Project description:We designed a new specific mRNA microarray targeting a subset of genes (748) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways and how they possibly differed between the closely related strains based on environment and host association. To better understand how the different environments might affect gene expressions, the samples were taken in depth profiles, at night and day, during a cruise in the South China Sea.
Project description:Recent advances in RNA sequencing (RNA-Seq) have enabled the discovery of novel transcriptomic variations that are not possible with traditional microarray-based methods. Tissue and cell specific transcriptome changes during pathophysiological stress, in disease cases versus controls and in response to therapies are of particular interest to investigators studying cardiometabolic diseases. Thus, knowledge on the relationships between sequencing depth and detection of transcriptomic variation is needed for designing RNA-Seq experiments and for interpreting results of analyses. Using deeply sequenced RNA-Seq data derived from adipose of a healthy individual before and after systemic administration of endotoxin (LPS), we investigated the sequencing depths needed for studies of gene expression and alternative splicing (AS). We found that to detect expressed genes and AS events, ~100 million (M) filtered reads were needed. However, the requirement on sequencing depth for the detection of LPS modulated differential expression (DE) and differential alternative splicing (DAS) was much higher. To detect 80% of events, ~300M filtered reads were needed for DE analysis whereas at least 400M filtered reads were necessary for detecting DAS. Although the majority of expressed genes and AS events can be detected with modest sequencing depths (~100M filtered reads), the estimated gene expression levels and exon/intron inclusion levels were less accurate. We report the first study that evaluates the relationship between RNA-Seq depth and the ability to detect DE and DAS in human adipose. Our results suggest that a much higher sequencing depth is needed to reliably identify DAS events than for DE genes. Random sampling the RNA-seq data in different depth for gene and alternative-splicing analysis
Project description:We have developed an endovascular catheter-based device for sampling of the endothelium, intended for RNA-seq analysis. With an outer diameter of 0.23 mm it is capable of reaching peripheral vessels for endothelial sampling, and favourably compares to other approaches with stent retrievers or similar tools. Here, we have collected samples from liver and kidney vessels from swine and performed RNA-sequencing to validate the sample quality.
Project description:Copy number profiling of 1000 Genomes Phase 3 inidividuals using the Agilent 1M aCGH arrays Two color experiment. NA10851 used as reference against 2534 other individuals from the phase 3 of the 1000 Genomes project
Project description:The risk of large, devastating tsunamis in the South China Sea and its surrounding coastal region is commonly underestimated or unrecognized due to the difficulty of differentiating tsunami from storm deposits. As a consequence, few convincing records have documented tsunami deposits in this region. Here we report preliminary evidence from Xisha Islands in the South China Sea for a large tsunami around AD 1024. Sand layers in lake sediment cores and their geochemical characteristics indicate a sudden deposition event around AD 1024, temporally consistent with a written record of a disastrous event characterized by high waves in AD 1076. Heavy coral and shell fossils, which are older than AD 1024, deposited more than 200 meters into the island, further support the occurrence of a high-energy event such as a tsunami or an unusually large storm. Our results underscore the importance of acknowledging and understanding the tsunami hazard in this area.