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Old 02-27-2019, 04:34 AM   #1
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Location: Israel

Join Date: Jan 2019
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Default ERCC spike-ins for prokaryotes

I see that many people use ERCC spike-ins with prokaryotes, but looking at the manufacturer description I see that they only mention that it is good for eukaryotes...

I found some articles that asses the validity of the ERCC in eukaryotes, but never on prokaryotes...

So can I use it in prokaryotes? anyone found an article assessing the validity of ERCC in prokaryotes?

**I'm specifically interested in e.coli, and I really need spike ins because I suspect that most of the genes will express differently between the two conditions... If for example all the genes will be 2 times more expressed in condition A than in condition B, without spike-ins the differential expression will look like there was no change. If you have other suggestions for this scenario besides ERCC, I would love to know... **
Adiro is offline   Reply With Quote
Old 02-27-2019, 05:33 AM   #2
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Location: UK

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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?
Bukowski is offline   Reply With Quote
Old 02-28-2019, 04:51 PM   #3
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I'd be careful about using them for Prokaryotes. Many of them are actually bacterial genes, mostly B.subtilis if I remember correctly, but also some antibiotic resistance genes descended from Affy controls. I'd download the fastas and align to your genome of interest before using them.
cmbetts is offline   Reply With Quote

ercc spike ins, rnaseq, spike-in

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