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== Welcome to the MIT BIOMICRO CENTER ==


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== BioMicro Center News ==


=== 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 [[BioMicroCenter:Microarray|microarrays.]] Affymetrix will be retiring their old labeling kits later this year and we have been [[BioMicroCenter:Microarrays#Technology_Updates|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 [[BioMicroCenter:People|Manlin or myself.]]
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In addition to microarrays, we have also upgraded to the latest kits from Illumina for [[BioMicroCenter:Sequencing|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.  [[BioMicroCenter:Genome_Seq|We have placed some of the preliminary analyses on our website under the genomic sequencing section.]]
== ABOUT THE BIOMICRO CENTER ==


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.
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>


Lastly, we are still in the process of [[BioMicroCenter:RenoPlans|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 [[BioMicroCenter:RenoPlans|on our website]] along with all of our monthly updates.
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"''


== PUBLICATIONS ==


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Publications from [https://www.ncbi.nlm.nih.gov/sites/myncbi/stuart.levine.1/bibliography/47165401/public/?sortby=pubDate&sdirection=descending Stuart Levine]
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===RECENT & UPCOMING CHANGES===
 
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== 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:News2010|2010]]'''
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<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
== RECENT CHANGES TO THE WEBSITE ==
 
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Latest revision as of 05:26, 28 March 2023

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

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Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

ABOUT THE BIOMICRO CENTER

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 Department of Biology, the Koch Institute for Integrative Cancer Research, the Department of Biological Engineering and the 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.

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"
  • CEHS "This work was funded by the National Institute of Environmental Health Sciences of the NIH under award P30-ES002109"

PUBLICATIONS

Publications from Stuart Levine

PREVIOUS NEWSLETTERS

2017+
2016
2015
2014
2013
2012
2011
2010

RECENT CHANGES TO THE WEBSITE

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