|
|
| (79 intermediate revisions by 6 users not shown) |
| Line 1: |
Line 1: |
| {{BioMicroCenter}} | | {{BioMicroCenter}} |
|
| |
|
| | . |
| | == Welcome to the MIT BIOMICRO CENTER == |
| | |
| | {| |
| | |valign=top style="width:60%;padding-right:10px;"| |
| == BioMicro Center News == | | == BioMicro Center News == |
| {|
| |
| |rowspan=2 valign=top style="width:60%;padding-right:10px;"|
| |
|
| |
|
| == 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.<BR><BR>
| |
|
| |
|
| 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, [[BioMicroCenter:Sequencing|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.<BR><BR>
| |
| A couple quick final announcements:
| |
| * Pricing for the next fiscal year is now on the [[BioMicroCenter:PricingFY2013|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!
| |
|
| |
|
| | |valign="top"| |
| | |
| | == ABOUT THE BIOMICRO CENTER == |
|
| |
|
| == APRIL 19, 2012 ==
| | The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [http://biology.mit.edu Department of Biology], the [http://ki.mit.edu Koch Institute for Integrative Cancer Research], the [http://be.mit.edu Department of Biological Engineering] and the [http://cehs.mit.edu MIT Center for Environmental Health Sciences.] The BioMicro Center provides MIT faculty members with integrated facilities for high-throughput data-intensive genomics, bioinformatic analysis, as well as large-scale database storage, management, data mining and data modeling required to fully implement systems approaches to investigate a broad spectrum of biological problems. The BioMicro Center is designed to maximize the likelihood of successfully designing, implementing, and analyzing systems biology data. With an expert staff available for consultation and collaboration, including several full time bioinformatics scientists and experimentalist with significant experience in systems biology, ample resources exist to assist MIT researchers in any aspect of the research project. This unique cross-disciplinary collaboration leverages resources, spreading institutional commitment, and providing an environment that strongly encourages intellectual rapport between scientists that contributes to the success of projects. This collaborative environment creates a unique opportunity for interactions of biologists and biological engineers who study a broad range of problems. Investigators are able to adopt novel techniques to address their topics of interest as well as develop new collaborations throughout the institute. <BR><BR> |
| 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.
| | Experimental and analytical work done in the BioMicro Center is funded by the NIH and must be made available through the NIH's open access policy. All Koch Institute and CEHS labs '''must''' acknowledge their core grants for work done in the core with the following language. |
| | * KI ''"This work was funded by the National Cancer Institute of the NIH under award P30-CA14051"'' |
| | * [[BioMicroCenter:CEHS13|CEHS]] ''"This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"'' |
|
| |
|
| 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.
| | == PUBLICATIONS == |
|
| |
|
| |valign="top"|
| | Publications from [https://www.ncbi.nlm.nih.gov/sites/myncbi/stuart.levine.1/bibliography/47165401/public/?sortby=pubDate&sdirection=descending Stuart Levine] |
|
| |
|
| == PREVIOUS NEWSLETTERS == | | == PREVIOUS NEWSLETTERS == |
| | | '''[[BioMicroCenter:News2017+|2017+]]'''<BR> |
| | | '''[[BioMicroCenter:News2016|2016]]'''<BR> |
| | '''[[BioMicroCenter:News2015|2015]]'''<BR> |
| | '''[[BioMicroCenter:News2014|2014]]'''<BR> |
| | '''[[BioMicroCenter:News2013|2013]]'''<BR> |
| | '''[[BioMicroCenter:News2012|2012]]'''<BR> |
| '''[[BioMicroCenter:News2011|2011]]'''<BR> | | '''[[BioMicroCenter:News2011|2011]]'''<BR> |
| '''[[BioMicroCenter:News2010|2010]]''' | | '''[[BioMicroCenter:News2010|2010]]''' |
