BioMicroCenter:News

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=== September 16, 2011 ===
+
== OCTOBER 9, 2012 ==
 +
A quick, almost all Illumina, update:<BR><BR>
-
Dear users,
+
First, the Illumina loaner [[BioMicroCenter:Sequencing#HiSeq_2000|HiSeq]] is now up and running and we are running at full speed. Our last full flowcell in the queue is loading this week so we should finally be back to normal (hopefully).  We cannot prevent instrument failure but at least any issues should have less of a negative impact for the 6 weeks or so while the loaner is here (in other words, if you have time sensitive samples, now is the time to get them in).<BR><BR>
-
I hope everyone had a great summer. I have a few updates for on recent changes in the BioMicro Center.
+
Second, our [[BioMicroCenter:Sequencing#MiSeq|MiSeq]] is scheduled for its upgrade in the next two weeks. This will make two changes. First, the number of reads per run will increase significantly – from ~5m to ~15m. Secondly, the upgrade will add a third tier of read lengths – 500nt. The 500nt run will cost a few hundred more than the 300nt run and will take a second day, but will give us read lengths longer than anything else in the BioMicro Center.<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 providedWe 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.
+
Third, Illumina is having a user meeting on Thursday over at the [http://whereis.mit.edu/?go=L11 Hyatt]. The meeting is likely to be at least moderately technical but is free if you are interested in goingRegistration is at: http://eventregistration.illumina.com/d/scqsm0/4W<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.
+
  "The Boston User Group Meeting: Continuing advances in Illumina’s genomic analysis technologies are rapidly changing the way scientists
 +
  in a variety of disciplines  approach their research. Through a series of local user group meetings, Illumina is providing an opportunity
 +
  for our customers to showcase their research as well as a forum to discuss protocol optimization and bioinformatics solutions. Additionally,  
 +
  you will hear about the latest updates to our products and enhancements to the Illumina Next Generation Sequencing workflow, as well as have  
 +
  the opportunity to interact with key vendors who provide products that support the NGS workflow.  Continental breakfast, breaks, and lunch
 +
  will be provided."
-
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, a couple quicker notes:
-
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.  
+
* We frequently update our [[BioMicroCenter:Forms|forms]] on the website (and not the file name). We typically do this after there has been some kind of communication based error. For submissions, please make sure you have the most recent one by downloading them regularly.
 +
* We have a position open in the lab for a technical assistant. If you know anyone who you think would be a good fit for the BioMicro Center who is looking for a position, please ask them to [http://sh.webhire.com/servlet/av/jd?ai=631&ji=2645644&sn=I apply (mit-00009096)].
 +
<BR><BR>
-
Best regards,
+
== SEPTEMBER 19, 2012 ==
-
-Stuart Levine
+
We hope everyone had a great summer. A couple of updates for you:<BR><BR>
-
--
+
First, and most importantly, I know a lot of you have been affected by very long Illumina turnaround times for HiSeq samples, and especially those for long reads. Our HiSeq has had a very large run of failures this summer and it is affecting everyone. Short reads have been able to sneak through between the failures, so the problem is not quite as bad there, but we have been working very hard with Illumina to get the HiSeq back running efficiently. I can finally report some good news on this front. First, Illumina is shipping us a second HiSeq this week to help us clear through the back log.  In addition, we are enormously grateful to the Biopolymer core at the KI which has taken several of our backlogged flowcells and is helping us work through the queue. Hopefully, these changes will allow us to get on top of our queue and get sequencing turn around back to where it should be. <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/
+
 +
On a more positive note, we have been able to significantly increase our throughput in quality control for Illumina over the past few months. First, we have begun using the Advanced Analytical Fragment Analyzer (donated by the Dept. of Biology) to replace the Agilent Bioanalyzer for Illumina libraries. The fragment analyzer uses capillary electrophoresis to measure fragment length and quantity of DNA and RNA molecules much the same way the BioAnalyzer does. However, unlike the bioanalyzer, it can run unattended, allowing us to process more samples per day. It also appears to have a lower failure rate and a broader dynamic range, both key elements in our analysis. In addition, through a collaboration with the new KI High Throughput Screening Core, we have been able to automate our qPCR analysis using the Tecan systems in the BioMicro Center. This is enabling us to run 384 well qPCRs in a much less labor intensive manner while maintaining high quality. We’re still recalibrating our cluster densities using the Tecans but we are very close to having the last few details ironed out. <BR><BR>
 +
Couple of other quick notes:
 +
- We’ve had a few additions to our staff with Scott Morin joining us as a technical assistant, replacing Kevin Thai, and Margaret Minnig and Kate Tracka joining us from Northeastern for the summer / fall.
 +
- The Technology Seminar Series will resume in the spring. We have been too focused on the Illumina issues to schedule the vendors this fall.
-
=== 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.
+
== JUNE 5, 2012 ==
 +
A couple major Illumina announcements to begin with. First, thanks to the generosity of Dr. Chris Love, the BioMicro Center now has an Illumina MiSeq available. The MiSeq is Illumina’s newest sequencer and is optimized for speed and long read lengths. The MiSeq flowcell contains a single lane with 5 million clusters. While this is well below the 200m reads per lane on the HiSeq, the small surface area enables it to run much faster with a cycle taking only 5 minutes. This means that a 150+150 paired end run can be done in a little over a day, instead of requiring two weeks or more of sequencing. The MiSeq is ideal for applications that do not require enormous read depth, such as microRNA analysis, resequencing of small genomes, barcode sequencing or sequencing amplicons. There are a number of caveats about the MiSeq that can impact your experiment, most notably that there is no separate control lane which means you need to be more careful about base balance, and we are happy to talk with you more about 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>
+
The second announcement is about our venerable GAIIs. As some of you may have noticed, submitting samples for the GAII has been an exercise in extreme patience as we have struggled to fill flowcells due to low demand. The addition of the MiSeq, and some fantastic efforts by Michael Gravina in the lab, has enabled us to rework how we are processing GAII flowcells. We have been able to create partial flowcells on the GAII by altering recipes and making a few minor “modifications”. This has allowed us to move from a model like the HiSeq, where we need a full flowcell before we run, to a model where we can run as soon as the samples pass quality control, more like the MiSeq. However, unlike the MiSeq, we can run multiple lanes at once. Also, running partial flowcells means we can skip parts of the imaging time which does speed up the sequencing (though not to the level of the MiSeq). Some critical caveats: First, these methods are not supported by Illumina, so we cannot offer to replace failed runs. Second, unlike the HiSeq, the PhiX lane is *not* included. You must choose to sequence a lane of PhiX if you want to do control normalization. Finally, this service is completely "a la carte" so the pricing schema is quite different. To go along with these changes, [[BioMicroCenter:Sequencing|we have completely reworked the Illumina page on our website]], so take a look there for more information about the MiSeq, the new GAII methods and pricing.<BR><BR>
 +
A couple quick final announcements:
 +
* Pricing for the next fiscal year is now on the [[BioMicroCenter:PricingFY2013|Website]]. Prices have generally moved lower, though there are slightly higher prices in a few areas.
 +
* The BioMicro Center will be running on a skeleton staff the week of June 11th (the week of the Building 68 retreat and the KI symposium). There will be some staff on hand but our throughput will be significantly lower than normal.
 +
* Finally, last month we said goodbye to Barbara Karamapalas who has been running our automation efforts. Stuart Levine will be handling the Tecans while we are looking for a replacement. We will also be having more turnover in the next couple months as well. Our current co-op, Linda Nguyen, will be leaving at the end of June to return to Northeastern and Kevin Thai will be stepping down in July to take a little bit of time off before he returns to MIT as a graduate student. We wish them all the best of luck and we’re looking very aggressively for their replacements!
-
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.
 
-
 
-
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]].
 
-
 
-
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]].
 
-
 
-
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>
 
 +
== APRIL 19, 2012 ==
 +
There have been a large number of changes in BioMicro to catch you up on in several different areas since my last newsletter. First, I need to begin by introducing Shmulik Motola, our new lab manager. Shmulik has been on board for several months now and is coordinating the flow of projects through the lab. Shmulik did his graduate work at the Weizmann Institute and was a Postdoctoral Associate in Dr. Ernest Fraenkel’s lab here at MIT. Shmulik is the go to person for questions you have about the status of your projects, Illumina queue times, etc. and can also help you with experimental design (shmulikm@mit.edu)
 +
Second, we have expanded our equipment repertoire with the purchase of a Sage BluePippin preparative electrophoresis system (http://www.sagescience.com/bluepippin/). The Pippin prep is an automated system for extracting bands from agarose gels. We are currently testing the system out and will be deploying it to several of our Illumina library preparation methods. We’re planning to use it as part of the RNAseq methodology to provide much tighter size distributions than the SPRIworks can manage. In addition, high percentage agarose gels should enable us to begin to offer library preparation for small RNA sequencing (contact Shmulik if you would like to volunteer for our beta). Because  the BluePippin has a pulse field feature, it should also be useful for building jumping libraries as well as isolating fragments for the new “long read” sequencing technologies, such as Oxford Nanopore. Of course, the Pippin prep is also available for your more “mundane” chores such as isolating bands for cloning.
 +
Finally, our BioInformatics team has had a major overhaul. Dr. Fugen Li left MIT at the end of last year and has been replaced by Dr. Ryan Abo from the Mayo Clinic and Dr. Vincent Butty from Dr. Chris Burge’s lab.  Both bring with them years of experience and, along with Dr. Huiming Ding, are available to help with any informatics challenges you have in your research, especially those related to sequencing. In addition to providing direct research support, we are looking forward to offering short classes on informatics beginning in the summer or fall. We’re in the planning stages now so if you have ideas on subjects you would like us to cover, please let us know.
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Revision as of 20:06, 9 October 2012

Image:BioMicroCenter-header6.jpg

Contents

BioMicro Center News

OCTOBER 9, 2012

A quick, almost all Illumina, update:

First, the Illumina loaner HiSeq is now up and running and we are running at full speed. Our last full flowcell in the queue is loading this week so we should finally be back to normal (hopefully). We cannot prevent instrument failure but at least any issues should have less of a negative impact for the 6 weeks or so while the loaner is here (in other words, if you have time sensitive samples, now is the time to get them in).

Second, our MiSeq is scheduled for its upgrade in the next two weeks. This will make two changes. First, the number of reads per run will increase significantly – from ~5m to ~15m. Secondly, the upgrade will add a third tier of read lengths – 500nt. The 500nt run will cost a few hundred more than the 300nt run and will take a second day, but will give us read lengths longer than anything else in the BioMicro Center.

Third, Illumina is having a user meeting on Thursday over at the Hyatt. The meeting is likely to be at least moderately technical but is free if you are interested in going. Registration is at: http://eventregistration.illumina.com/d/scqsm0/4W

 "The Boston User Group Meeting: Continuing advances in Illumina’s genomic analysis technologies are rapidly changing the way scientists 
 in a variety of disciplines  approach their research. Through a series of local user group meetings, Illumina is providing an opportunity 
 for our customers to showcase their research as well as a forum to discuss protocol optimization and bioinformatics solutions.  Additionally, 
 you will hear about the latest updates to our products and enhancements to the Illumina Next Generation Sequencing workflow, as well as have 
 the opportunity to interact with key vendors who provide products that support the NGS workflow.  Continental breakfast, breaks, and lunch 
 will be provided."

Finally, a couple quicker notes:

  • We frequently update our forms on the website (and not the file name). We typically do this after there has been some kind of communication based error. For submissions, please make sure you have the most recent one by downloading them regularly.
  • We have a position open in the lab for a technical assistant. If you know anyone who you think would be a good fit for the BioMicro Center who is looking for a position, please ask them to apply (mit-00009096).



SEPTEMBER 19, 2012

We hope everyone had a great summer. A couple of updates for you:

First, and most importantly, I know a lot of you have been affected by very long Illumina turnaround times for HiSeq samples, and especially those for long reads. Our HiSeq has had a very large run of failures this summer and it is affecting everyone. Short reads have been able to sneak through between the failures, so the problem is not quite as bad there, but we have been working very hard with Illumina to get the HiSeq back running efficiently. I can finally report some good news on this front. First, Illumina is shipping us a second HiSeq this week to help us clear through the back log. In addition, we are enormously grateful to the Biopolymer core at the KI which has taken several of our backlogged flowcells and is helping us work through the queue. Hopefully, these changes will allow us to get on top of our queue and get sequencing turn around back to where it should be.

On a more positive note, we have been able to significantly increase our throughput in quality control for Illumina over the past few months. First, we have begun using the Advanced Analytical Fragment Analyzer (donated by the Dept. of Biology) to replace the Agilent Bioanalyzer for Illumina libraries. The fragment analyzer uses capillary electrophoresis to measure fragment length and quantity of DNA and RNA molecules much the same way the BioAnalyzer does. However, unlike the bioanalyzer, it can run unattended, allowing us to process more samples per day. It also appears to have a lower failure rate and a broader dynamic range, both key elements in our analysis. In addition, through a collaboration with the new KI High Throughput Screening Core, we have been able to automate our qPCR analysis using the Tecan systems in the BioMicro Center. This is enabling us to run 384 well qPCRs in a much less labor intensive manner while maintaining high quality. We’re still recalibrating our cluster densities using the Tecans but we are very close to having the last few details ironed out.

Couple of other quick notes: - We’ve had a few additions to our staff with Scott Morin joining us as a technical assistant, replacing Kevin Thai, and Margaret Minnig and Kate Tracka joining us from Northeastern for the summer / fall. - The Technology Seminar Series will resume in the spring. We have been too focused on the Illumina issues to schedule the vendors this fall.


JUNE 5, 2012

A couple major Illumina announcements to begin with. First, thanks to the generosity of Dr. Chris Love, the BioMicro Center now has an Illumina MiSeq available. The MiSeq is Illumina’s newest sequencer and is optimized for speed and long read lengths. The MiSeq flowcell contains a single lane with 5 million clusters. While this is well below the 200m reads per lane on the HiSeq, the small surface area enables it to run much faster with a cycle taking only 5 minutes. This means that a 150+150 paired end run can be done in a little over a day, instead of requiring two weeks or more of sequencing. The MiSeq is ideal for applications that do not require enormous read depth, such as microRNA analysis, resequencing of small genomes, barcode sequencing or sequencing amplicons. There are a number of caveats about the MiSeq that can impact your experiment, most notably that there is no separate control lane which means you need to be more careful about base balance, and we are happy to talk with you more about it.

The second announcement is about our venerable GAIIs. As some of you may have noticed, submitting samples for the GAII has been an exercise in extreme patience as we have struggled to fill flowcells due to low demand. The addition of the MiSeq, and some fantastic efforts by Michael Gravina in the lab, has enabled us to rework how we are processing GAII flowcells. We have been able to create partial flowcells on the GAII by altering recipes and making a few minor “modifications”. This has allowed us to move from a model like the HiSeq, where we need a full flowcell before we run, to a model where we can run as soon as the samples pass quality control, more like the MiSeq. However, unlike the MiSeq, we can run multiple lanes at once. Also, running partial flowcells means we can skip parts of the imaging time which does speed up the sequencing (though not to the level of the MiSeq). Some critical caveats: First, these methods are not supported by Illumina, so we cannot offer to replace failed runs. Second, unlike the HiSeq, the PhiX lane is *not* included. You must choose to sequence a lane of PhiX if you want to do control normalization. Finally, this service is completely "a la carte" so the pricing schema is quite different. To go along with these changes, we have completely reworked the Illumina page on our website, so take a look there for more information about the MiSeq, the new GAII methods and pricing.

A couple quick final announcements:

  • Pricing for the next fiscal year is now on the Website. Prices have generally moved lower, though there are slightly higher prices in a few areas.
  • The BioMicro Center will be running on a skeleton staff the week of June 11th (the week of the Building 68 retreat and the KI symposium). There will be some staff on hand but our throughput will be significantly lower than normal.
  • Finally, last month we said goodbye to Barbara Karamapalas who has been running our automation efforts. Stuart Levine will be handling the Tecans while we are looking for a replacement. We will also be having more turnover in the next couple months as well. Our current co-op, Linda Nguyen, will be leaving at the end of June to return to Northeastern and Kevin Thai will be stepping down in July to take a little bit of time off before he returns to MIT as a graduate student. We wish them all the best of luck and we’re looking very aggressively for their replacements!


APRIL 19, 2012

There have been a large number of changes in BioMicro to catch you up on in several different areas since my last newsletter. First, I need to begin by introducing Shmulik Motola, our new lab manager. Shmulik has been on board for several months now and is coordinating the flow of projects through the lab. Shmulik did his graduate work at the Weizmann Institute and was a Postdoctoral Associate in Dr. Ernest Fraenkel’s lab here at MIT. Shmulik is the go to person for questions you have about the status of your projects, Illumina queue times, etc. and can also help you with experimental design (shmulikm@mit.edu)

Second, we have expanded our equipment repertoire with the purchase of a Sage BluePippin preparative electrophoresis system (http://www.sagescience.com/bluepippin/). The Pippin prep is an automated system for extracting bands from agarose gels. We are currently testing the system out and will be deploying it to several of our Illumina library preparation methods. We’re planning to use it as part of the RNAseq methodology to provide much tighter size distributions than the SPRIworks can manage. In addition, high percentage agarose gels should enable us to begin to offer library preparation for small RNA sequencing (contact Shmulik if you would like to volunteer for our beta). Because the BluePippin has a pulse field feature, it should also be useful for building jumping libraries as well as isolating fragments for the new “long read” sequencing technologies, such as Oxford Nanopore. Of course, the Pippin prep is also available for your more “mundane” chores such as isolating bands for cloning.

Finally, our BioInformatics team has had a major overhaul. Dr. Fugen Li left MIT at the end of last year and has been replaced by Dr. Ryan Abo from the Mayo Clinic and Dr. Vincent Butty from Dr. Chris Burge’s lab. Both bring with them years of experience and, along with Dr. Huiming Ding, are available to help with any informatics challenges you have in your research, especially those related to sequencing. In addition to providing direct research support, we are looking forward to offering short classes on informatics beginning in the summer or fall. We’re in the planning stages now so if you have ideas on subjects you would like us to cover, please let us know.

PREVIOUS NEWSLETTERS

2011
2010

RECENT CHANGES TO THE WEBSITE

24 October 2014

+      14:33 BioMicroCenter:News‎ (2 changes) . . (+39) . . (Page history) [Vincent L. Butty‎ (2×)]
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