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Old 07-12-2011, 12:10 PM   #1
Location: Maryland

Join Date: May 2011
Posts: 65
Default Poor yield with chemical RNA fragmentation?

Has anyone had problems with low RNA recovery after chemical fragmentation for mRNA seq? A collaborator says that he loses ~90% of his material when he fragments chemically. He says that covaris shearing of RNA provides a much greater yield. Has anyone else had the same experience?
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Old 07-12-2011, 12:50 PM   #2
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Location: USA

Join Date: Apr 2010
Posts: 102

Illumina kits uses chemical fragmentation for mRNA seq and they didn't see any problem with the yield of and so i don't think it is chemical fragmentation leads to low yield. Try to adjust the time of the fragmentation (typically 5 minutes).
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Old 07-13-2011, 12:57 AM   #3
Location: cambridge

Join Date: Apr 2010
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What kit was used for chemical fragmentation?
I used a commercial kit for fragmentation. The time was 15 mins. I tried fragmenting for 10 mins and increased it by 1 min up to 15 mins. I got the same result, all the RNA had been fragmented to below 100bp. I won't use this kit again.
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