Next Generation Sequencing
We are using Illumina’s highly parallel and high-throughput sequencing-by-synthesis technology. Our sequencers enable a wide range of applications due to their different throughput capacities. The performance of the sequencers allows sequencing results with fast run times. Our next-generation sequencing service includes all the steps from project design to analyses of the results.
We provide sequencing services in whole transcriptome, targeted RNA-sequencing, and in small RNA-analyses. We start analyses either from RNA or we can extract RNA from cells, tissues or FFPE blocks. Before sequencing, the quality and quantity of RNA are carefully monitored. We have expertise from different library preparation methods which we apply based on specific project requirements. The RNA-seq service covers all the steps from experimental design to bioinformatic analysis of the results. Transcriptome profiling from minute amount of sample material or from single cells is also possible.
BMGen provides both re-sequencing and de novo sequencing from small and large genomes. We start analyses either from DNA or we can extract DNA from customer’s samples. Services include whole genome, exome, focused or small PCR amplicon sequencing. Amplicon size in exome sequencing varies according to the selected off-the-shelf targets or targets designed by the customer. ChIPseq and CLIPSeq technologies allow survey of interactions between protein, DNA, and RNA, enabling the interpretation of regulation events of protein/nucleic acid interactions. Methylation sequencing enables the study of the epigenetic regulation of genome. Both whole genome and targeted bisulfite sequencing are provided by BMGen. Sequencing-based genome-wide target enrichment assays to study CNVs, LOH and targeted mutations are also possible.
BMGen provides DNA and RNA microarray services from Affymetrix and Agilent platforms. The services include gene expression analyses for mRNA and miRNA. Arrays to detect chromosomal aberrations with copy number variations are also available for cytological research. The service includes all the steps from project design and array platform selection to bioinformatic analyses of microarrays.
We provide computational analyses for both next-generation sequencing and microarray data. For both DNA-Seq and RNA-Seq, the analysis includes data pre-processing, variant discovery, and callset refinement which are carried out using GATK Best Practices. Microarray data analysis typically involves data filtering and normalization combined with statistical analysis. Further downstream analyses for next-generation sequencing and microarrays are tailored according to customer’s needs.
BMGen offers both Western blotting and immunofluorescence based protein detection services for customers. These services are available on request and are always tailored for customer’s needs. Apart from standard detection of proteins from customer’s samples we also perform antibody testing upon request.
BMGen also provides protein expression services using the Olink Proximity Extension Assay Technology that is based on detecting specific protein expression by antibodies that are linked with oligos. Each protein is detected by two antibodies, which are linked with complementary oligos. Binding of the oligos can be detected and protein expression is quantified using qPCR. Using Olink technology we can quantify up to 92 proteins from 90 samples in a single run.
Genetic Engineering Services
BMGen has access to and broad expertise in genome scale mouse and human lentiviral shRNA reagents for gene knockdown studies in context of target validation. Furthermore, we will have access to genome scale CRISPR reagents for gene knockout and editing projects, starting February 2016.
BMGen uses a biosafety level 2 virus production facility to provide retro-and lentiviral particles for generation of genetically altered cell lines.
BMGen collaborates and carries out contract research with pharmaceutical and biotech partners to generate and test next generation predictive biological models of epithelial cancers for target validation and drug discovery. The current pipeline of cancer models includes cell based 3D culture models grown in reconstituted extracellular matrices, ex vivo explant cultures from patient-derived tumors and various in vivo tumor models including xenograft and pdx models as well as genetically engineered mice.