Facilities & services

Bioinformatics

NGS data storage is provided. Raw fastq data is kept by default for 3 months; optionally, up to 5 years can be requested. The data is stored in a centralized computing facility where users can log in and apply analysis pipelines to their data. At current we offer a small number of data processing pipelines, including, variant calling, alignment, CNV calling and RNAseq analysis. Downstream analysis and interpretation is not included in our standard services. 

Consultancy

Expert advice on the possibilities, experimental design, platform, technologies and methods of choice, standard bioinformatics analysis, results / follow-up and / or reference to collaborating departments or researchers  

Digitial Droplet PCR

The newest acquisition of the CFG is a Bio-Rad QX200 ddPCR machine for Pathogen or Rare Mutation Detection (RMD).

DNA / RNA isolation

The CFG offers automated DNA and RNA isolation using a Qiagen Qiasymphony or FlexStar instrument for DNA extraction and a Qiacube instrument for RNA isolation. 

Lab automation

The CFG houses multiple lab automation robots from Beckman Coulter, Mosquito and Hamilton to enhance reproducibility, cost efficiency and to allow handling of low amounts of input material and/or reagents. Standardized liquid handling workflows are available for DNA-seq and RNA-seq experiments. Custom workflows for your application can be developed in a collaborative setup

Next Generation Sequencing

For NGS sequencing we offer both high throughput sequencing services (Illumina HiSeq 4000 / GeneStudio S5 Prime / Pacific Biosciences Sequel II) as well as fast turnaround sequencing services (Illumina-MiSeq / IonTorrent-PGM / Oxford Nanopore). 

Pricing

For collaborators and clients affiliated to the Amsterdam UMC we offer a reduced pricing scheme:

Pricing (internal link)

For external clients, please contact us for more information:

E-mail: cfg-info@amsterdamumc.nl
Telephone: +31(0)20-556 3846

Sanger sequencing

The CFG owns several ABI 3730 instruments for conventional Sanger Sequencing and Fragment Analysis. 

Single cell / nuclei sequencing

The CFG offers multiple workflows for (BSL-2) single cell gene expression analysis. The most recent acquisition is the 10X Chromium controller, which offers a well-established and standardized platform for single cell analysis. Furthermore, we are working workflows for single cell ATAC sequencing and single nuclei sequencing. 

Corona-maatregelen

We zetten ons in om ons ziekenhuis veilig te houden tijdens de coronacrisis.

Lees deze extra maatregelen goed door voordat u een van onze locaties bezoekt: