What happens when Illumina sequencing reagents run out?

[picabo]

Hello.

If I am sequencing a long read on an Illumina GA IIx and I forget to add fresh reagents, resulting in the reagents running out, what happens? Can I add them after I notice they ran out or is the run ruined?

Thank you.

[csc]

It will depend on how early you noticed that reagents ran out and what steps have occurred since they ran out. If you allow chemistry to occur without enough reagents (i.e. IMR or CLM), the phasing of your clusters is likely to get scrambled. If, lets say, you notice during an imaging cycle that it ran out of scan mix (but the chemistry steps preceding imaging were completed correctly), you can add more scan mix and then restart that imaging cycle without too much of an issue.

Use the reagent tracking feature and set a conservative cycle count so that the recipe will stop before running out of reagents.

[GW_OK]

If the reagents ran dry you might also get crystal formation in your tubes, causing blockages. And I don't think flowcells like being dry for very long, either. It sucks but I'd re-run it. You might still be able to get data out of what cycles were completed before he reagent issue, for what its worth.