Next-Generation Sequencing – Multimedia

Peripheral blood is widely used as starting material for biomarker discovery and validation using molecular biology technologies. The vast majority of currently published transcriptome data is based on RNA derived either from stabilized whole blood or peripheral blood mononuclear cells (PBMCs). Here, gene expression profiling studies and SOPs for fast, easy and specific manual or automated isolation of monocytes directly from whole blood are being described.

The goal: To get novel insights into the mechanisms of prostate adenocarcinoma by leveraging next generation sequencing (NGS) data, particularly human transcriptome data, through in silico data analysis and interpretation by Ingenuity’s IPA® software. CLC Genomics Workbench and CLC Genomics Server helped us assess short read RNA-Seq data.

Analysis of SIV next generation sequencing data for the estimation of escape rates in different animal groups and tissue compartments.

Standard mRNA amplifications for "All-Exon" microarrays and for bacterial RNAs are impossible with small samples and with degraded RNAs, because removal of rRNAs must precede universal, non-selective RNA amplification. This pre-treatment with magnetic beads is cumbersome, requires high amounts of starting material, is not universal for all species and degraded RNAs are not suitable.

In mid-2009 The Nickerson Lab in the Department of Genome Sciences at the University of Washington faced the daunting task of rapidly scaling up their next generation sequencing laboratory. Given the enormous amount of data to be generated, a critical part of this scale-up was picking the right LIMS solution. This system needed to handle data flow from sample submission to results reporting.

1. Combination of protoplast transient expression system and Nickel resin based purification is an useful approach for chromatin enrichment that can be used to identify transcription factor’s potential target genes. 2.Comparison our ChIP-on-chip target genes with in vivo binding targets using two whole genome tiling array platforms showing high degree of overlap between two methods.

We present evidence that miRNA precursors are present in the single-celled green alga Chlamydomonas reinhardtii and that they give rise to mature miRNAs that regulate target genes by post-transcriptional RNA cleavage.

We have developed a web-based database, "PRIMe (Platform for RIKEN Metabolomics)," which contains powerful tools for researchers to analyze gene co-expression data and mass spectral data. PRIMe has been developed with the main aim of facilitating integrated analysis for transcriptomics and metabolomics.

Combined with extensive bioinformatics analyses, our joint analysis of transcriptomics and metabolomics data has generated interesting findings which led to further laboratory verification, such as potential genes associated with alkaloid production.

MolPAGE (Molecular Phenotyping to Accelerate Genomic Epidemiology) is an EU consortium with almost twenty collaborating universities and companies throughout Europe. One of the aims of MolPAGE is to find early onset biomarkersfor type 2 diabetes (T2DM) and cardio-vascular diseases(CVD).