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Old 02-19-2014, 04:07 AM   #3
Jubs
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Location: Germany

Join Date: Jun 2013
Posts: 6
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Hi Jimmie and doc2r,

I'm about to try this method also and I'm glad I found this thread in time. Did you have any success in cleaning up for mtDNA? Or did the authors gave any suggestions?

For now I'm considering a double-wash on the nuclei and qPCR for mtDNA sequences to see how enriched they are in relation to the rest. That should give an idea on how many washes are needed to get rid of most mtDNA and, most importantly, how much of the good stuff I lose when washing more than once.

When analyzing their original data I also found the 60% of the reads mapping to chrM, which reduces a lot the amount of reads that are actually usable. Funny they don't mention this in the paper...

Our sequencing facility experts said that use of biotin probes for getting rid of ribosomal dna would not be so straightforward because smaller genDNA fragments would also get pulled down... but I never tried this before so I wouldn't know how they would actually behave.

Thanks!
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