Editing BioMicroCenter:News2012 (section)

== SEPTEMBER 19, 2012 ==
We hope everyone had a great summer. A couple of updates for you:<BR><BR>

First, and most importantly, I know a lot of you have been affected by very long Illumina turnaround times for HiSeq samples, and especially those for long reads. Our HiSeq has had a very large run of failures this summer and it is affecting everyone. Short reads have been able to sneak through between the failures, so the problem is not quite as bad there, but we have been working very hard with Illumina to get the HiSeq back running efficiently. I can finally report some good news on this front. First, Illumina is shipping us a second HiSeq this week to help us clear through the back log.  In addition, we are enormously grateful to the Biopolymer core at the KI which has taken several of our backlogged flowcells and is helping us work through the queue. Hopefully, these changes will allow us to get on top of our queue and get sequencing turn around back to where it should be. <BR><BR>

On a more positive note, we have been able to significantly increase our throughput in quality control for Illumina over the past few months. First, we have begun using the Advanced Analytical Fragment Analyzer (donated by the Dept. of Biology) to replace the Agilent Bioanalyzer for Illumina libraries. The fragment analyzer uses capillary electrophoresis to measure fragment length and quantity of DNA and RNA molecules much the same way the BioAnalyzer does. However, unlike the bioanalyzer, it can run unattended, allowing us to process more samples per day. It also appears to have a lower failure rate and a broader dynamic range, both key elements in our analysis. In addition, through a collaboration with the new KI High Throughput Screening Core, we have been able to automate our qPCR analysis using the Tecan systems in the BioMicro Center. This is enabling us to run 384 well qPCRs in a much less labor intensive manner while maintaining high quality. We’re still recalibrating our cluster densities using the Tecans but we are very close to having the last few details ironed out. <BR><BR>

Couple of other quick notes:
- We’ve had a few additions to our staff with Scott Morin joining us as a technical assistant, replacing Kevin Thai, and Margaret Minnig and Kate Tracka joining us from Northeastern for the summer / fall. 
- The Technology Seminar Series will resume in the spring. We have been too focused on the Illumina issues to schedule the vendors this fall.