BioMicroCenter:News2016

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MARCH 2016

Dear users,

I wanted to bring you up to date on a number of major changes in the BioMicro Center. We've been spending the last several months focused extensively on improving turn around time and on reducing the cost of library preparation significantly. While not all of our efforts are ready for primetime, we do have several significant changes that I hope will be of interest.

The largest change is the addition of a second NextSeq500 and a second MiSeq. We are increadibly grateful to Li-Huei Tsai, Miriam Heiman, Michael Birnbaum and Biological Engineering for these additional instruments. Their addition has significantly reduced our turn around time and we've been able to keep our queue time for both instruments to under a week, which is a dramatic improvement over last year. It also allows us to have instrument redundancy for the inevitable machine failures.

A second change we are rolling out is a modification to our library pooling that can significantly lower the QC costs for an experiment. We have been experimenting using fluorometric measurements of the individual samples before pooling. This cuts out a day in preparing libraries for sequencing and reduces the costs as well. We have been using this internally for a couple of months and the results are on par with what we were observing using qPCR of the individual constituents. We will be making this available to everyone now as a new option "IlluminaQC-Rapid" through iLabs and it can be marked on our latest downloadable forms. This will cost half of a regular quality control reaction but will remove the guarantee of the pooling, as it is a less rigorous check of the quality of the sample. We would discourage using this method if there is signficant variation in the samples within a project, but it is a good method when you are pooling large numbers of libraries prepared in parallel where you have high confidence in the preparation.

Finally, we are rolling out a brand new eukaryotic RNAseq library preparation method that will significantly reduce preparation costs. High throughput 3' digital gene expression (HT-3'DGE) uses a very early indexing step to tag each sample, allowing us to significantly reduce the cost of the experiment - preps will cost $1200 for 24 samples and $4000 for a whole plate. We have been working on this protocol (based on the Soumillon et al.,doi: http://dx.doi.org/10.1101/003236) as part of a new collaboration with the KI High-Throughput Screening Core. It is NOT appropriate for all situations, but can be a huge savings where it is applicable. As with all of our high-throughput methods, samples can drop out and will not be rerun if they do.

Thank you all for your patience as we worked through a number of issues with the sequencers this fall. As a heads up, we will be having a lot of staff turnover this summer as some of our staff are moving on to other positions and graduate school. We are already hiring new staff and we hope to minimize any disruptions.