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:To elucidate miRNA-mediated temporal crosstalk during productive infection, we identified genome-wide miRNA target sites using Argonaute-crosslinking and immunoprecipitation followed by high-throughput sequencing (AGO-CLIPseq) in human cytomegalovirus (HCMV)-infected cells and evaluated the targeting efficacy by applying our new AGO-CLIPseq enrichment (ACE)-scoring algorithm.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:Using Next-generation sequencing of total RNA isolated from human cytomegalovirus virions we have analyzed host (human) snoRNA molecules.
Project description:Using Next-generation sequencing of total RNA isolated from human cytomegalovirus virions we have identified host (human) tRNA molecules.
Project description:The proteome of the SS13 isolate assigned to the Chromatiaceae family was assessed by shotgun proteomics using a pan-proteomics database for the genus Rheinheimera and a whole genome sequencing -derived database.
Project description:Purpose: To identify interactions of the viral DNA-binding protein, UL34, with the viral genome during lytic-phase replication. Methods: Human fibroblasts were infected with human cytomegalovirus expressing Myc-tagged UL34 in biological duplicate. At 48 hours post infection, ChIP was performed with anti-Myc tag antibody (Cell Signaling) and the resulting DNA fragments were sequenced on Illumina MiSeq. Reads were trimmed and duplicates removed. Reads passing quality filter were aligned to a custom reference genome containing both the human genome with the human cytomegalovirus genome as an additional chromosome to prevent read assignment bias with CLC Genomics Workbench verison 9.0. Enrichment of UL34 in the viral origin of lytic replication (oriLyt) was calculated by dividing read counts from the ChIP'd samples (Myc-UL34-1, Myc-UL34-2) by those from non-ChIP whole cell lysate (Input) with a 125bp sliding window (25bp overhang) after adjusting for total read count variances. An additional sample containing DNA that was subjected to the ChIP protocol in the absence of antibody (No Antibody) was compared to the Input to determine background enrichment. Results: Several peaks were identified when comparing the Myc-UL34-ChIP samples to Input. UL34 is bound to the viral oriLyt at 48 hours post infection near the three previously defined UL34-binding sites to varying degrees, as well as additional locations within the region. No peaks were identified when comparing the No Antibody and Input samples.
