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{{BioMicroCenter}}
{{BioMicroCenter}}


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== Welcome to the MIT BIOMICRO CENTER ==


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===JANUARY/FEBRUARY NEWSLETTER===
== BioMicro Center News ==
=== JANUARY 2017 ===
BMC is officially moving almost all of our sample intake to [https://mit.ilabsolutions.com iLabs]. We have spent the past several months moving the forms for Illumina library prep, sequencing and Pacbio sequencing over to the new system and testing it out - thank you to the labs that helped us with our beta testing! You can find BMC in iLabs at https://mit.ilabsolutions.com/ in the KI Genomics Core / MIT BioMicro Center section. The new forms are under "Request Services". All projects using MIT cost objects should use iLabs going forward. Projects being billed to outside groups or by PO should continue to use the forms on the website.<BR><BR>


January/February 2009 - HIGHLIGHTS
The [[BioMicroCenter:Covaris|Covaris E220]] is now up and running. We will be having a [[BioMicroCenter:Technology_Seminar_Series|seminar for it on January 11th]] (details TBA). Our Covaris rep will be on hand that day to help you set up your protocols as well. Please let Jon or myself know if you would like to schedule time. There is no charge for this retraining. <BR><BR>
* New BioMicro Website at http://web.mit.edu/biomicro
* New plate reader available for use in 68-252d.
* Tecan EVO robotic training Feb 14th
* BioMicro Center Renovation in February


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.]]
The price for SYBR green is decreasing significantly to $25/ml. In the fall, we compared a number of new providers based on their ability to quantify Illumina libraries. Of the two we tested, one preformed as well as KAPA (the other did not). KAPA, in turn, was able to lower the cost of their SYBR significantly which we prefer as it will maintain consistency. Due to the lower cost, we are also removing the pooling charges from Illumina sequencing - those costs are being absorbed into the QC costs instead. The Roche SYBR did not match this lower cost and we will be discontinuing our bulk purchases of it.<BR><BR>


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]].
Finally, we are introducing a significantly cheaper library prep for [[BioMicroCenter:DNA_HTL|very high-throughput experiments]]. We have been collaborating closely with [http://ttplabtech.com/liquid-handling/mosquito_hv/ TTP Labtech to adapt their Mosquito] liquid handler for core facility settings. Our first method is NexteraXT. Using the Mosquito, we have been able to reduce the reaction volume by an order of magnitude. A 96 well plate will cost <$15/sample and a 384 well plate is under $7.50/sample. These new methods are ideally suited for single cell and amplicon work but are NOT well suited for de novo assembly as the library complexity is lower due to the lower amount of input DNA. TTP will be giving the [[BioMicroCenter:Technology_Seminar_Series|seminar in February]].


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.


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.


-Stuart Levine
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== 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 [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 offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina platform (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms are also part of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the [http://ki.mit.edu Koch Institute] as the [http://ki.mit.edu/sbc/microarray MicroArray Technologies Core] and as part of the [http://ki.mit.edu/sbc/bioinformatics Bioinformatics and Computing Core] and the [http://cehs.mit.edu MIT Center for Environmental Health Sciences] as part of the [http://cehs.mit.edu/facilities.html#Genomics_and_Bioinformatics_Core Genomics and Imaging Core]<BR><BR>
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===RECENT & UPCOMING CHANGES===
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"''


{{BioMicroCenter:News/Changes/Content}}
== PUBLICATIONS ==
Please note the publication aspect of OWW is not working. This section is disabled.
<!--
'''2015'''<BR><BR>
<biblio>
#Paper1 pmid=25837992 <!- SL.JW Essig->
#Paper2 pmid=25477501 <!- VB Boyer->
#Paper3 pmid=25561496 <!- AJ Sharp->
#Paper4 pmid=26163349 <!- HD.CW Hynes->
#Paper5 pmid=26341558 <!- AJ.CW Gertler Jacks->
#Paper6 pmid=26510153 <!- VB Saeij->
#Paper7 pmid=26522011 <!- HD Chisholm->
</biblio>
'''2014'''<BR><BR>
<biblio>
#Paper1 pmid=24501120 <!- RPA Walker->
#Paper2 pmid=24501121 <!- RPA Walker->
#Paper3 pmid=24249727 <!- VB Saeij->
#Paper4 pmid=24757057 <!- RPA.VB Samson->
#Paper5 pmid=24763590 <!- HD Chisholm->
#Paper6 pmid=24899568  <!- VB.SL Dedon->
#Paper7 pmid=24931974 <!- VB Burge->
#Paper8 pmid=24413286 <!- RPA.SL Tannenbaum Fox->
#Paper9 pmid=25333635 <!- VB.SL Boyer->
#Paper10 pmid=25197050 <!- JW.CW Amon->
#Paper11 pmid=25037231 <!- CW Hynes->
#Paper12 pmid=25337879 <!- AJ Jacks->
#Paper13 pmid=24954536 <!- AJ Jacks2->
#Paper14 pmid=24788094 <!- AJ Sharp->
#Paper15 pmid=24711431 <!- AJ Jacks3->
#Paper16 pmid=24630729 <!- AJ Jacks4->
#Paper17 pmid=25477501 <!- VB Boyer2->
#Paper18 pmid=25348403 <!- RPA.SL Dedon ->


 
</biblio>


<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
'''2013'''<BR><BR>
<biblio>
#Paper1 pmid=23662897 <!- BMC Paper->
#Paper2 pmid=23657361 <!- HD Chisholm->
#Paper3 pmid=23352431 <!- HD.VB Boyer->
#Paper4 pmid=23630078 <!- CW.AJ Sharp->
#Paper5 pmid=23523371 <!- CW Jacks->
#Paper6 pmid=23990805 <!- SL.VB Boyer->
#Paper7 pmid=24009526 <!- CW Lees->
#Paper8 pmid=23873940 <!- CW Jacks2->
#Paper10 pmid=24134150 <!- SL.RPA Tannenbaum->
#Paper11 pmid=24367253 <!- VB Saeij->
#Paper12 pmid=23703590 <!- SM Fraenkel ->
</biblio>
'''2012'''<BR><BR>
<biblio>
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
#Paper2 pmid=22847430 <!-SL Saeij->
#Paper3 pmid=22102570 <!-HD Chisholm->
</biblio>
'''2011'''<BR><BR>
<biblio>
#Paper1 pmid=21892155 <!-SL Sur->
</biblio>
'''2010'''<BR><BR>
<biblio>
#Paper1 pmid=20720539 <!-SL Young->
#Paper2 pmid=20581084 <!-SL Zwaka->
</biblio>
'''2009'''<BR><BR>
<biblio>
#Paper1 pmid=19531355 <!-SL Amon->
</biblio>


{|
-->
|-
|'''[[BioMicroCenter:News/2008|2008]]'''
|-
|{{BioMicroCenter:News/2008/Content}}
<!-- Remove Comments when Jan 2009 Newsletter is ready
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|'''[[BioMicroCenter:News/2009|2009]]'''
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|{{BioMicroCenter:News/2009/Content}}
Remove Comments when Jan 2009 Newsletter is ready -->
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== PREVIOUS NEWSLETTERS ==
'''[[BioMicroCenter:News2015|2015]]'''<BR>
'''[[BioMicroCenter:News2014|2014]]'''<BR>
'''[[BioMicroCenter:News2013|2013]]'''<BR>
'''[[BioMicroCenter:News2012|2012]]'''<BR>
'''[[BioMicroCenter:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2010|2010]]'''
<br>
<br>
<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
 
== RECENT CHANGES TO THE WEBSITE ==
{{BioMicroChanges}}
{{BioMicroChanges}}


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Revision as of 09:52, 3 January 2017

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

.

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

JANUARY 2017

BMC is officially moving almost all of our sample intake to iLabs. We have spent the past several months moving the forms for Illumina library prep, sequencing and Pacbio sequencing over to the new system and testing it out - thank you to the labs that helped us with our beta testing! You can find BMC in iLabs at https://mit.ilabsolutions.com/ in the KI Genomics Core / MIT BioMicro Center section. The new forms are under "Request Services". All projects using MIT cost objects should use iLabs going forward. Projects being billed to outside groups or by PO should continue to use the forms on the website.

The Covaris E220 is now up and running. We will be having a seminar for it on January 11th (details TBA). Our Covaris rep will be on hand that day to help you set up your protocols as well. Please let Jon or myself know if you would like to schedule time. There is no charge for this retraining.

The price for SYBR green is decreasing significantly to $25/ml. In the fall, we compared a number of new providers based on their ability to quantify Illumina libraries. Of the two we tested, one preformed as well as KAPA (the other did not). KAPA, in turn, was able to lower the cost of their SYBR significantly which we prefer as it will maintain consistency. Due to the lower cost, we are also removing the pooling charges from Illumina sequencing - those costs are being absorbed into the QC costs instead. The Roche SYBR did not match this lower cost and we will be discontinuing our bulk purchases of it.

Finally, we are introducing a significantly cheaper library prep for very high-throughput experiments. We have been collaborating closely with TTP Labtech to adapt their Mosquito liquid handler for core facility settings. Our first method is NexteraXT. Using the Mosquito, we have been able to reduce the reaction volume by an order of magnitude. A 96 well plate will cost <$15/sample and a 384 well plate is under $7.50/sample. These new methods are ideally suited for single cell and amplicon work but are NOT well suited for de novo assembly as the library complexity is lower due to the lower amount of input DNA. TTP will be giving the seminar in February.


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 offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina platform (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms are also part of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Institute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core

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

Please note the publication aspect of OWW is not working. This section is disabled.

PREVIOUS NEWSLETTERS

2015
2014
2013
2012
2011
2010

RECENT CHANGES TO THE WEBSITE

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18 April 2024

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