NGI during Covid-19 outbreak

NGI is still up and running during the Covid-19 pandemic, but we are experiencing some limitations in terms of personnel and key reagents. Each NGI node is following its respective host university recommendations and will continue operation until further notice.

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SMARTer ThruPLEX DNA-seq

Library preparation for DNA, ideal for preparing libraries from small amounts of input material. Works well for shotgun libraries, ChIP DNA and FFPE samples, amongst others.

The ThruPLEX DNA-seq chemistry is engineered and optimized to generate DNA libraries with high molecular complexity from low-input samples.

Sample requirements for common sample types

Genomic DNA
  • Sample type: DNA
  • Concentration: 1-10 ng/μL
  • Volume: >15 μL
  • Material needed for 1 prep: 40 ng
  • We ask for: Gel picture or FragmentAnalyzer trace
FFPE
  • Sample type: DNA
  • Concentration: 20-50 ng/μL
  • Volume: >15 μL
  • Material needed for 1 prep: 200 ng
  • We ask for: Gel picture or FragmentAnalyzer trace
ChIP-ed DNA
  • Sample type: ChIP-ed DNA
  • Concentration: 0.2-10 ng/μL
  • Volume: >15 μL
  • Material needed for 1 prep: 1 ng
  • We ask for: BioAnalyzer trace

These input requirements are for illustrative purposes only. Please get in touch with one of our project coordinators to discuss your samples if in doubt.

What we do with your samples

Once your samples arrive at NGI, we start by performing a reception control step in which we make sure the sample meets our requirements.

If the samples fail this quality control step, we will contact you to discuss possible options. Should you choose to proceed with samples not fulfilling the criteria it will be at your own risk, NGI will only make one attempt at library preparation and if the prep does not work you will have to pay for the library preparation anyway.

If the samples pass reception control, the samples will be queued for library preparation.

Library preparation

Single-tube reaction that starts with low input double-stranded DNA (0.05 ng to 50 ng). The genomic DNA is fragmented before library preparation. For already fragmented DNA molecules (such as ChIP-DNA), the initial fragmentation step is omitted.

Stem-loop adapters are blunt end ligated to repaired input DNA. These molecules are extended then amplified to include barcodes using a high-fidelity polymerase to yield an indexed Illumina NGS library.

Library QC and sequencing

We evaluate the concentration of the library using qPCR and inform you of the QC status of each sample. Once the libraries have passed this QC step, they are normalised, pooled, and queued for sequencing.

The sequencing will be carried out following the setup stated in the agreement.

Applications
Relevant Technologies
Bioinformatics Pipelines
Method Status

Service

We are routinely running this method. Please visit the Order Portal to place an order.

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