consultancy

Consultancy service

For expertise advice on your NGS-based research and the possibilities USF offers to get the most out of your samples: request a meeting at our consulting hour, each Friday at 1:30pm. Experimental design, technology, platform and library preparation choice, standard bioinformatics analysis, results and follow-up experiments are discussed. The facility manager ensures to bring the right experts from any of the participating organisations to the table.

You can request a meeting at useq@umcutrecht.nl.

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Bioinformatics Data Analysis

Data analysis

We facilitate routine primary data analysis, including basic QC and conversion of sequencing runs. In addition, demultiplexing is offered for a standard set of indexes as described here.

For further analysis, please contact our collaborators of the UMCU Bioinformatics Expertise Core (UBEC).

Data encryption

To ensure a safe data transfer we encrypt your data using OpenPGP encryption. In order for us to do this please follow the instructions here.

Data storage

The data download link will be active for one week. Please ensure proper handling when you are unable to download the data yourself!

Data storage is supported for a maximum of two months, after this period data will be deleted without prior notice. Users are responsible for long term storage and back up of their data.

 

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SNP Fingerprinting

We offer SNP fingerprinting service for human samples: a measurement of genetic variation of Single Nucleotide Polymorphisms (SNPs). This application can be used for genotyping, gender confirmation and sample tracking.

In our automated SNP fingerprinting workflow we use TaqMan OpenArray technology in combination with the QuantStudio 12K Flex Real-Time PCR System: a nanoliter fluidics platform for low volume, solution phased reactions. We employ the OpenArray Barcode Panel 32A, including 29 autosomal and 3 Y-chromosomal SNPs. Per array we can interrogate 45 samples, low input needed (minimal concentration of 5 ng/ul, with a minimal volume of 10 ul).

 

Pricing

Service fees include costs for chemicals, operator time and troubleshooting.

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DNA / RNA isolation

Obtaining high quality sequencing data starts with high quality DNA and RNA. We use the Qiagen Symphony robot for its proven robust high quality automated isolation of whole tissue, cells, organoids, blood and other body fluids. Standard services include human and mouse samples. Please contact us to discuss possibilities for samples of other species.

 

Sample requirements

We request samples to be submitted as either snapfrozen tissue, dry cell / organoid pellet, or dissolved in 200 ul ATL buffer (for DNA), dissolved in 400 ul RLT+ buffer (for RNA, stored at -80C), dissolved in 400 ul Trizol (for RNA, stored at -80C).

The maximum capacity of the robot is 96 samples per run/day, we require a minimum of 8 samples to start a run.

 

Requester is responsible for collection of primary sample. Note that samples will be stored for a maximum of 2 months and subsequently discarded without further notice.

 

Pricing

Service fees include costs for chemicals, operator time and quality control.

 

 

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Library Preparation

We facilitate the following library preparation methods using standard Illumina reagents, both as manual and automated (Neoprep) workflow:

For DNA:

  • TruSeq DNA Nano LT (manual)
  • TruSeq DNA Nano (Neoprep, automated)

For RNA:

  • TruSeq Stranded total RNA, ribo zero for human/mouse/rat (manual)
  • TruSeq Stranded mRNA polyA (manual)
  • TruSeq Stranded mRNA polyA (Neoprep, automated)

A maximum of 24 TruSeq indexes is available. Please contact us if you would like to use custom indexes. Bioinformatics demultiplexing service is supported for a restricted set of indexes.

 

Sample requirements

For DNA library preparation we request a minimum of 200 ng in 50 ul, measured with a fluorometric quantitation analysis (e.g. Qubit).

 

For RNA library preparation polyA-based (both Neoprep and manual) we request a minimum of 200 ng in 12.5 ul.

For RNA library preparation ribo zero (manual) we request a minimum of 500 ng in 15 ul.

RNA concentration should be measured with a fluorometric quantitation analysis (e.g. Qubit) and RNA quality should be at least RIN 8 (RNA Integrity Number).

 

Requester is responsible for collection of primary sample. Note that samples will be stored for a maximum of 2 months and subsequently discarded without further notice.

 

Pricing

Service fees include costs for chemicals, operator time, quality control (assessed with Bioanalyzer 2100 and Qubit) and troubleshooting.

 

Disclaimer

Library quality is mainly influenced by sample input quality. Users are responsible for ensuring that the quality of primary samples is high enough for successful library preparation. We will contact users when we have any doubt about input or library quality. Reagents that have been used will be charged, even if samples cannot be prepped and/or sequenced.

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Next Generation Sequencing

USEQ operates a broad range of sequencing platforms, each with unique characteristics. Technical and cost characteristics determine the best fit for your experiment. Service fees include costs for chemicals, operator time, quality control, maintenance, lab information management system (LIMS) and troubleshooting. Please refer to the FAQ page for sample requirements.

Currently, we operate the following Illumina platforms and configurations:

  • HiSeq2500 (1 machine)
  • NextSeq500 (3 machines)
  • MiSeq (1 machine)
  • MiniSeq (1 machine)

On this page you can find an overview per platform of the most widely used run modi, configurations and expected output*. Other run modi and custom recipes are possible as well, upon consultation with USEQ.

 

*Please note that high quality of sequence libraries is crucial in order to obtain maximum output. For samples submitted as ready to sequence libraries, USEQ cannot take any responsibility for data quality and quantity. 

 

NGS platforms and additional services

 

Illumina HiSeq2500

Applications: genome, exome, transcriptome sequencing
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Illumina NextSeq500

Applications: genome, exome, transcriptome sequencing
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Illumina MiSeq

Applications: targeted and small genome sequencing
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Illumina MiniSeq

Applications: targeted sequencing
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In addition, we provide access to the newest sequencing platforms:

 

Oxford Nanopore Sequencing

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Whole Genome Sequencing

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Services

We provide support for a broad range of services, including Next Generation Sequencing, sample preparation, DNA/RNA isolation, SNP fingerprinting, basic data analysis. A comprehensive state-of-the-art infrastructure is available, including NGS sequencers, liquid handling robotics, bioinformatics tools and ICT. Displayed below are our current standard services, please contact us for extra services.