Feb 27, 2012
The Genomic Core Facility will move from C2 to H2 on March the 5th. [More]
Feb 27, 2012
Genomic Core Facility is the name we use from now on. [More]
Dec 21, 2011

Facility opening hours during Christmas and Newyear.

The wetlab will be open on 22nd from 9.30-11.00 for sample hand-in. Also on 28th and the 29th sample hand-in the lab will be open. The wetlab will be closed on Friday 23, Monday 27, and Friday the 30th of December. We open again on Monday Januari 2nd. Bioinformatic support is present during most working days except Thursdays - make appointments to be sure. Merry Christmas and a Happy Newyear to all of the users.

[More]
Nov 21, 2011
The second HiSeq2000 that we have acquired in May 2011 showed up with an error message in the homing of the tray carrying the flowcells. Replacement material has been provided by Illumina and will be installed on Wednesday, November 16th 2011. This will impair the runschedule for 1 week. [More]
Jul 12, 2011
Focus has been adjusted and new software is installed. [More]
Jul 7, 2011
We observe a focus problem using version 3 Sequence Chemistry with Single Read Version 1.5 Flowcells. [More]
Jun 14, 2011
The test runs that have been run for the last two weeks on the second Hiseq were succesful although we faced that some out of focus tiles were present. [More]
May 26, 2011
At this moment we run 4 Flowcells simulataneously! [More]
May 10, 2011
The second HiSeq2000 is now being put together and tested technically by Illumina technitians. [More]
Apr 19, 2011
The second Hiseq2000 has been shipped to the NKI [More]
Mar 31, 2011
The Hiseq2000 is being serviced [More]
Feb 24, 2011
We are in the process of acquiring a second Hiseq2000 for the NKI. [More]
Feb 24, 2011
The HiSeq2000 sequencing machine runs two flowcells (FC) simultaneous. [More]
Oct 5, 2010
HiSeq2000 update. The Hiseq2000 sequencing tool has arrived at the facility. It will be installed in the first half of October.
[More]
Feb 27, 2010
The Facility has moved from G2H2 to C2.009. [More]
Jan 1, 2010

In house printing of several platforms has been phased out since januari 2010.

[More]

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.