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== Welcome to the MIT BIOMICRO CENTER ==
{|
|valign=top style="width:60%;padding-right:10px;"|
== BioMicro Center News ==
== BioMicro Center News ==
{|
=== JULY 2017 ===
|rowspan=2 valign=top style="width:60%;padding-right:10px;"|  
We have several exciting developments to tell you about over the next few months. This month, we have some major changes in our QC with the addition of an [[BioMicroCenter:FemtoPulse|AATI FemtoPulse]] and an upgrade of the [[BioMicroCenter:Advanced_analytical_Fragment_analyzer| AATI Fragment Analyzer]]. <BR><BR>


=== September 16, 2011 ===
[[BioMicroCenter:FemtoPulse|AATI FemtoPulse]] is a redesigned version of the Fragment Analyzer that significantly expands its capabilities. The new instrument can detect nucleic acid down to concentrations of 5 fg/ul – approximately 5000 molecules of a 1kb fragment. In addition, it will incorporate a pulse field generator allowing it to separate fragments of over 200kb.  Advanced Analytical has provided us an early instrument in the hope of identifying novel applications that require this extreme sensitivity. The Femto Pulse was donated to the BioMicro Center by the MIT Center for Environmental Health Sciences. We will be scheduling a Technology Seminar to introduce the FemtoPulse in the fall.<BR><BR>


Dear users,
Next week we will also be upgrading our [[BioMicroCenter:Advanced_analytical_Fragment_analyzer|AATI Fragment Analyzer]] from a 12 capillary to a 48 capillary machine to address consistent and increasing backlogs on the instrument. This expanded capacity will allow us to batch many more samples on each run. A side effect of this upgrade is we will need to likely move some smaller projects back to the Agilent BioAnalyzer to avoid wasting reagents.  For the moment, we will not be adjusting the rates of batched samples.<BR><BR>


I hope everyone had a great summer. I have a few updates for on recent changes in the BioMicro Center.
Deployment of the Femto Pulse and upgrade of the Fragment Analyzer will occur this coming Monday to Wednesday. During this time, there may be some delays while the instruments are installed and serviced. We will also use this time to upgrade the iLab sample submission system, so we ask for your patience while we roll these changes out.<BR><BR>


First, we will be running the Technology Seminar Series again this year. This seminar series is designed to showcase a different technology in the facility each month and to bring you up to date on the latest advances and future directions of the technology in the BioMicro Center. The seminar is on Tuesdays at noon in 68-181 and lunch will be provided. 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. The first session will be in just under two weeks with Tecan presenting on the robotics systems we have in the core. The full schedule is being maintained on our website at http://openwetware.org/wiki/BioMicroCenter:Technology_Seminar_Series.
=== APRIL 2017 ===
We have used the sunsetting of the [[BioMicroCenter:Neoprep|Illumina Neoprep]] as an opportunity to re-evaluate all of our library prep methodologies with an eye on significantly reducing library preparation costs. We’re now ready to roll out hand preparation for these methods as well as some of our automation to help smooth the transition. We plan to bring in scientists from the different manufacturers we’ve been looking at through our Technology Seminar Series to answer any questions you may have. For all of the methods, we will have a single sample price as well as a batch price that will be significantly cheaper per sample. Below are the RNAseq methods that are already locked in.
{|border="1"
|Method / Kit
|Per sample ||Per 24 ||Per 96 / 384
|-
|polyA RNA (>50ng):<BR>Kapa Hyperprep
|$150 ||$2,000 (est) ||NA
|-
|3’Digital Gene Expression
|NA ||$1,200 ||$4,000
|-
|Ribosomal Depletion (human/mouse):<BR>Kapa RiboGone
|$225 || TBD || TBD
|-
|Ribosomal Depletion (other):<BR>Illumina Ribozero + Kapa Hyperprep
|$250 || TBD || NA
|-
|Low input polyA:<BR>Clontech SMARTseq v4
|$300 || $1,600 || $2,500 / $5,000
|-
|Low input ribosomal depletion (human/mouse) <BR> Clontech ZapR kit
  |$200 || TBD || TBD
|}
Please note that we do not consider this problem ‘solved’ and we are continuing to work on adapting new protocols with the aim of lowering cost while maintaining quality. We also are not yet complete with the process of getting everything listed in iLabs which will happen over the next couple weeks. The Neoprep will be shut down on July 31.<BR><BR>


Second, we are just rolling out our newest service: Automated chromatin IP. Over the past few months we have been evaluating the IP-Star technology from Diagenode. We’ve had enough success that the instrument has been purchased and we are now offering ChIP services. The IP-star takes as input sonicated crosslinked chromatin from ~5 million cells and antibody, and ends with purified DNA. The DNA can be used for either gene specific analysis or can be carried directly in to Illumina library preparation and ChIP-seq. We have validated one set of buffer conditions that have worked robustly but the system is capable of handling a broad range of alternative conditions and can even be used to test several conditions simultaneously. I do want to point out that this is still an experimental technology and remains sensitive to most of the complexities of ChIP (requiring good antibodies and chromatin preparations) so our “guarantee” of success is much more limited than most of our other technologies, but we have seen some very promising results from our early adopters.
A second area we continue to address is data storage. With recent expansions to the systems, we are able to significantly lower our data storage costs for next year. Active storage will now be $200/TB/y while archival storage (read only) will be at $100/TB/y.<BR><BR>


Finally, for those of you following the Agilent BioAnalyzer saga, we’re hoping we are at the end of it now and that the high sensitivity DNA chips are back on line. We’re still cleaning up our backlog so sample processing remains slower than we would like but I’m hoping within a week we’ll be back to normal. I do want to thank the technicians in the lab who have been working extra hours on an extremely frustrating problem to get the issue resolved.  
Finally, many of you may have heard about a recent issue of “index switchng” or “pad swapping” on Illumina sequencers from a bioRxiv preprint from Stanford or social media (http://biorxiv.org/content/early/2017/04/09/125724). We have been well aware of this issue for many years and that it is endemic in all Illumina sequencers (we called it “barcode swapping” in house). Fortunately for us, the non-patterned flowcells (such as MiSeq, NextSeq and HiSeq2000) have a significantly lower issue with this than the newer instruments. Even so, the low level of index switching we have observed (~0.1% of reads for most runs) is a primary reason we have resisted mixing libraries from different labs on single sequencing lanes. If you have any questions/concerns about this instrument ‘feature’, we are happy to discuss it with you. Our hope is the new emphasis on this issue for the patterned flowcells will result in improved methodologies that further lower the likelihood of barcode swaps.  


As always, this newsletter is only sent to people who have used the BioMicro Center within the past couple years, so feel free to forward this on to anyone else who might be interested.  
=== 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>


Best regards,
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>
-Stuart Levine


--
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>
--
Stuart Levine, PhD
BioMicro Center Director                              slevine@mit.edu
Massachusetts Institute of Technology                617-452-2949
77 Massachusetts Ave. 68-304d                    (f) 617-258-xxxx
Cambridge, MA 02139                              (c) 617-312-1286
http://web.mit.edu/biomicro/


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]].




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


I hope everyone is having a great summer. I have a few updates for on recent changes in the BioMicro Center.
|valign="top"|
 
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>
 
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
 
=== May 24, 2011 ===
 
 
Dear users,


We have a number of updates to let you all know about that have happened in the last few months.
== ABOUT THE BIOMICRO CENTER ==


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]].
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>


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]].
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"''


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]].
== PUBLICATIONS ==
Please note the publication aspect of OWW is not working. This section is disabled.
<!--
'''2015'''<BR><BR>
<biblio>
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#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->
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'''2014'''<BR><BR>
<biblio>
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#Paper16 pmid=24630729 <!- AJ Jacks4->
#Paper17 pmid=25477501 <!- VB Boyer2->
#Paper18 pmid=25348403 <!- RPA.SL Dedon ->


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.
 
</biblio>


Thank you all for your support,
'''2013'''<BR><BR>
<biblio>
#Paper1 pmid=23662897 <!- BMC Paper->
#Paper2 pmid=23657361 <!- HD Chisholm->
#Paper3 pmid=23352431 <!- HD.VB Boyer->
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'''2012'''<BR><BR>
<biblio>
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'''2011'''<BR><BR>
<biblio>
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'''2010'''<BR><BR>
<biblio>
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#Paper2 pmid=20581084 <!-SL Zwaka->
</biblio>
'''2009'''<BR><BR>
<biblio>
#Paper1 pmid=19531355 <!-SL Amon->
</biblio>


-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>
 
 
 
 
|valign="top"|


== PREVIOUS NEWSLETTERS ==
== PREVIOUS NEWSLETTERS ==
 
'''[[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:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2010|2010]]'''
'''[[BioMicroCenter:News2010|2010]]'''

Revision as of 11:39, 21 July 2017

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

.

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

JULY 2017

We have several exciting developments to tell you about over the next few months. This month, we have some major changes in our QC with the addition of an AATI FemtoPulse and an upgrade of the AATI Fragment Analyzer.

AATI FemtoPulse is a redesigned version of the Fragment Analyzer that significantly expands its capabilities. The new instrument can detect nucleic acid down to concentrations of 5 fg/ul – approximately 5000 molecules of a 1kb fragment. In addition, it will incorporate a pulse field generator allowing it to separate fragments of over 200kb. Advanced Analytical has provided us an early instrument in the hope of identifying novel applications that require this extreme sensitivity. The Femto Pulse was donated to the BioMicro Center by the MIT Center for Environmental Health Sciences. We will be scheduling a Technology Seminar to introduce the FemtoPulse in the fall.

Next week we will also be upgrading our AATI Fragment Analyzer from a 12 capillary to a 48 capillary machine to address consistent and increasing backlogs on the instrument. This expanded capacity will allow us to batch many more samples on each run. A side effect of this upgrade is we will need to likely move some smaller projects back to the Agilent BioAnalyzer to avoid wasting reagents. For the moment, we will not be adjusting the rates of batched samples.

Deployment of the Femto Pulse and upgrade of the Fragment Analyzer will occur this coming Monday to Wednesday. During this time, there may be some delays while the instruments are installed and serviced. We will also use this time to upgrade the iLab sample submission system, so we ask for your patience while we roll these changes out.

APRIL 2017

We have used the sunsetting of the Illumina Neoprep as an opportunity to re-evaluate all of our library prep methodologies with an eye on significantly reducing library preparation costs. We’re now ready to roll out hand preparation for these methods as well as some of our automation to help smooth the transition. We plan to bring in scientists from the different manufacturers we’ve been looking at through our Technology Seminar Series to answer any questions you may have. For all of the methods, we will have a single sample price as well as a batch price that will be significantly cheaper per sample. Below are the RNAseq methods that are already locked in.

Method / Kit Per sample Per 24 Per 96 / 384
polyA RNA (>50ng):
Kapa Hyperprep 		$150 $2,000 (est) NA
3’Digital Gene Expression NA $1,200 $4,000
Ribosomal Depletion (human/mouse):
Kapa RiboGone 		$225 TBD TBD
Ribosomal Depletion (other):
Illumina Ribozero + Kapa Hyperprep 		$250 TBD NA
Low input polyA:
Clontech SMARTseq v4 		$300 $1,600 $2,500 / $5,000
Low input ribosomal depletion (human/mouse)
Clontech ZapR kit 		$200 TBD TBD

Please note that we do not consider this problem ‘solved’ and we are continuing to work on adapting new protocols with the aim of lowering cost while maintaining quality. We also are not yet complete with the process of getting everything listed in iLabs which will happen over the next couple weeks. The Neoprep will be shut down on July 31.

A second area we continue to address is data storage. With recent expansions to the systems, we are able to significantly lower our data storage costs for next year. Active storage will now be $200/TB/y while archival storage (read only) will be at $100/TB/y.

Finally, many of you may have heard about a recent issue of “index switchng” or “pad swapping” on Illumina sequencers from a bioRxiv preprint from Stanford or social media (http://biorxiv.org/content/early/2017/04/09/125724). We have been well aware of this issue for many years and that it is endemic in all Illumina sequencers (we called it “barcode swapping” in house). Fortunately for us, the non-patterned flowcells (such as MiSeq, NextSeq and HiSeq2000) have a significantly lower issue with this than the newer instruments. Even so, the low level of index switching we have observed (~0.1% of reads for most runs) is a primary reason we have resisted mixing libraries from different labs on single sequencing lanes. If you have any questions/concerns about this instrument ‘feature’, we are happy to discuss it with you. Our hope is the new emphasis on this issue for the patterned flowcells will result in improved methodologies that further lower the likelihood of barcode swaps.

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.

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07:38 Xning098 talk contribs uploaded File:XiNingDrawnSetup2.png ‎
     
07:35 Xning098 talk contribs uploaded a new version of File:Figure 2 Set-up1.png ‎
     
07:24 Xning098 talk contribs uploaded File:DrawnElectoosmoticflow.jpeg ‎
     05:25  Ernesto-Perez-Rueda:Contact‎ diffhist −94‎ Ernesto Perez-Rueda talk contribs

25 April 2024

      23:55  Flow and Pattern Asymmetries‎‎ 46 changes history −21‎ [Courtneychau‎ (46×)]
     
23:55 (cur | prev) −14‎ Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
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23:55 (cur | prev) −31‎ Courtneychau talk contribs (→‎Stokes Flow)
     
23:54 (cur | prev) −151‎ Courtneychau talk contribs (→‎Stokes Flow)
     
23:50 (cur | prev) +184‎ Courtneychau talk contribs (→‎References)
     
23:46 (cur | prev) 0‎ Courtneychau talk contribs (→‎Active Mixing Methods)
     
23:46 (cur | prev) +1‎ Courtneychau talk contribs (→‎Passive Mixing Methods)
     
23:45 (cur | prev) 0‎ Courtneychau talk contribs (→‎Chaotic Advection)
     
23:44 (cur | prev) 0‎ Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
23:43 (cur | prev) +28‎ Courtneychau talk contribs (→‎Stokes Flow)
     
23:39 (cur | prev) +1‎ Courtneychau talk contribs (→‎Stokes Flow) Tag: Manual revert
     
23:38 (cur | prev) −1‎ Courtneychau talk contribs (→‎Stokes Flow)
     
23:37 (cur | prev) +11‎ Courtneychau talk contribs
     
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23:33 (cur | prev) 0‎ Courtneychau talk contribs (→‎References)
     
23:30 (cur | prev) +3‎ Courtneychau talk contribs (→‎Passive Mixing Methods)
     
23:28 (cur | prev) −426‎ Courtneychau talk contribs
     
23:16 (cur | prev) +1,656‎ Courtneychau talk contribs (→‎References)
     
23:14 (cur | prev) 0‎ Courtneychau talk contribs (→‎Applications of Asymmetric Flow)
     
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23:10 (cur | prev) 0‎ Courtneychau talk contribs (→‎Chaotic Advection)
     
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23:04 (cur | prev) −179‎ Courtneychau talk contribs (→‎Applications of Asymmetric Flow)
     
23:03 (cur | prev) +16‎ Courtneychau talk contribs (→‎Pneumatic Valves and Mixers)
     
23:02 (cur | prev) +16‎ Courtneychau talk contribs (→‎Active Mixing Methods)
     
23:02 (cur | prev) −334‎ Courtneychau talk contribs (→‎Active Mixing Methods)
     
22:56 (cur | prev) −415‎ Courtneychau talk contribs (→‎Passive Mixing Methods)
     
22:52 (cur | prev) −115‎ Courtneychau talk contribs (→‎Herringbone Mixer)
     
22:52 (cur | prev) −457‎ Courtneychau talk contribs (→‎Passive Mixing Methods)
     
22:38 (cur | prev) 0‎ Courtneychau talk contribs (→‎Microfluidic Mixers)
     
22:35 (cur | prev) −315‎ Courtneychau talk contribs (→‎Mixing on the Microfluidic Scale)
     
22:14 (cur | prev) 0‎ Courtneychau talk contribs (→‎Stokes Flow)
     
22:12 (cur | prev) 0‎ Courtneychau talk contribs (→‎Péclet Number (Pe))
     
22:11 (cur | prev) +6‎ Courtneychau talk contribs (→‎Reynolds Number (Re))
     
22:10 (cur | prev) +2‎ Courtneychau talk contribs (→‎Diffusion and Advection)
     
22:07 (cur | prev) +2‎ Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
22:05 (cur | prev) +2‎ Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
22:04 (cur | prev) +4‎ Courtneychau talk contribs (→‎Fundamentals of Mixing)
     
22:02 (cur | prev) +471‎ Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
21:52 (cur | prev) +78‎ Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
21:50 (cur | prev) +6‎ Courtneychau talk contribs (→‎Asymmetries in Microfluidics)
     
21:44 (cur | prev) −1‎ Courtneychau talk contribs (→‎Twists and Bends)
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