Genomics Core Facility (location H2)

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

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.

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.