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Old 07-12-2011, 11:10 AM   #1
eab
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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, 11:50 AM   #2
upendra_35
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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 07-12-2011, 11:57 PM   #3
niceday
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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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