GENERAL GENOMICS SERVICE SEQUENCING AND GENOTYPING UNIT

Equipment

The Sequencing and Genotyping Unit of the University of the Basque Country UPV / EHU has technicians and advanced equipment in automated sequencing and genotyping of DNA markers. It has several platforms of SNP genotyping to suit a wide range of formats Number SNP vs. Number. samples (including the newest TaqMan OpenArray and Biomark HD System Fluidigm) allowing to suit the needs of large variability of projects (from a few samples and / or SNPs, to hundreds simultaneously).

The unit has a laboratory designed following the recommendations of good laboratory practice. Furthermore, the quality of Sequencing and Genotyping is confirmed by international companies of genetic analysis through participation in various annual exercises in quality control and standardization of results.

The users of Sequencing and Genotyping Unit of Genomics Facility are researchers in the network of Basque Science, Technology and Innovation, as well as biotechnology companies and public and private institutions throughout the state and Europe, involved in activities related in the genetic analysis applied to basic research, applied research and / or clinical diagnosis.

The high-performance equipment at the disposal of the Genomics laboratory enables variations in the genome to be identified on a large scale via the automated management of the reactions deemed necessary for these analytical processes. Below is provided a list of the most important equipment:

  • GeneAmp PCR System 9700 and Veriti thermocyclers (Applied Biosystems)
  • Two Starlet liquid dispensation robots made by Hamilton
  • DNA extraction robots (KingFisher Duo Prime System).
  • Spectrophotometer (Nanodrop 1000 and 8000) and Fluorometer (FLx800 and QuBit).
  • Pippin Prep (Sage Science) - DNA Size Selection for NGS.
  • LabChip GX Touch 24 Nucleic Acid Analyzer.
  • 3130xl sequencers (Applied Biosystems)
  • 7900HT Fast real-time PCR (Applied Biosystems) with Zymark coupled plate charger robot.
  • Real time PCR CFX96 (Bio-rad)
  • DNA microarray platform: 2100 Bioanalyzer, hybridization furnace and Agilent G2565BA Microarray Scanner, and Spot Blot2 Protein Edition robot for microarray printing made by ArrayIt.
  • Juno Platform and BioMark HD System from  Fluigdim (see the document)
  • NGS: MiSeq desktop sequencer (ILLUMINA) sequencer
  • NGS: NextSeq desktop sequencer (ILLUMINA) sequencer

The laboratories of the Sequencing and Genotyping Unit, which it shares with the Gene Expression Unit, are a recently-created laboratory that has been designed in accordance with the recommendations set out for laboratory good practices. They are distributed in plants 1 and 2 of the Animal Biotechnology Center (Maria Goyri building), located in the scientific park of the UPV/EHU (Leioa Campus).

All processes are treated independently in order to prevent any risk of cross contamination. The laboratory is arranged over four separate areas set aside for: DNA extraction, PrePCR processes, PostPCR processes, and the result-reading equipment and data-analysis room. The laboratory as a whole is equipped with transition cabins and a contamination prevention system by means of pressure gradient between areas.

SOME OF THIS EQUIPMENT HAS BEEN CO-FUNDED BY THE BASQUE GOVERNMENT OR BY THE EUROPEAN UNION VIA THE EUROPEAN REGIONAL DEVELOPMENT FUND

HIGH-PRECISION QUANTIFICATION


Nanodrop ND-100


FLX800 (Plate reader fluorimeter)

RNA QUALITY ANALYSIS AND MIGRATION STANDARD FOR AMPLIFIED DNA FRAGMENTS AND DIGESTION

          
Agilent 2100z bioanalyzer

STARLET DISPENSATION ROBOTS MADE BY HAMILTON

3 units (1 nucleic acid extraction, 1PrePCR, 1 PostPCR)

          

THERMOCYCLERS

  • GeneAMP 9700 APPLIED BIOSYSTEMS: 2 dual-head units and 1 single-head unit of 96.

          

  • 2 VERITI APPLIED BIOSYSTEMS units: flexibility of PCR Standard or Fast mode programmes and head with 6 independent temperature-programming blocks.

          

  • 3 units of ABIPRISM AUTOMATIC SEQUENCERS: 310, 3100avant and 3130xl

7900HT FAST REAL-TIME PCR WITH ZYMARK ROBOT

7900HT FAST REAL-TIME PCR WITH ZYMARK ROBOT

SCANNER made by AGILENT G2565BA

NGS: MiSeq DESKTOP SEQUENCER (ILLUMINA) SEQUENCER