Asked this question on Twitter and thought I would share answers here via Storify. I am putting it below the fold to allow people to avoid the Storify embed if they want to.
//storify.com/phylogenomics/correcting-for-rrna-copy-in-qpcr-data.js[View the story “Correcting for rRNA copy # in qPCR data” on Storify]
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Author: Jonathan Eisen
I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis
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I have seen these papers cited when correcting for rRNA gene copy number:
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the
Ribosomal RNA Operon Copy Number Database. Nucl. Acids Res., 29,
181-184.
Lee ZM-P, Bussema C, Schmidt TM (2009) rrnDB: documenting the number
of rRNA and tRNA genes in bacteria and archaea. Nucleic Acids Res, 37,
D489-D493.
However, I wonder if anyone has ever thought about how ploidy would affect 16S rDNA qPCR? For example:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016392
If some species typically have 20 genome copies per cell and others have 1 genome copy per cell, this would make conversion of gene copy numbers to cells pretty much impossible unless you measure the ploidy for every species in your system. And if you don't do the conversion, then what do gene copy numbers mean?
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Thanks .. and agree that ploidy could be a big big big problem.
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