Expired flowcell

TonyBrooks · 10-04-2011, 08:41 AM

We have a couple of expired flowcells in our fridge (manufactured 13 months ago). Has anyone here run a flowcell that is past it's best before date and got decent data? How far expired was it? I'm seriously anti "throw things away" and I'd like to use it.

I'm wondering if it'll be the same as Affymetrix arrays (which are still fine years after expiry).

NextGenSeq · 10-04-2011, 03:31 PM

We ran a GAIIX flowcell that was ~2months expired and it worked terribly.

simonandrews · 10-05-2011, 12:35 AM

How expensive is it to get as far as the first base report with a flowcell? If the reagent cost to that stage isn't too bad you could try it and just bail out if the clusters look poor. As long as your cluster generation is OK I'd think that the rest of the sequencing would be OK from that point.

behavin · 10-06-2011, 01:09 PM

We had a HiSeq v1 flow cell that was WITHIN its expiration window (I think it was about 8 months old) and when we ran it the outside edges of each lane looked horrible, intensities were low across the board, and the Q30's were pretty bad compared to what we're used to.

NextGenSeq · 10-07-2011, 07:40 AM

That sounds like their old manufacturing problem. Illumina had bad lots of flowcells in 2010 where the edges had a problem with the oligo deposition.

MRSeq · 02-07-2012, 10:13 PM

Hello, I have nothing to contribute, but I am also very interested in that question. Collaborating facility has a HiSeQ 2000 flowcell (old type) that is 6 months expired and would let us play with it for free. But what should we expect? Terrible problems or normal quality? We have to decide within days should we risk good samples and use it as a purely technical exercise? I would love to hear from somebody with experience with "expired" HiSeQ flowcell.

TonyBrooks · 02-09-2012, 02:39 AM

Surely if it's free you should just give it a go. Keep the denatured hyb solution and if it looks terrible, you can still repeat the sequencing.
I can't see any reason why it would generate incorrect information. You may just get more technical issues, such as low cluster numbers or low quality scores. If anything is really bad it should get removed by the filters before it hits any analysis pipeline.

obiwan · 02-16-2012, 04:26 PM

Yes, we've run a single-end flow cell for the GAIIx with good results. Its expiration date was 8/20/2010 and we ran it in April 2011. More recently (Jan 2012) we ran another flow cell with the same expiration date. I can't say qualitatively that it was good (the PhiX lane failed), but I did see clusters in the other 7 lanes.

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10-04-2011, 08:41 AM	#1
TonyBrooks Senior Member Location: London Join Date: Jun 2009 Posts: 298	Expired flowcell We have a couple of expired flowcells in our fridge (manufactured 13 months ago). Has anyone here run a flowcell that is past it's best before date and got decent data? How far expired was it? I'm seriously anti "throw things away" and I'd like to use it. I'm wondering if it'll be the same as Affymetrix arrays (which are still fine years after expiry).

10-04-2011, 03:31 PM	#2
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	We ran a GAIIX flowcell that was ~2months expired and it worked terribly.

10-05-2011, 12:35 AM	#3
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	How expensive is it to get as far as the first base report with a flowcell? If the reagent cost to that stage isn't too bad you could try it and just bail out if the clusters look poor. As long as your cluster generation is OK I'd think that the rest of the sequencing would be OK from that point.

10-06-2011, 01:09 PM	#4
behavin Member Location: TN Join Date: Oct 2011 Posts: 11	We had a HiSeq v1 flow cell that was WITHIN its expiration window (I think it was about 8 months old) and when we ran it the outside edges of each lane looked horrible, intensities were low across the board, and the Q30's were pretty bad compared to what we're used to.

10-07-2011, 07:40 AM	#5
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	That sounds like their old manufacturing problem. Illumina had bad lots of flowcells in 2010 where the edges had a problem with the oligo deposition.

02-07-2012, 10:13 PM	#6
MRSeq Member Location: USA Join Date: May 2009 Posts: 11	Hello, I have nothing to contribute, but I am also very interested in that question. Collaborating facility has a HiSeQ 2000 flowcell (old type) that is 6 months expired and would let us play with it for free. But what should we expect? Terrible problems or normal quality? We have to decide within days should we risk good samples and use it as a purely technical exercise? I would love to hear from somebody with experience with "expired" HiSeQ flowcell.

02-09-2012, 02:39 AM	#7
TonyBrooks Senior Member Location: London Join Date: Jun 2009 Posts: 298	Surely if it's free you should just give it a go. Keep the denatured hyb solution and if it looks terrible, you can still repeat the sequencing. I can't see any reason why it would generate incorrect information. You may just get more technical issues, such as low cluster numbers or low quality scores. If anything is really bad it should get removed by the filters before it hits any analysis pipeline.

02-16-2012, 04:26 PM	#8
obiwan Junior Member Location: Berkeley,CA Join Date: Feb 2012 Posts: 1	Yes, we've run a single-end flow cell for the GAIIx with good results. Its expiration date was 8/20/2010 and we ran it in April 2011. More recently (Jan 2012) we ran another flow cell with the same expiration date. I can't say qualitatively that it was good (the PhiX lane failed), but I did see clusters in the other 7 lanes.