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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Loop Genomics sequencing

Loop genomics can provide both transcript counting and phasing for full length mRNA using short-reads on Illumina sequencers

Sample requirements

  • >5 μl of >=10 ng/μl if sample is total RNA
  • RNA Integrity Number (RIN) >=7
  • >5 μl of >= 1ng/μl if sample is enriched mRNA
  • Samples need to be in multiples of 8

How to evaluate the sample quality

  • Bioanalyzer to get RIN
  • qbit to get RNA concentration measurement

If you are not able to carry out these steps, or your samples are below the required thresholds, please get in touch.

What we do with your samples

Depending on whether full-length transcripts or transcript counts are needed, we will use the “counting” or the “phasing” protocols

Expected results

Depending on whether full-length transcripts or transcript counts are needed we will use the “counting” or the “phasing” protocol.

  • Phasing: Assembled transcript contigs, each derived from a unique mRNA molecule in the RNA sample. This application needs no previous knowledge of the transcriptome of the species from which the sample is derived.
  • Counting: A list of counts for a set of reference transcripts supplied by the user or in the case of human, from a reference library of known transcripts

Bioinformatics

The Loop Analysis software is installed at NGI. We will run either the analysis of a “counting” or a “phasing” library

Applications
Relevant Technologies
Bioinformatics Pipelines
Method Status

Pilot

We are currently testing this method. Please contact us to find out more.

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