Bioinformatics and Expression Analysis (BEA)

Regional facility of national interest

Bioinformatics and Expression Analysis (BEA) provides services for genomic analysis based on the Affymetrix, Agilent, Illumina and ABI platforms for microarrays, sequencing and qPCR. This includes gene expression and transcriptome analysis, DNA-binding analysis, epigenetic analysis including DNA-methylation and miRNA analysis, genome wide SNP and copy number variation analysis and different Illumina sequencing applications. The service is complete and ranges from experimental planning, sample extraction and quality control, to actual analysis and bioinformatic support. BEA offers training and education in genomic technologies including associated data analysis. For more information please visit http://www.bea.ki.se/

SERVICES

  • Bioinformatic support and data analysis. BEA provides services for planning, experimental design and analysis of data with commercial or developed computational tools. Services include educational support and practical training in the use of software and analysis methods.
  • Epigenetic analysis. Illumina 450 K Methylation arrays, Affymetrix and Agilent miRNA arrays, ChIP on Chip applications with Affymetrix and Agilent tiling arrays.
  • Expression analysis. Affymetrix and Agilent microarray analysis in different formats.
  • Genotyping and CNV analysis. Affymetrix SNP 6.0 arrays, Agilent CGH arrays and Illumina Infinium beadarrays for genetic variation analysis.
  • qRT-PCR analysis. Gene expression and genotyping qPCR using TaqMan chemistry. Different options with custom 96- or 384-well and Taqman low density arrays (TLDA) formats.
  • RNA and DNA quality control. Purification and extraction services for different biological specimen. RNA/DNA concentration and content quality control.
  • Sequencing analysis. Illumina NGS services including library construction. In house sequencing with the MiSeq platform. Coordination of larger sequencing projects on the Illumina HiSeq platforms. Bioinformatic support.

APPLICATIONS

  • Gene expression profiling and transcriptome mapping with different methods and microarray platforms.
  • Epigentic analysis including Global DNA methylation analysis, ChIP applications and miRNA analysis.
  • Genome wide association analysis (GWAS) and Copy number analysis (CNV).
  • RNA sequencing, ChIP sequencing and targeted re-sequencing.

EQUIPMENT

  • DNA/RNA handling equipment. Agilent 2100 Bioanalyzer system, Agilent 2200 TapeStation system, Qiagen QIAcube sample preparation robot, Qiagen Tissuelyser sample disruptor.
  • Microarray scanners. Affymetrix Genechip 3000 and GeneTitan system, Agilent G2565CA microarray system and Illumina iScan microarray system.
  • qRT-PCR. Applied Biosystems 7900HT fast real-time PCR system.
  • Robotics. Biomek FXP laboratory automation workstation.
  • Sequencing. Illumina Miseq benchtop sequencer.