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Old 02-02-2017, 01:38 PM   #1
kgoglin
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Default mRNA jaggeed peaks in profiles on Bioanalzyer

An mRNA profile on Bioanalyzer can take slightly unusual forms. Rarely do we see a perfect clean hump (see attached). Sometimes we get a hump with many jagged sharp peaks and within the same sample set the jagged sharp peaks disappear or are lessened. See the samples attached where the top three samples have a more smooth hump compared to the others. What are these jagged sharp peaks? Are certain mRNAs selected for? (We used Ribo-Zero for rRNA depletion from the Total RNA)

These samples were submitted to the core so I don't know the underlying experiment which may be affecting the mRNA profile.

The researcher did notice a difference in sequence data coming from these three samples. They said "There seems to be a large proportion (30%) of unmappable (unidentifiable) reads in 3 particular libraries out of the 9 Borrelia libraries. I am wondering if there may be anything out of the ordinary for these 3 libraries during library construction and/or sequencing (e.g. RNA quantity, etc.)". Nothing was strange about the library prep protocol; the only thing we noticed was these mRNA profiles.
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File Type: jpg mRNA profile.jpg (61.6 KB, 13 views)
File Type: jpg mRNA_jagged_peaks.jpg (84.5 KB, 15 views)
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Old 02-02-2017, 04:54 PM   #2
nucacidhunter
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I do not know if there is any typical electrophoretic profile for rRNA depleted total RNA except that I would not expect to see rRNA peaks. I assume profile will depend on the transcript population present in the sample and vary quite widely depending on many biological factors.

I wonder if they have done any BLAST or any other similarity search on those un-mappable reads which might give clues about their origin.
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