Difference between revisions of "BioMicroCenter:News"

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== Welcome to the MIT BIOMICRO CENTER ==
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{|
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|valign=top style="width:60%;padding-right:10px;"|
 
== BioMicro Center News ==
 
== BioMicro Center News ==
{|
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=== JULY 2017 ===
|rowspan=2 valign=top style="width:60%;padding-right:10px;"|  
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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>
 +
 
 +
[[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>
  
== OCTOBER 9, 2012 ==
+
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>
A quick, almost all Illumina, update:<BR><BR>
 
  
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>
+
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>
  
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>
+
=== 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
 +
|-
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|polyA RNA (>50ng):<BR>Kapa Hyperprep
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|$150 ||$2,000 (est) ||NA
 +
|-
 +
|3’Digital Gene Expression
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|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>
  
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 going.  Registration is at: http://eventregistration.illumina.com/d/scqsm0/4W<BR><BR>
+
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>
  
  "The Boston User Group Meeting: Continuing advances in Illumina’s genomic analysis technologies are rapidly changing the way scientists
+
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.  
  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:
+
=== 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>
  
* 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.
+
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>
* 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>
 
  
== SEPTEMBER 19, 2012 ==
+
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>
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>
+
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]].
  
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.
 
  
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|valign="top"|
  
== JUNE 5, 2012 ==
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== ABOUT THE BIOMICRO CENTER ==
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>
 
  
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>
+
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>
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!
 
  
 +
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"''
  
== APRIL 19, 2012 ==
+
== PUBLICATIONS ==
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)
+
Please note the publication aspect of OWW is not working. This section is disabled.
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<!--
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'''2015'''<BR><BR>
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<biblio>
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#Paper1 pmid=25837992 <!- SL.JW Essig->
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#Paper2 pmid=25477501 <!- VB Boyer->
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#Paper3 pmid=25561496 <!- AJ Sharp->
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#Paper4 pmid=26163349 <!- HD.CW Hynes->
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#Paper5 pmid=26341558 <!- AJ.CW Gertler Jacks->
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#Paper6 pmid=26510153 <!- VB Saeij->
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#Paper7 pmid=26522011 <!- HD Chisholm->
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</biblio>
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'''2014'''<BR><BR>
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<biblio>
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#Paper1 pmid=24501120 <!- RPA Walker->
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#Paper2 pmid=24501121 <!- RPA Walker->
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#Paper3 pmid=24249727 <!- VB Saeij->
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#Paper4 pmid=24757057 <!- RPA.VB Samson->
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#Paper5 pmid=24763590 <!- HD Chisholm->
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#Paper7 pmid=24931974 <!- VB Burge->
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#Paper8 pmid=24413286 <!- RPA.SL Tannenbaum Fox->
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#Paper9 pmid=25333635 <!- VB.SL Boyer->
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#Paper10 pmid=25197050 <!- JW.CW Amon->
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#Paper11 pmid=25037231 <!- CW Hynes->
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#Paper12 pmid=25337879 <!- AJ Jacks->
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#Paper13 pmid=24954536 <!- AJ Jacks2->
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#Paper14 pmid=24788094 <!- AJ Sharp->
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#Paper15 pmid=24711431 <!- AJ Jacks3->
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#Paper16 pmid=24630729 <!- AJ Jacks4->
 +
#Paper17 pmid=25477501 <!- VB Boyer2->
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#Paper18 pmid=25348403 <!- RPA.SL Dedon ->
  
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.
+
 
 +
</biblio>
  
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.
+
'''2013'''<BR><BR>
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<biblio>
 +
#Paper1 pmid=23662897 <!- BMC Paper->
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#Paper2 pmid=23657361 <!- HD Chisholm->
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#Paper3 pmid=23352431 <!- HD.VB Boyer->
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#Paper4 pmid=23630078 <!- CW.AJ Sharp->
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#Paper5 pmid=23523371 <!- CW Jacks->
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#Paper6 pmid=23990805 <!- SL.VB Boyer->
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#Paper7 pmid=24009526 <!- CW Lees->
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#Paper8 pmid=23873940 <!- CW Jacks2->
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#Paper10 pmid=24134150 <!- SL.RPA Tannenbaum->
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#Paper11 pmid=24367253 <!- VB Saeij->
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#Paper12 pmid=23703590 <!- SM Fraenkel ->
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</biblio>
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'''2012'''<BR><BR>
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<biblio>
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#Paper1 pmid=22981692 <!-SL Boyer: Heart->
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#Paper2 pmid=22847430 <!-SL Saeij->
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#Paper3 pmid=22102570 <!-HD Chisholm->
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</biblio>
 +
'''2011'''<BR><BR>
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<biblio>
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#Paper1 pmid=21892155 <!-SL Sur->
 +
</biblio>
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'''2010'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=20720539 <!-SL Young->
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#Paper2 pmid=20581084 <!-SL Zwaka->
 +
</biblio>
 +
'''2009'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=19531355 <!-SL Amon->
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</biblio>
  
|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]]'''

Latest revision as of 11:39, 21 July 2017

BioMicroCenter-header6.jpg

BIOMICRO GENOMICS HIGH-THROUGHPUT COMPUTING TOOLS QUICK LINKS

.

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"

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22 October 2017

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