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| | == Welcome to the MIT BIOMICRO CENTER == |
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| |rowspan=2 valign=top style="width:55%;padding-right:10px;"| | | |valign=top style="width:60%;padding-right:10px;"| |
| | == BioMicro Center News == |
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| === Aug 9, 2010 ===
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| Dear Users,<br>
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| There have been a number of significant changes in the BioMicro Center in the past few months and there will be more to come. To keep you up to date, I will again be sending out a newsletter every month or two with highlights of what is going on. Unlike previous newsletters, these will only be sent to those who have used the facility within the past year or so, so be sure to spread the word if you see items that might be of interest to others in your lab!
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| ====New equipment====
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| A number of pieces of new equipment have been added to the BioMicro Center, particularly in the area of high throughput screening. First, through an equipment grant sponsored by Wendy Gilbert, we have added a second robotic fluidics machine that is specifically geared for screening 96 and 384 well plates. Unlike the older robot, this Tecan has a plate manipulating arm that allows it to handle much larger experiments. We also have added the Fluidigm Biomark which has been relocated from E17 and we are also in the evaluation phase for the Nanostring nCounter. Both of these machines allow you to look at a large number of genes / SNPs across a large number of samples. The Biomark is a nanofluidic RT-PCR machine that creates large matrices (either 48x48 or 96x96) of samples and primers, allowing you to do close to 10,000 RT-PCR reactions on a plate. The nCounter uses a “code set” of up to 800 genes to hybridize to dozens or hundreds of samples, then visualizes the single molecule interactions. The nCounter is particularly interesting in that it does not require conversion of the sample to cDNA, or even purification of the RNA. Information about all of these instruments can be found on our website.
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| ====New services====
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| We are happy to announce the beginning of sample preparation services for Illumina sequencing. We are introducing this service starting with double stranded DNA fragments (>100bp) such as de novo genomic sequencing, resequencing, ChIP-seq and RNA-seq that has been converted to cDNA. The service includes QC, end-repair, adaptor ligation, size selection and enrichment. Once samples are prepared, they are validated and added directly to the Illumina sequencing queue. Right now, this service is limited, but we are hoping to introduce multiplexing and RNA samples in the near future.
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| ====Upcoming Events====
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| With so many changes both in new equipment and upgrades to current equipment we wanted to create an opportunity for you to learn more about the assays available in the facility. To help with this, we will be sponsoring a “Technology Seminar Series” this fall. The weekly seminars will be at noon on Mondays (lunch will be provided). Each week we will showcase a different technology in the facility and bring you up to date on the latest advances and future directions of the technology. We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly.
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| I hope you are having a great summer!<br>
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| -Stuart
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| === May 13, 2010 ===
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| In order to increase the space available for equipment in the BioMicro Center, we are doing a little more remodeling. Please note the following changes:
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| * The freezers have been relocated to the 304 hallway
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| * The RT-PCR machines will be moving to the 316 entry.
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| We hope this change will make accessing the [[BioMicroCenter:RTPCR|RT-PCR]] machines easier and will also create room for the [[BioMicroCenter:Tecan_Freedom_Evo|new Tecan EVO 150]], scheduled to arrive in early June. Keep an eye on this page for future updates!
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| === April 19, 2010 === | | |valign="top"| |
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| 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.
| | == ABOUT THE BIOMICRO CENTER == |
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| 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. | | 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> |
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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.
| | 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"'' |
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| === April 1, 2010 === | | == PUBLICATIONS == |
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| 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!
| | 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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| === March 2010 === | | == PREVIOUS NEWSLETTERS == |
| 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.
| | '''[[BioMicroCenter:News2017+|2017+]]'''<BR> |
| | | '''[[BioMicroCenter:News2016|2016]]'''<BR> |
| {| border=1 align="right"
| | '''[[BioMicroCenter:News2015|2015]]'''<BR> |
| ! ILLUMINA SEQUENCING
| | '''[[BioMicroCenter:News2014|2014]]'''<BR> |
| !width=100| MIT - current
| | '''[[BioMicroCenter:News2013|2013]]'''<BR> |
| !width=100| MIT - April 1, 2010
| | '''[[BioMicroCenter:News2012|2012]]'''<BR> |
| !width=100| unit
| | '''[[BioMicroCenter:News2011|2011]]'''<BR> |
| ! Notes
| | '''[[BioMicroCenter:News2010|2010]]''' |
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| | Single End (36nt)
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| |align="right"| $805
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| |align="right"| $860
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| |align="center"| per lane
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| | inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
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| | Paired End (36+36nt)
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| |align="right"| $1,385
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| |align="right"| $1,450
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| |align="center"| per lane
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| | Add'l 36nt
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| |align="right"| $295
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| |align="right"| $300
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| |align="center"| per lane
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| | Sample Multiplexing
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| |align="right"| $0
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| |align="right"| $50
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| |align="center"| per 10 samples combined
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| | Combined over the whole order. Only applies to samples combined by BCM technicians.
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| | Repriming
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| |align="right"| $200
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| |align="right"| $300
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| |align="center"| per flow cell
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| | Uses 6nt. Cost is divided by number of lanes requiring repriming. Repriming is required for standard Illumina multiplexing.
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| |}
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| Non-MIT rates are 30% higher for academic institutions and 50% highers for non-academic institutions. Priority is given to samples from CORE facilities.
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| ===RECENT & UPCOMING CHANGES=== | | == RECENT CHANGES TO THE WEBSITE == |
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| {{BioMicroCenter:News/Changes/Content}}
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| <B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
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| {|
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| |'''[[BioMicroCenter:News/2009|2009]]'''
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| |-
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| |{{BioMicroCenter:News/2009/Content}}
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| |'''[[BioMicroCenter:News/2008|2008]]'''
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| |-
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| |{{BioMicroCenter:News/2008/Content}}
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| |}
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| <br>
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| <B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
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| {{BioMicroChanges}} | | {{BioMicroChanges}} |
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| |} | | |} |
