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{{BioMicroCenter}}
{{BioMicroCenter}}


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== Welcome to the MIT BIOMICRO CENTER ==


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== BioMicro Center News ==


=== April 19, 2010 ===


Starting next month, the [http://mit.edu/ki/index.html Koch Institute] and the MIT BioMicro Center will be hosting a [http://www.nanostring.com/ Nanostring] nCounter system on a trial basis. The [http://www.nanostring.com/products/ncounter/ nCounter system] is a [http://www.nanostring.com/applications/technology/ single molecule visualizer] that quantitatively detects RNA and other nucleic acids using a hybridization system in a highly multiplex manner. The system uses color-coded molecular barcodes to digitally count nucleic acid molecules in solution. The system does not use enzymes for detecting the nucleic acids, allowing direct measurements of mRNA from a variety of input materials including degraded RNA or crude cell lysates.


The instruments will be located in the BioMicro Center and will be available to all members of the MIT community. We will be using this time to gauge the level of interest in the nCounter and whether it would be a viable system to purchase.
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If you are interested in learning more, we will be hosting a seminar with [http://www.nanostring.com/ Nanostring] representatives on April 30th. The seminar will be at 11am in 68-181. Nanostring representatives will be available after the talk to discuss the instruments and specific applications. More information is in the [[Media:Nanostring_abstract.pdf‎|ABSTRACT]] for the talk.
== ABOUT THE BIOMICRO CENTER ==


=== April 1, 2010 ===
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>


Thanks to the generosity of a grant from the [http://www.moore.org/ Moore Foundation] to Dr. Penny Chisholm and ARRA funding to Dr. Chris Burge the BioMicro Center will be significantly expanding our sequencing capacity over the next 4-6 months. The first step of this expansion begins today with the addition of a new [http://www.illumina.com/systems/genome_analyzer_iix.ilmn GAIIx] and [http://www.illumina.com/systems/genome_analyzer/cbot.ilmn cBot] from Illumina. We are working hard to get ''"Ryland"'' and ''"Agustus Gloop"'' up and running and we hope to be able to shorten our queue times very soon!
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"''


=== March 2010 ===
== PUBLICATIONS ==
Due to an increase in the cost of Illumina reagents, increase in data file size, and the complexity of sample preps, we have had to increase, slightly, the cost of Illumina sequencing. These new rates will be effective on samples submitted after April 1, 2010. Samples already in the queue will use the current rates.


{| border=1 align="right"
Publications from [https://www.ncbi.nlm.nih.gov/sites/myncbi/stuart.levine.1/bibliography/47165401/public/?sortby=pubDate&sdirection=descending Stuart Levine]
! ILLUMINA SEQUENCING
!width=100| MIT - current
!width=100| MIT - April 1, 2010
!width=100| unit
! Notes
|-
| Single End (36nt)
|align="right"| $805
|align="right"| $860
|align="center"| per lane
| inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
|-
| Paired End (36+36nt)
|align="right"| $1,385
|align="right"| $1,450
|align="center"| per lane
|
|-
| Add'l 36nt
|align="right"| $295
|align="right"| $300
|align="center"| per lane
|-
| Sample Multiplexing
|align="right"| $0
|align="right"| $50
|align="center"| per 10 samples combined
| Combined over the whole order. Only applies to samples combined by BCM technicians.
|-
| Repriming
|align="right"| $200
|align="right"| $300
|align="center"| per flow cell
| Uses 6nt. Cost is divided by number of lanes requiring repriming. Repriming is required for standard Illumina multiplexing.
|-
|}
<BR>
Non-MIT rates are 30% higher for academic institutions and 50% highers for non-academic institutions. Priority is given to samples from CORE facilities.


== 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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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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16 April 2024

     10:20  Yarn Microfluidics - Roger Dirth‎‎ 12 changes history +442 [Rcostello‎ (12×)]
     
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15 April 2024

     23:43  User:Yanbin Huang‎‎ 2 changes history +170 [Yanbin Huang‎ (2×)]
     
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     22:11  The paper that launched microfluidics - Xi Ning‎‎ 14 changes history +9,705 [Xning098‎ (14×)]
     
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     18:16  Multilayer Paper Microfluidics - Madyson Redder‎‎ 15 changes history +4,948 [Mredder‎ (15×)]
     
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