BioMicroCenter:News

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BioMicro Center News

JANUARY 9, 2013

Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.

First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.

During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.

Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week. If you have any concerns, please do not hesitate to contact me.


OCTOBER 9, 2012

A quick, almost all Illumina, update:

First, the Illumina loaner HiSeq is now up and running and we are running at full speed. Our last full flowcell in the queue is loading this week so we should finally be back to normal (hopefully). We cannot prevent instrument failure but at least any issues should have less of a negative impact for the 6 weeks or so while the loaner is here (in other words, if you have time sensitive samples, now is the time to get them in).

Second, our MiSeq is scheduled for its upgrade in the next two weeks. This will make two changes. First, the number of reads per run will increase significantly – from ~5m to ~15m. Secondly, the upgrade will add a third tier of read lengths – 500nt. The 500nt run will cost a few hundred more than the 300nt run and will take a second day, but will give us read lengths longer than anything else in the BioMicro Center.

Third, Illumina is having a user meeting on Thursday over at the Hyatt. The meeting is likely to be at least moderately technical but is free if you are interested in going. Registration is at: http://eventregistration.illumina.com/d/scqsm0/4W

 "The Boston User Group Meeting: Continuing advances in Illumina’s genomic analysis technologies are rapidly changing the way scientists 
 in a variety of disciplines  approach their research. Through a series of local user group meetings, Illumina is providing an opportunity 
 for our customers to showcase their research as well as a forum to discuss protocol optimization and bioinformatics solutions.  Additionally, 
 you will hear about the latest updates to our products and enhancements to the Illumina Next Generation Sequencing workflow, as well as have 
 the opportunity to interact with key vendors who provide products that support the NGS workflow.  Continental breakfast, breaks, and lunch 
 will be provided."

Finally, a couple quicker notes:

  • We frequently update our forms on the website (and not the file name). We typically do this after there has been some kind of communication based error. For submissions, please make sure you have the most recent one by downloading them regularly.
  • We have a position open in the lab for a technical assistant. If you know anyone who you think would be a good fit for the BioMicro Center who is looking for a position, please ask them to apply (mit-00009096).



SEPTEMBER 19, 2012

We hope everyone had a great summer. A couple of updates for you:

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.

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.

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.


JUNE 5, 2012

A couple major Illumina announcements to begin with. First, thanks to the generosity of Dr. Chris Love, the BioMicro Center now has an Illumina MiSeq available. The MiSeq is Illumina’s newest sequencer and is optimized for speed and long read lengths. The MiSeq flowcell contains a single lane with 5 million clusters. While this is well below the 200m reads per lane on the HiSeq, the small surface area enables it to run much faster with a cycle taking only 5 minutes. This means that a 150+150 paired end run can be done in a little over a day, instead of requiring two weeks or more of sequencing. The MiSeq is ideal for applications that do not require enormous read depth, such as microRNA analysis, resequencing of small genomes, barcode sequencing or sequencing amplicons. There are a number of caveats about the MiSeq that can impact your experiment, most notably that there is no separate control lane which means you need to be more careful about base balance, and we are happy to talk with you more about it.

The second announcement is about our venerable GAIIs. As some of you may have noticed, submitting samples for the GAII has been an exercise in extreme patience as we have struggled to fill flowcells due to low demand. The addition of the MiSeq, and some fantastic efforts by Michael Gravina in the lab, has enabled us to rework how we are processing GAII flowcells. We have been able to create partial flowcells on the GAII by altering recipes and making a few minor “modifications”. This has allowed us to move from a model like the HiSeq, where we need a full flowcell before we run, to a model where we can run as soon as the samples pass quality control, more like the MiSeq. However, unlike the MiSeq, we can run multiple lanes at once. Also, running partial flowcells means we can skip parts of the imaging time which does speed up the sequencing (though not to the level of the MiSeq). Some critical caveats: First, these methods are not supported by Illumina, so we cannot offer to replace failed runs. Second, unlike the HiSeq, the PhiX lane is *not* included. You must choose to sequence a lane of PhiX if you want to do control normalization. Finally, this service is completely "a la carte" so the pricing schema is quite different. To go along with these changes, we have completely reworked the Illumina page on our website, so take a look there for more information about the MiSeq, the new GAII methods and pricing.

A couple quick final announcements:

  • Pricing for the next fiscal year is now on the Website. Prices have generally moved lower, though there are slightly higher prices in a few areas.
  • The BioMicro Center will be running on a skeleton staff the week of June 11th (the week of the Building 68 retreat and the KI symposium). There will be some staff on hand but our throughput will be significantly lower than normal.
  • Finally, last month we said goodbye to Barbara Karamapalas who has been running our automation efforts. Stuart Levine will be handling the Tecans while we are looking for a replacement. We will also be having more turnover in the next couple months as well. Our current co-op, Linda Nguyen, will be leaving at the end of June to return to Northeastern and Kevin Thai will be stepping down in July to take a little bit of time off before he returns to MIT as a graduate student. We wish them all the best of luck and we’re looking very aggressively for their replacements!


APRIL 19, 2012

There have been a large number of changes in BioMicro to catch you up on in several different areas since my last newsletter. First, I need to begin by introducing Shmulik Motola, our new lab manager. Shmulik has been on board for several months now and is coordinating the flow of projects through the lab. Shmulik did his graduate work at the Weizmann Institute and was a Postdoctoral Associate in Dr. Ernest Fraenkel’s lab here at MIT. Shmulik is the go to person for questions you have about the status of your projects, Illumina queue times, etc. and can also help you with experimental design (shmulikm@mit.edu)

Second, we have expanded our equipment repertoire with the purchase of a Sage BluePippin preparative electrophoresis system (http://www.sagescience.com/bluepippin/). The Pippin prep is an automated system for extracting bands from agarose gels. We are currently testing the system out and will be deploying it to several of our Illumina library preparation methods. We’re planning to use it as part of the RNAseq methodology to provide much tighter size distributions than the SPRIworks can manage. In addition, high percentage agarose gels should enable us to begin to offer library preparation for small RNA sequencing (contact Shmulik if you would like to volunteer for our beta). Because the BluePippin has a pulse field feature, it should also be useful for building jumping libraries as well as isolating fragments for the new “long read” sequencing technologies, such as Oxford Nanopore. Of course, the Pippin prep is also available for your more “mundane” chores such as isolating bands for cloning.

Finally, our BioInformatics team has had a major overhaul. Dr. Fugen Li left MIT at the end of last year and has been replaced by Dr. Ryan Abo from the Mayo Clinic and Dr. Vincent Butty from Dr. Chris Burge’s lab. Both bring with them years of experience and, along with Dr. Huiming Ding, are available to help with any informatics challenges you have in your research, especially those related to sequencing. In addition to providing direct research support, we are looking forward to offering short classes on informatics beginning in the summer or fall. We’re in the planning stages now so if you have ideas on subjects you would like us to cover, please let us know.

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19 December 2014

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