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== Welcome to the MIT BIOMICRO CENTER ==


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|valign=top style="width:60%;padding-right:10px;"|  
==DECEMBER NEWSLETTER==
== 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 [[BioMicroCenter:FemtoPulse|AATI FemtoPulse]] and an upgrade of the [[BioMicroCenter:Advanced_analytical_Fragment_analyzer| AATI Fragment Analyzer]]. <BR><BR>


Happy Holidays,
[[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>


We have had a very busy month and have been moving very quickly to reinvigorate the BioMicro Center. Last week, we welcomed Allison Perrotta who has joined us as a technical associate. Allison is a graduate of UNH and has spent the past year working for EPIX pharmaceuticals. She will be working with Manlin on handling Affymetrix microarrays and Illumina sequencing samples.  Please feel free to say hi the next time you come by the center.
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>


This month, I would like to highlight three areas BioMicro is currently focusing on where I would be very interested in receiving feedback from our users. The first is our effort to speed up the turnaround time for Affymetrix arrays. In addition to adding more hands, we have the opportunity to double our number of active fluidics stations for free by pre-ordering a (large) number of GeneChips.  The concern with placing such a large order is that some of the arrays will not be used. In order to minimize this risk, it would be very helpful if anyone who is planning on using Affymetrix arrays in the next 4-6 months could send me an email with an estimate of the number and types of arrays you are thinking of using. We will then use these estimates in planning our pre-order.
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 role these changes out.<BR><BR>


Second, in addition to improving our Affymetrix turn around time, we are also re-activating our high throughput liquid handling robot (a Tecan Evo 150). Because we have not used this robot in several years, we will be scheduling a training session in the next few weeks once we get the robot back under a service agreement. Once the machine is operational, we will make it available to anyone who has been trained to use it and will be posting signups for it on our website. If you are interested in learning more about the current functionalities of the Tecan or would be interested in coming to the training session, please send me an email.  
=== 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>


Finally, several labs have approached us regarding computational resources, specifically about data storage. We are currently examining several different options that would allow us to provide data storage on an “as needed” basis to our users. One idea we are investigating is to provide server space on BioMicro managed machines at a fairly low cost (~$400 - $600 per year per terabyte). This fee would include all administrative costs as well as daily TSM backups (normally $65/month), and would allow our users to purchase only the amount of memory they need. However, because of the vast array of different storage devices on the market, it would be very helpful if we knew how many labs would be interested in this type of a service. So, again, if you would consider this type of a service, or have any questions, please send me an email.
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>


Thank you all in advance for your feedback. I really do appreciate your help in improving the work we do in the BioMicro Center. We do have many other projects going on right now including a complete revamp of our website and a renovation of the BioMicro Center lab space that I hope to be able to tell you more about soon. Once again, my door is always open and I hope to be chatting with you.
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.  


Best Regards,<br>
=== JANUARY 2017 ===
-Stuart Levine
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>
|valign="top" width="35%"|
== RECENT AND UPCOMING CHANGES ==
[[BioMicroCenter:Sequencing| Illumina/Solexa Sequencing]] -- ''*New*'' <BR><BR>
[[BioMicroCenter:3primeIVT| New Affymetrix labeling ]] -- ''*New*'' <BR><BR>
[[BioMicroCenter:Information_about_Tecan_Freedom_Evo| Tecan EVO high-throughput ]] -- ''Coming Jan '09'' <BR><BR>
[[BioMicroCenter:RenoPlans| BioMicro Center Renovation ]] -- ''Coming Feb '09'' <BR><BR>


|-
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>
|valign="top" width="35%"|
 
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>
 
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]].
 
 
 
|valign="top"|
 
== 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>
 
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"''
 
== PUBLICATIONS ==
Please note the publication aspect of OWW is not working. This section is disabled.
<!--
'''2015'''<BR><BR>
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#Paper6 pmid=26510153 <!- VB Saeij->
#Paper7 pmid=26522011 <!- HD Chisholm->
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#Paper2 pmid=24501121 <!- RPA Walker->
#Paper3 pmid=24249727 <!- VB Saeij->
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#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 ->
 
 
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'''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->
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#Paper7 pmid=24009526 <!- CW Lees->
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#Paper11 pmid=24367253 <!- VB Saeij->
#Paper12 pmid=23703590 <!- SM Fraenkel ->
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'''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->
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'''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>
 
-->
 
== 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>
 
== RECENT CHANGES TO THE WEBSITE ==
{{BioMicroChanges}}


== OLD NEWSLETTERS ==
|}
'''2008'''<br>
[[BioMicroCenter:NewsDec08|December 2008]]<br>
[[BioMicroCenter:NewsNov08|November 2008]]<br>
|}

Revision as of 06:46, 20 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 role 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.

PREVIOUS NEWSLETTERS

2015
2014
2013
2012
2011
2010

RECENT CHANGES TO THE WEBSITE

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6 May 2024

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19:41 (cur | prev) +24‎ Xning098 talk contribs (→‎Breast Cancer: Overview)
     
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     21:12  (Upload log)‎ [Xning098‎ (3×)]
     
21:12 Xning098 talk contribs uploaded File:Whatman® FTA® cards.png ‎
     
21:03 Xning098 talk contribs uploaded File:Diagram-Shows-the-Technique-of-FNAC.png ‎
     
20:18 Xning098 talk contribs uploaded File:Guthrie test .png ‎
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