high conservation in various tissues where their expression levels exhibited some dynamic variations during grapevine development. Significantly, it was found the phenomena that some Vv-miRNA families exist one key member that act as the main regulator of their target genes during grapevine development.
Project description:In the present study, we were interested in gene expression changes in the pectoralis muscle of juvenile king penguins during the transition from terrestrial to marine life. Strictly terrestrial during their first year after hatching, king penguin chicks must then depart to sea to reach nutritional emancipation and pectoralis muscle is largely involved in penguin adaptation to the marine environment. To compare these transcriptomic profiles, we realized heterologous hybridization on Affymetrix GeneChip Chicken Genome Arrays, as the chicken is the closest model species for which microarrays are available. The development of a new algorithm, MaxRS, allow us to determine differentially expressed genes implicated in energetic metabolism or involved in cellular defense against reactive oxygen species and associated injuries.
Project description:Enterotoxigeneic Escherichia coli (ETEC) is a leading cause of diarrhoeal infections in young children living in endemic regions in low and middle-income countries and adults travelling to these destinations. CFA/I fimbriae have been identified as the predominant colonisation factor associated with human ETEC infections. Here we used used Transposon-directed insertion-site sequencing (TraDIS) and transcriptomic analysis to identify the essential genome of the prototypical CFA/I expressing ETEC strain H10407 and uncover the survival mechanisms that enhance persistence of ETEC isolates in water and within mammalian hosts. RNA transcription profiles of H10407 were identified under different in vitro growth conditions including aerobic growth in neutral LB media (pH7); aerobic growth in acidic media (pH5); aerobic growth in alkaline media (pH9); anaerobic growth in neutral LB media (pH7); and survival in fresh water. Research work including RNA preparation and bioinformatics and statistical analyses were conducted at the Wellcome Trust Sanger Institute (WTSI) and the Westmead Institute for Medical Research (WIMR), the University of Sydney. The sequencing data was generated in the Bioscience Core Laboratory at King Abdullah University of Science and Technology (KAUST).
Project description:Both exogenously supplied and transgenic induced cytokinin production can effectively delay senescence of broccoli florets during postharvest storage. However, a substantial comparison between the mechanisms of these two treatments on delaying broccoli florets senescence was absent. Here, we conduct microarray analysis on broccoli florets of N6-benzylaminopurine treated and ipt-transgenic broccoli that harbor a senescence-associated-gene promoter triggering isopentenyltransferase gene expression during postharvest storage. Analysis used RNA of Green King inbred line 104 as control sample for comparison to the experimental samples of ipt-transgenic line 102, 103 and parental line Green King as well as 10 ppm BA treated Green King at harvest and after postharvest storage at 25 centigrade in the dark for 4 days.
Project description:In the present study, we were interested in gene expression changes in the pectoralis muscle of juvenile king penguins during the transition from terrestrial to marine life. Strictly terrestrial during their first year after hatching, king penguin chicks must then depart to sea to reach nutritional emancipation and pectoralis muscle is largely involved in penguin adaptation to the marine environment. To compare these transcriptomic profiles, we realized heterologous hybridization on Affymetrix GeneChip Chicken Genome Arrays, as the chicken is the closest model species for which microarrays are available. The development of a new algorithm, MaxRS, allow us to determine differentially expressed genes implicated in energetic metabolism or involved in cellular defense against reactive oxygen species and associated injuries. Data from NI and SA penguin juveniles are already on GEO n°GSE17725