Central Microarray and Deep Sequencing Core Facility

The facility is set-up to support users from within the Netherlands Cancer Institute (NKI/AvL). We are financially supported by the Center for Biomedical Genetics (CBG), the Cancer Genomics Centre (CGC) and by internal funding. Our policies are fine-tuned in close collaboration with the NKI microarray committee.

The competitive high level of scientific research that is performed in the NKI requires that supporting facilities work at the same level with high accuracy and appropriate speed. To maintain the facilities’ accuracy and at the same time reduce the turnaround time for the experiments we make a distinction between our main stream high throughput activities and the other work we do.  

For Main stream activities we aim and expect to deliver results within a period of 3 weeks or less.  We do request that users follow the guidelines in sample preparation and sample delivery to qualify to enter the mainstream lines.

We have terminated lines of activities that lacked general support or that are out-dated and we have replaced them by alternative means (like deep sequencing) or by buying or acquiring services elsewhere.  For example, we phased-out most of the in-house printing of microarrays.

To be able to maintain a short mainstream activity turnaround time, all other activities are performed as quickly as possible, be it with lower priority.  Mainstream activities can only be applicable to projects of maximal 24 samples per user and for samples that pass our standard QC levels. Larger series demand a different time schedule and very large projects may even require technical assistance from the research department involved.

MAIN stream activities:

Gene expression analysis on the catalog Illumina WG6-V3 human, human HT12, mouse WG6-V2 bead array platforms.

Gene expression analysis on the catalog array platforms of Agilent for Drosophila or Zebrafish

Comparative Genome Hybridization of pre-labeled DNA samples on the Nimblegen platform using the MAUI hybridization station (12-plex arrays).

miRNA expression on commercial arrays of Exiqon (miRCURY LNA™ microRNA Array, v.11.0).

Hybridization of pre-labeled samples for DAM-id or ChIP-chip in the TECAN hybridization stations on custom or catalog Nimblegen arrays. Custom arrays are provided to the CMF by the user.

Shearing/homogenization of fractions (DNA/RNA/tissue) by the Covaris acoustic implosion method.

BioAnalyzer analysis of RNA or DNA

SIDE stream/Innovative research activities:

Illumina BeadArray platforms (DASL, Golden Gate, Infinium)

miRNA experiment on the Agilent 8-pack platform or Illumina 24 pack platform.

Printing (in house) of custom sets of microarrays for development of novel applications.

Deep Sequencing of ChIP samples,  Dam-id samples, RNA-Seq, DGE, Mate-Pair sequencing, de novo sequencing, barcode sequencing, all with options of indexing samples

Capture and (re-sequencing) by either solid state platforms (Nimblegen or Agilent) or by liquid state platform (SureSelect of Agilent).

Bio-informatic support:

We aim to support users of the facility throughout the processes of data acquisition, data analysis and data storage. Application and development of Sequencing Analysis software is one of the main points of interest, however we are also improving the central database CMFdb for the latest improvements and the addition of the direct Illumina MIAME upload to ArrayExpress.