How long can cDNA libraries be frozen for?

[RM_Tanner]

Hello,

My question is:

How long can RNA-seq libraries be frozen at -20C after initial sequencing? Can a frozen RNA-seq library be re-sequenced 6 months later with high quality?

I spoke to someone at our local sequencing facility, and she indicated that she has frozen libraries and re-sequenced them 3 months later with no problems. Does anyone know if a library can be frozen for 6-12 months?


Background information:

Our lab is going to conduct a large amount of RNA seq experiments (we have close to 100 samples, including replicates). However, we cannot afford to sequence all of our samples deeply.

We want to sequence one replicate per condition (10-15 million reads) to see where interesting changes are occuring. We would then re-sequence those interesting conditions with replicates (50 million reads each).

However, we want our initial libraries frozen for later re-sequencing, to avoid paying for extra library preps and sequenced reads.

[Chipper]

I have sequenced some libraries that were > 1 y old without problem but of course it is no guarantee. But in this case it does not make sense to me to take one replicate to 15 M reads instead of 3x5M.

[cmbetts]

I've also sequenced libraries >1yr with no obvious ill effects.

That being said, I agree with Chipper that (assuming these are biological replicates) you'll get higher quality data sequencing all of your replicates such that you still only get 10-15M each condition.

[jwfoley]

I agree with everything said. If the frozen libraries stayed frozen the whole time, you should be able to measure their longevity in decades, not months. But N = 1 is only going to give you spurious results that you'll waste even more money on, not to mention the turnaround time for sequencing. If you really want to save money, save it on the sequencing depth, not the replication. http://bioinformatics.oxfordjournals.../30/3/301.long