Project description:Metabolomics data collected for high biomass fecal and saliva samples on quadrupole-Orbitrap mass spectrometer to validate a standardized method for sample accession, DNA and metabolite extraction using single tubes (Matrix tubes).
Project description:Western blotting (WB) is widely used to test antibody specificity, but the assay has low throughput and precision. Here we show that an inverted version of WB allows parallel readout with antibody arrays, shotgun mass spectrometry (MS) and immunoprecipitation followed by MS (IP-MS). The pipeline provides means for large-scale implementation of concepts proposed by an international working group on antibody validation (IWGAV).
Project description:Metabolomics data collected for high biomass fecal and saliva samples on quadrupole-Orbitrap mass spectrometer to validate a standardized method for sample accession, DNA and metabolite extraction using single tubes (Matrix tubes).
Project description:HiCUP is a pipeline for processing sequence data generated by Hi-C, a technique used to investigate the three-dimensional organisation of a genome. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also provides an easy-to-interpret yet detailed quality control report that may be used by researchers to refine their experimental protocol for future studies. The software is freely available and has already been used for processing Hi-C data in several recently published peer-reviewed research articles. This experiment investigates the impact of using HiCUP to remove putative PCR amplification products in heavily duplicated Capture Hi-C libraries. Examination of three Capture Hi-C libraries
Project description:HiCUP is a pipeline for processing sequence data generated by Hi-C, a technique used to investigate the three-dimensional organisation of a genome. The pipeline maps data to a specified reference genome and removes artefacts that would otherwise hinder subsequent analysis. HiCUP also provides an easy-to-interpret yet detailed quality control report that may be used by researchers to refine their experimental protocol for future studies. The software is freely available and has already been used for processing Hi-C data in several recently published peer-reviewed research articles. This experiment investigates the impact of using HiCUP to remove putative PCR amplification products in heavily duplicated Capture Hi-C libraries.
Project description:We report a novel modular pipeline (iMir) for comprehensive analysis of miRNA-Seq data, from linker removal and sequence quality check to differential expression and biological target prediction, integrating multiple open source modules and resources linker together in an automated flow. Development of an integrated pipeline (iMir) for comprehensive analysis of miRNA-Seq experiment.