High Content Genomics and Bioinformatics

The facility has several  computer workstations dedicated to data analysis and makes use of the high performance computing facility hosted at the IGTP data processing center. Besides our in house laboratory infrastructure  to carry on sample quality control and preparation for high content genomic analysis assays the unit is coordinated with centralized genomics core facilities such as the CRG-CNAG.

Automated Illumina Infinium assay platform

HiScan Illumina Infinium assay platform

Used for array based genomewide SNP genotyping, copy number and LOH analysis, and DNA methylation profiling.

HiScan (Illumina) array scanner is a confocal scanner with 0.375 micron spatial resolution  and two lasers at  532 and 660 nm wavelengths. Allows imaging and data extraction for Infinium beadarray assays to measure  fluorescent signal from probes profiling up to 5.000.000  genomic positions per sample simultaneously.

Evo-150  (Tecan) liquid handling robot is equiped with 8 fixed tips and set up for automated sample processing for Illumina infinium assays. Allows parallel handling of up to 384 samples.

Robotic liquid handling

Sciclone NGS (PerkinElmer) liquid handling robot

Robot with 96 disposable tip head and plate gripper. Protocols for automated  execution of molecular biology applications, especially for next generation sequencing (NGS). Allows parallel handling of up to 96 samples  simultaneously. Used for NGS library preparation and quantification and 384 microwell plate qPCR setup.

Nucleic acid quantification and shearing

Qubit (Thermofisher)

Single tube fluorometer. Used for precise nucleic acid quantification from 1-20 µl of sample. Discriminates single from double stranded DNA, and from RNA.

S2 (Covaris) ultrasonicator

Ultrasound mechanical  processor based on adaptive focused acoustics. Used for genomic DNA and chromatin fragmentation, nucleic acid extraction from paraffin fixed tissue. Processes one sample at a time.

Bioinformatic data analysis computing

HP xw8600, xw4600, Z600, Z440 (Hewlet Packard) workstations

High performance computing workstations  with Linux operating system. Used for local computation or remote access to centralized nodes and storage systems hosted at the IGTP scientific computing data processing center (HPC) for bioinformatic analysis of genomic data generated by arrays and NGS.

Dell Precision T7500 (Dell) - Ion PGM Server

High performance  computing server with Linux operating system and Ion Torrent Suite software for run control and analysis of Ion Torrent next generation sequencing data

Automated nucleic acid analysis and size selection

Bioanalyzer 2100 (Agilent)

Automated lab-on-a-chip microfluidic chip nano-electrophoresis system. Used for analysis of DNA and RNA integrity and size assessment, and smallRNA qualitative profiling. Allows procesing of up to 11-12 samples per run.

Pippin Prep (SAGE)

Automated gel electrophoresis and elution system. Used for  size selection of DNA libraries in next generation sequencing applications libraries. Allows simultaneous separation of up to 4 library pools per run and predefined size fraction elution using independent settings per pool.

Next generation sequencing

Ion Torrent PGM (Personal Genome Machine, ThermoFisher) next generation sequencer

Massively parallel sequencing instrument based on proton detection sensors miniaturized fluidics laid on microchips. It can generate up to 5.000.000 sequencing reads up to 400 nt long per run from as many as 384 pooled samples simultaneously. Used for RNA and DNA sequencing applications on Ion chips 314, 316 and 318.

Prior to the run, clonal amplification of sequencing libraries by emulsion PCR is perfomed on Ion Torrent One Touch2 (ThermoFisher) automated emulsion PCR system followed by enrichment of template positive microspheres using Ion Torrent ES (Enrichment System, ThermoFisher) liquid handling instrument.