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== Welcome to the MIT BIOMICRO CENTER ==
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== BioMicro Center News ==
== BioMicro Center News ==
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=== JANUARY 2017 ===
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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>


=== JULY 2, 2011 ===
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>
Dear users,


I hope everyone is having a great summer. I have a few updates for on recent changes in the BioMicro Center.
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>


First, by popular demand we are announcing that our RNA seq sample preparation service is officially accepting samples. This service requires 100ng of high quality eukaryotic RNA as input and is based on the Illumina TruSeq RNAseq kits coupled with the SPRIworks sample preparation robot. The initial price is $350/sample, which is a little more than then price of a microarray preparation. While the service is open, we are still in the tweaking stage and we are evaluating a number of different protocols that could reduce the total RNA amount or lower the quality of the RNA needed. We do hope to have these questions resolved in the very near future, but the quality of the data we have been getting has been sufficient that we wanted to open the service up to everyone.<BR><BR>
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]].


Second, prices for all of our services were updated on July 1st. Many prices are decreasing. A few key things to notice:
* Agilent microarray prices are dropping to be significantly lower than Affymentrix. A full experiment can cost $350/array.
* HiSeq lane prices have decreased – particularly for paired end samples. GAII prices have also dropped a little.
* Robotics usage prices are now set in two hour blocks instead of on a “per session” basis.
* Fluidigm usage prices will be rising to help defray repair costs.
The full list can be found '''[[BioMicroCenter:Pricing|on our pricing page]]<BR><BR>


Finally, this month we have a number of personnel changes. Katie Sullivan and Justin Elliot will be returning to Northeastern with our thanks for six months of hard work, and our new co-ops Jessica Lebowitz and Kaitlyn Sanders, will be starting on July 5th. Jessica and Kaitlyn will be taking over operation of the BioAnalyzer/LabChip and other sample quality control services. In addition, we will be adding a new bioinformaticist, Dr. Huming Ding, to the Center in early July. Dr. Ding comes to us from the University of Toronto where he worked extensively with Dr. Charlie Boone on high throughput screening of genetic interactions and will be helping us establish pipelines for analyzing Illumina data. Please say hello and make them feel welcome the next time you stop by!<BR><BR>
Best regards and have a happy Fourth of July!<BR>
-Stuart Levine


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=== May 24, 2011 ===
== 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>


Dear users,
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"''


We have a number of updates to let you all know about that have happened in the last few months.
== 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 ->


First, we have continued to expand our [[BioMicroCenter:Illumina Library Preparation|DNA sample preparation services]]  . Over the past few months, we have been experimenting with the Nextera sample prep kit to complement our SPRIworks service. Where the SPRIworks system uses sonicated DNA, the Nextera kit is built to handle intact genomic DNA, using a transposase to fragment the DNA and is particularly suitable for applications that use entire genomic DNA, including copy number variation and de novo and resequencing projects. In addition, we have taken advantage of recent work from the Broad to improve our library representation by modifying our amplification protocol. The Nextera service is now available through BioMicro for the same price as the SPRIworks system and includes molecular [[BioMicroCenter:Multiplex|barcoding]] of the library. For more information about the Nextera system, please email  [[BioMicroCenter:People|Ryan Sinapius]].
 
</biblio>


In the [[BioMicroCenter:Microarrays|microarray]] area, we have made significant improvements to our Agilent microarray service. First, we have upgraded our scanner to 2um resolution, which will allow scanning of Agilent’s newest 1 million feature arrays. This has been coupled with an upgrade of the scanning and analysis software that can now handle additional quality controls. In addition, we have been working with Agilent to bring down the prices of their microarrays and we will be able to offer them at a significant discount beginning in July that will bring the [[BioMicroCenter:Pricing|price]] of microarray analysis down significantly. For more information about changes in the Agilent platform, please talk with [[BioMicroCenter:People|Manlin Luo]].
'''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>


Finally, in response to user demand we have purchased a number of licenses for TIBCO Spotfire Analytics. Spotfire is a widely used data analysis and visualization tool. It can handle a number of clustering functions and statistical tests and has very robust graphical capabilities. If you are interested in trying out Spotfire, please contact [[BioMicroCenter:People|Stephen Goldman]].
-->
 
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.
 
Thank you all for your support,
 
-Stuart Levine
 
=== Jan 2011 ===
Dear Users,<BR><BR>
I hope everyone had a great holiday. We have a couple updates as we begin the year.<BR><BR>
One of our goals for this year is to reduce our turnaround time as much as we can. We’ve taken a couple steps in this direction (though we have a long way to go!). First, we have brought a number of additional technicians on board. Michael Gravina joins us from Alnylam and will be working on the Illumina platform. Barbara Karampalas is joining us part time to work on automation. In addition we added two new coop students, Katie Sullivan and Justin Elliott, who will be taking Eris’ place as he returns to Northeastern, and we are looking to make an additional hire in the bioinformatics area (in collaboration with the Koch Institute Bioinformatics and Computing Core). Make sure you say hello the next time you stop by.<BR><BR>
In addition to new staff, we have also upgraded some of our equipment. This week we are adding a new Caliper LabChip system. The LabChip is a high throughput version of the Agilent BioAnalyzer (which uses Caliper technology) and can process hundreds of samples in a batch. Our on-site testing with the LabChip had a significant effect on the speed at which we were able to handle quality control. In order to automate the process, we will have to increase the minimum volume of sample we accept (to 5ul). For most applications, simply diluting your samples 2 fold prior to submission will be sufficient. We will be using the LabChip to handle high sensitivity DNA and standard RNA samples while small RNA, pico RNA and protein samples will continue to be run on the BioAnalyzer.  Prices for the LabChip and the BioAnalyzer will be the same but we will be able to offer discounts on large sample submissions that are run on the Caliper. <BR><BR>
Finally, we are in the finishing stages of beta testing our new RNA-seq sample prep service.  An addition to our existing DNA sample prep, we will be able to accept submissions of total RNA for sequencing just as we do for microarrays. Our current protocol is derived from Chris Burge’s lab but we are also testing kits from NuGEN for digital gene expression (DGE) which we hope will offer microarray quality results for considerably lower costs. If you are interested in helping out and have samples you are willing to contribute, please contact Ryan Sinapius who is coordinating the effort. <BR><BR>
As a reminder, this email only goes out to people who are have used the BioMicro Center within the past couple years. Please feel free to forward this message on to anyone else who might be interested.<BR><BR>
Thank you all for your support,<BR><BR>
-Stuart Levine<BR><BR>
 
 
 
 
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== PREVIOUS NEWSLETTERS ==
== 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]]'''
'''[[BioMicroCenter:News2010|2010]]'''
<br>


<br>
== RECENT CHANGES TO THE WEBSITE ==
== 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

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25 April 2024

     00:22  The paper that launched microfluidics - Xi Ning‎‎ 7 changes history +4,723 [Xning098‎ (7×)]
     
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24 April 2024

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23 April 2024

     15:33  "Pick and Place" Assembly of Parts Using PDMS - Amy Lim, Rylie Costello‎‎ 6 changes history +837 [Rcostello‎ (6×)]
     
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22 April 2024

     19:28  "Pick and Place" Assembly of Parts Using PDMS - Amy Lim, Rylie Costello‎‎ 2 changes history −2 [Rcostello‎ (2×)]
     
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