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Old 02-27-2019, 05:33 AM   #2
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Location: UK

Join Date: Jan 2010
Posts: 390

I don't think they say it's only good for eukaryotes, just that it mimics the nature of eukaryotic transcripts in terms of nucleotide content, size distribution, polyadenylation etc. I think the bigger concern using them for prokaryotes is probably that a chunk of the ERCC spike ins are derived from bacterial sequences in the first place.

If you're concerned about the derivation of the ERCC sequences, then there are artificial spike-in's available: (I would link to the sequins site, but there appears to be a configuration issue on their webserver)

Given that you "already see many people use ERCC spike-ins with prokaryotes" what kind of additional validity are you looking for?
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