The laboratory has all the necessary equipment to perform high throughput DNA sequencing on Illumina Genome Analyzer platform and microarray experiments, using both in-house prepared microarrays and Agilent and Affymetrix chips.
High throughput sequencing experiments are carried out using two Illumina Genome Analyzer IIx sequencers and a Cluster Generation station, which performs library amplification and flowcell preparation. Sample quality assessment and library validation are performed using Agilent 2100 Bioanalyzer, LightCycler 480 qPCR system (Roche), Qubit fluorometer (Invitrogen) and Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
Some of the equipment involved in microarray work includes Affymetrix GeneChip system (GeneChip Scanner 30007G, GeneChip Hybridization Oven 640, and GeneChip Fluidics Station 400), Agilent G2565 Microarray Scanner, 4200A GenePix scanner (Axon Instruments), multiple hybridization ovens, etc. The laboratory is capable of manufacturing custom microarrays using MicroGrid II arrayer (BioRobotics) that have been used for projects ranging from gene expression analysis in Arabidopsis, to studies of glycosaminoglycan-protein interactions and of the dynamics of DNA hybridization in real time.
The Laboratory has developed an extensive computational infrastructure that allows us to carry out image analysis and sequence data extraction using the Illumina Sequence Analysis Pipeline. We are also capable to perform some computation-intensive secondary analyses such as identification of binding sites for DNA-interacting proteins (ChIP-Seq), genome assembly, transcriptome analysis (RNA-Seq), etc. A local copy of UCSC Genome Browser allows us to visualize high throughput sequencing data within the context of genomic annotations in a flexible way. Resolver software suite (Rosetta Biosoftware) is available to our users for the analysis of microarray-based gene expression data. Additional microarray and HTS software tools and analysis packages, both public and commercial, are also available.