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Not sure if this is the right forum for such a question, but please refer me to the correct one, if possible.

Does anyone has experience in working and detecting transposable elements using High-throughput techniques?

We would like to identify the sequence of our TE and were wondering if this is possible via such methods (bulk- or scRNASeq)?

any ideas of others methods to run reach this goal would be appreciated.

thanks

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With RNA-seq you will capture only retrotransposons. If that's your goal, then I would suggest enriching isolated RNA somehow, (e.g. using microbeads that have a library of complementary sequences). Keep in mind: Some RNAseq workflows require polyadenylated RNA.

Why not use whole genome sequencing? Blumenstiel 2014

Or why not do something like this (it's just a quick idea, please back check with professionals):

  1. Design multiple primers against Long Terminal Repeats or Terminal Inverted Repeats
  2. Amplify transposons from Genomic DNA from drosophila
  3. Excise Band from gel, extract transposon sequences of preferred size
  4. Fragment DNA
  5. Ligate sequencing adapters. Amplify. Your high throughput sequencing library is now done
  6. Apply to sequencer

Please know that switching from bulk to single cell might increase your cost by a factor 50. (One cell costs very roughly 100 dollars, so sequencing 100 cells costs 10 000). So you need a good reason to switch to single cell.

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  • $\begingroup$ thanks for the answer and also the link to the paper. It looks interesting. I didn't plan on doing scRNA, it was just to know if this might be a better option than bulk. Just to understand it better, you mention I can only identify retrotransposons with RNA-Seq. Is this because of the polyadenylation necessity? $\endgroup$ Sep 19, 2022 at 6:26
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    $\begingroup$ RNAseq sequences RNA. It doesn‘t need polyA, necesserily. It only measures Retrotransposons since retrotransposons are the only transposons that are RNA at some point in their lifetime. $\endgroup$
    – markur
    Sep 19, 2022 at 7:44
  • $\begingroup$ @AssaYeroslaviz - note that the most differences between RNAseq and other NGS techniques lies in library-generation (includes e.g. reverse transcription). The sequencer itself always sequences a 'similar' DNA-library in the end that was ligated to adapters, no matter if the isolated source is mRNA, gDNA, miRNA, PCR-products, etc. $\endgroup$
    – markur
    Sep 19, 2022 at 9:35

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