BioMicroCenter:News

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===JANUARY/FEBRUARY NEWSLETTER===
 
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January/February 2009 - HIGHLIGHTS
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'''May 2009 - HIGHLIGHTS '''
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* New BioMicro Website at http://web.mit.edu/biomicro
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* Improvements in Microarray Processing
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* New plate reader available for use in 68-252d.
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* Improvements in Illumina Sequencing
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* Tecan EVO robotic training Feb 14th
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* Pilot project for large scale data storage
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* BioMicro Center Renovation in February
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* BioMicro Center renovation ongoing.
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It has been a very busy month in the BioMicro Center and we have a number of improvements to share with everyone. First, this month we have activated our new website (http://web.mit.edu/biomicro). This page has information about all of the resources available at the BioMicro Center as well as forms for download, calendars to schedule time on our machines and prices. The website is also set up as a wiki on the OpenWetWare platform to create a repository for information to help optimize experiments and to help shape the site to make it more useful to you. We are continuing to improve the site so check back often. You can [[Join|sign up for a wiki account.]]
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It has been a few months since our last update and I would like to share with everyone several improvements we have made in some of our core technologies.  
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This month we also introduced the Varioskan plate reader. This plate reader can handle plates from 6 to 384 wells and can do fluorometrics, lumisetrics and photometrics at most wavelengths between 200 and 1000nm (there is some variability depending on the application). The Varioskan is also capable of doing real time kinetic experiments and has the ability to add up to three reagents to the plate. The Varioskan is currently located in 68-252d. More information, including data validation and a calendar to schedule time on the Varioskan can be found on [[BioMicroCenter:Varioskan|our website]].
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One large change has been in our handling of microarrays. Affymetrix will be retiring their old labeling kits later this year and we have been evaluating different technologies to replace the old kits. We have tried out new kits for both eukaryotes and prokaryotes and have been pleased with the results. Both new kits require significantly less sample input (<100 ng total RNA) and are easier to handle larger numbers of samples. We are also looking at other labeling techniques that would require even less input RNA (<1ng or even from single cells). More information can be found on our website. If you are interested in some of the newer technologies, please contact Manlin or myself.
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We are also proceeding apace with our activation of the Tecan EVO robotic liquid handler. The EVO is able to automate most routine molecular biology protocols for high-throughput. We have scheduled a training session for the EVO on February 14th with the staff from Tecan. If you are interested in learning about the EVO or the types of reactions that can be run on the machine, or in attending the training session, please contact me.  
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In addition to microarrays, we have also upgraded to the latest kits from Illumina for next-generation sequencing. These new kits replace the old cleavage buffer with a new formulation that allows for much longer reads. We have preformed some tests with these new kits and have been able to achieve read lengths of 144nt (72nt each from the front and back) with over 90% of the reads showing 1 error or less at densities of typically >5 million reads per lane.  We have placed some of the preliminary analyses on our website under the genomic sequencing section.
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Lastly, we are beginning the process of remodeling the BioMicro Center lab space to create more room. We are planning on doing this stepwise so as to have as minimal an impact on our services as possible, though access to portions of the lab may be restricted at times. The final layout is also [[BioMicroCenter:RenoPlans|on our website]] along with all of our monthly updates.  
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We have also started a pilot program to help labs handle the large amounts of data produced by these high-throughput methodologies in response to requests from several labs. We have purchased a new storage server and are providing space on the server at $500 per terabyte per year. The server is set up to be able to be accessed from all three major operating systems (Linux, Windows and Mac) and the data is backed up using MIT’s TSM (normally $65/mo).  Space on this pilot server is limited and will be allocated on a first come / first served basis. Please contact Stephen Goldman or myself if you have questions. More information about this program can be found in the computing section of our website.
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-Stuart Levine
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Lastly, we are still in the process of remodeling the BioMicro Center lab space. Thank you all for your patience as we have been in transition and we hope by the end of this month to have the process completed.  The final layout is also on our website along with all of our monthly updates.

Revision as of 16:21, 9 May 2009

Image:BioMicroCenter-header6.jpg


May 2009 - HIGHLIGHTS

  • Improvements in Microarray Processing
  • Improvements in Illumina Sequencing
  • Pilot project for large scale data storage
  • BioMicro Center renovation ongoing.

It has been a few months since our last update and I would like to share with everyone several improvements we have made in some of our core technologies.

One large change has been in our handling of microarrays. Affymetrix will be retiring their old labeling kits later this year and we have been evaluating different technologies to replace the old kits. We have tried out new kits for both eukaryotes and prokaryotes and have been pleased with the results. Both new kits require significantly less sample input (<100 ng total RNA) and are easier to handle larger numbers of samples. We are also looking at other labeling techniques that would require even less input RNA (<1ng or even from single cells). More information can be found on our website. If you are interested in some of the newer technologies, please contact Manlin or myself.

In addition to microarrays, we have also upgraded to the latest kits from Illumina for next-generation sequencing. These new kits replace the old cleavage buffer with a new formulation that allows for much longer reads. We have preformed some tests with these new kits and have been able to achieve read lengths of 144nt (72nt each from the front and back) with over 90% of the reads showing 1 error or less at densities of typically >5 million reads per lane. We have placed some of the preliminary analyses on our website under the genomic sequencing section.

We have also started a pilot program to help labs handle the large amounts of data produced by these high-throughput methodologies in response to requests from several labs. We have purchased a new storage server and are providing space on the server at $500 per terabyte per year. The server is set up to be able to be accessed from all three major operating systems (Linux, Windows and Mac) and the data is backed up using MIT’s TSM (normally $65/mo). Space on this pilot server is limited and will be allocated on a first come / first served basis. Please contact Stephen Goldman or myself if you have questions. More information about this program can be found in the computing section of our website.

Lastly, we are still in the process of remodeling the BioMicro Center lab space. Thank you all for your patience as we have been in transition and we hope by the end of this month to have the process completed. The final layout is also on our website along with all of our monthly updates.


RECENT & UPCOMING CHANGES

Illumina/Solexa Sequencing -- *New*
New Affymetrix labeling -- *New*
Notes from the ABRF
Tecan EVO high-throughput -- Training Feb 12, 2009
BioMicro Center Renovation -- Coming Feb '09


PREVIOUS NEWSLETTERS

2009
May
January / February
2008
December
November


RECENT CHANGES TO THE WEBSITE <\BIG><\B>


22 July 2014

+      15:16 BioMicroCenter:Software‎ (3 changes) . . (+744) . . (Page history) [Jingzhi Zhu‎ (3×)]

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