Instrumentation and Platforms available at BEA

BEA – the core facility for Bioinformatics and Expression Analysis is a Swedish national genomic service facility located at the Karolinska Institute. Clinical and translational scientists depend on complex instrumentation and educated laboratory technicians to perform high quality research. To fulfill this demand, BEA offers access to an extensive repertoire of genomic technologies to help scientists, investigators and the biotech community to conduct and explore their research in the most efficient and economical way. Specifically, BEA provides services and consultation for genomic analyses based on the latest Affymetrix, Agilent, Illumina and ABI platforms for sequencing, microarray analysis and qPCR. This includes a number of different types of genomic analyses; Gene expression and transcriptome analyses in standard and custom formats for different model organisms, Epigenetic analysis including bisulfite DNA-methylome and miRNA analysis, Genome wide SNP and copy number variation analysis, FFPE and small sample extractions and amplifications, NGS library preparations and sequencing . The services, which are complete, range from experimental planning to extensive bioinformatics support including access to software, hardware and resources for NGS analysis. At present, the core facility is financed by grants from the Karolinska Institutet, the Science for Life Laboratory and by user fees. For further information about the core facility and the technologies, please visit http://www.bea.ki.se

Instrumentation and Platforms available at BEA

BEA Staff

Services at BEA Experimental Planning, Data Analysis and Bioinformatics

Fredrik Fagerström-Billai, David Brodin, Susann Fält, Jessica Lindvall, Patrick Müller, Malin Nilsson, Marika Rönnholm, Indranil Sinha and Karin Dahlman-Wright.

Department of Biosciences and Nutrition, Novum, Karolinska Institutet, SE-141 57 Huddinge, Sweden

GeneTitan Scanner

Iscan Scanner

Biomek FXP

GCS 3000 Scanner

QIAcube Robot

7900 HT qRT-PCR

Agilent Microarray Scanner

The aim of BEA is to provide an extensive repertoire of genomic technologies to ongoing research projects at Swedish universities. Services are based on the Affymetrix, Agilent, Illumina and ABI platforms for microarray analysis, qPCR and Sequencing services. Standardized services ranges from experimental planning, nucleic acid purification and quality control, amplification and labeling preprocessing, library preparation, microarray hybridization and scanning, clustering and sequencing and bioinformatic support. •Nucleic acid preparation and Quality Control. •Gene expression analysis with different microarray platforms, species and formats.•Exon microarray analysis of alternative splicing.•Genome-wide association studies (GWAS) and Copy Number Variant (CNV) analysis•Bisulfite DNA methylation analysis (Illumina 450K methylation analysis). •miRNA profiling with different platforms and capture methods.•ChIP-on-chip and transcriptome mapping with tiling arrays.•Library preparations and NGS sequencing services on Illumina MiSeq and HiSeq 2000•ChIP-sequencing, mRNA sequencing, small RNA sequencing and transcriptome sequencing services.

BEA will assist in experimental planning, data analysis and downstream bioinformatics for all our applications. Our aim is to provide the customer with data in a format that is as accessible as possible without the need for further processing. We use software from the platform vendor as well as a number of commercial and non-commercial programs.

BEA’s data analysis support is free of charge and can be divided in basic and extended analysis. The basic analysis is always included in the service, and the extended analysis will be performed in agreement with the customer.

From left to right: Fredrik Fagerström Billai (Group leader), Susanne Fält (Research engineer), Jessica Lindwall (Bioinformatician), David Brodin (Bioinformatician), Karin Dahlman-Wright (Scientific director), Marika Rönnholm (Research engineer), Malin Nilsson (Research engineer), Patrick Müller (Research engineer)

At BEA there are many different genetic analyses and different types of microarrays to choose from. The figure shows the types of microarray and assays which are possible to run with the three different platforms available at BEA namely Affymetrix, Illumina and Agilent.

www.bea.ki.se

MiSeq Sequencer

HiSeq 2000 Sequencer

Basic Analysis:Experimental Design: Support in deciding number of replicates, experimental groups etc.Quality Control : Assessment of sample data to make sure the quality is sufficient.Preprocessing : Depending on platform this may include normalization, background correction,

summarization, alignment, peak finding etc.

Statistical Testing: Significanse testing for finding differences between experimental groups.Annotations: The latest annotations provided by the vendor will be added to the analyzed

data.

Extended Analysis:Visualizations: Support in creating various visualizations like heat maps, PCA plots, pathways

etc.

Functional Analysis: Enrichment testing for exploring associations with biological networks, gene ontologies, diseases, upstream regulators etc.

Data Publishing: Submitting data to public resources like Gene Expression Omnibus