Genomics Core Facility (location H2)

Note: Because of Hemelvaartsdag there will be no sample hand in on thursday morning, this weeks sample hand in will be at fridaymorning between 10:00 and 11:30.

The facility is set-up to support users from within the Netherlands Cancer Institute (NKI/AvL).

Main stream activities:

Deep Sequencing of ChIP samples, RNA-Seq, Small hairpin library screen seq (Mission/TRC), small RNA seq, de novo sequencing, barcode sequencing, all with options of indexing samples. We use TruSeq protocols and standard Illumina sample preparation kits.

Capture and sequencing by liquid phase platform (SureSelect of Agilent). We use capture baits for catalog Whole Exome (Mouse and Human), Kinome and for custom sets of genes.

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

BioAnalyzer analysis of RNA or DNA

Mainstream activities are applicable to projects of maximal 24 samples per user that pass our standard QC levels. Larger series require a different time schedule, very large projects may even require technical assistance from the research department involved.

We do request that users follow the guidelines deepseq in sample preparation and sample delivery to qualify to enter the mainstream lines. That means delivery of samples on Thursday mornings between 10 and 11.30 am and with the appropriate sample forms.

Side stream activities:

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 to be provided to the CMF by the user.

Comparative Genome Hybridization of DNA samples on the 12x135K Nimblegen platform using the MAUI hybridization station (12-plex arrays). DNA must be pre-labeled by the user.

Gene expression analysis on the catalog Illumina human HT12 V4 and mouse WG6-V2 bead array platforms.

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

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

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.

We do request that users follow the  guidelines microarrays in sample preparation and sample delivery to qualify to be accepted by the facility. That means delivery of samples on Thursday mornings between 10 and 11.30 am and with the appropriate sample forms.

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. We keep improving the central database CMFdb which supports the MIAME upload to ArrayExpress.

We provide access to the software Nimblescan, Nexus and Ingenuity (send mail to inquire how).

Resources:

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 collaboration with the NKI microarray committee.