BioMicroCenter:News

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(OCTOBER 9, 2012)
(PUBLICATIONS)
(30 intermediate revisions not shown.)
Line 1: Line 1:
{{BioMicroCenter}}
{{BioMicroCenter}}
-
== BioMicro Center News ==
+
.
 +
== Welcome to the MIT BIOMICRO CENTER ==
 +
 
{|
{|
-
|rowspan=2 valign=top style="width:60%;padding-right:10px;"|  
+
|valign=top style="width:60%;padding-right:10px;"|  
 +
== BioMicro Center News ==
 +
=== MARCH 2014 ===
 +
A couple highlights of things going on in the center.
 +
* We are resuming the [[BioMicroCenter:Technology_Seminar_Series|Technology Seminar Series]] this week with Roche speaking on Wednesday at lunch. The talk will focus on non-standard applications of the Light Cycler (SNP detection, etc).
 +
* The Fraenkel lab has very kindly donated their [[BioMicroCenter:Covaris|Covaris sonicator]] to the core and we will be putting it under a service contract. We will need to put in place a small fee to cover the cost of the contract - likely starting in July. Training for new users will be available through [[BioMicroCetner:People|Shmulik]].
 +
* We’ve generally had positive feedback about our new AA/BioA form and we’re expanding the new excel forms to include Illumina sequencing. [[BioMicroCenter:Forms|This new form will cover most types of sample preparation.]]
 +
* Illumina is raising the prices on all of their sequencing reagents starting April 1. We lowered our prices very aggressively last year so, in order to break even, [[BioMicroCenter:Pricing#SEQUENCING|we will have adjust our prices slightly higher.]]
-
== OCTOBER 9, 2012 ==
+
===  JANUARY, 2014 ===
-
A quick, almost all Illumina, update:<BR><BR>
+
I hope everyone had a fantastic holiday. We have several updates to let you know about. Since there are a few more than usual, I’m just going to give you the bullet list which you can check out on our website.
-
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>
+
* Upgrade the [[BioMicroCenter:Software#BMC-BCC_Pipeline|basic analysis pipeline for Illumina]] – corrects some bugs, mostly with data overwrite problems, improves speed and provides more QC data, including GC bias checks on all HiSeq runs.  
 +
* New Co-op students -  [[BioMicroCenter:People|Ani Webb and Sam Kaplan]] started this week.
 +
* New protocol for the Advanced Analytical allows us to do [[BioMicroCenter:Advanced_analytical_Fragment_analyzer|picoRNA]] samples on the machine. This cuts the cost of the analysis in half. We can still do the analysis on the BioAnalyzer if you prefer.
 +
* If you run a lot of AA samples, you can lower your cost significantly by submitting the samples preloaded in a plate for the machine (contact us at biomicro@mit.edu if you are interested in this).
 +
* Testing out a [[BioMicroCenter:Forms|new sample submission form]] based on Excel instead of Word. We’re piloting it with the BioAnalyzer form.
 +
* We’re also trying to improve communication by sending database snapshots to users doing Illumina sequencing to make sure we have all the data entered correctly.
 +
* Data storage costs have gone down significantly to [[BioMicroCenter:Pricing|$280/TB/y]]
 +
* There are several IAP sessions highlighting software packages available from the MIT libraries. These include [ http://student.mit.edu/searchiap/iap-BD6D0CF8E096B284E0400312852F4A61.html Ingenuity Pathway Analysis,] [http://student.mit.edu/searchiap/iap-BD6D0CF8DC3DB284E0400312852F4A61.html GeneGO,] and our own [http://student.mit.edu/searchiap/iap-9289af8d41aa4e8e01425c9c633508c6.html training session on using Rous]
-
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>
 
-
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>
+
=== SEPTEMBER 12, 2013 ===
-
  "The Boston User Group Meeting: Continuing advances in Illumina’s genomic analysis technologies are rapidly changing the way scientists
+
I hope everyone had a great summer. A couple new things to tell you about with the start of the academic year. First, we have two new bioinformatics scientists on board. [[BioMicroCenter:BioInformaticsStaff|Dr. Duan Ma]] comes to us from the Dept of Biostatistics at Washington University as well as several years in industry where she worked on a broad variety of bioinformatics problems as well as cloud computing solutions. [[BioMicroCenter:BioInformaticsStaff|Dr. Jie Wu]] did his PhD in computational biology Cold Spring Harbor where he focused on developing algorithms for RNAseq. Both Jie and Duan are located in [http://whreis.mit.edu 68-317], so please stop by and say hello.<BR><BR>
-
  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:
+
One new product to tell you about is new [http://www.illumina.com/products/miseq-reagent-kit-v3.ilmn MiSeq v3 kits] which just came out. These kits increase read counts to 25m from the current 15m maximum. The kits only come in 150 and 600 nt sizes and are somewhat more expensive than the current reagents. The changes to the MiSeq do not help v2 kits and they cannot reach the 25m threshold. We will be offering both the v2 and v3 kits for a short while, but our expectation is the v2 kits will be discontinued by Illumina in the not so distant future. New pricing for the v3 kits is up on our [[BioMicroCenter:Pricing pricing site.]]<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.
+
Also on the sequencing front, we have some evidence that the CG bias issues we were seeing on the HiSeq may not have been totally resolved. We are in the middle of implementing some significant changes in our control lane chemistry in collaboration with Illumina. These will at least allow us to monitor the situation very aggressively and detect any changes in GC bias by using a more complex mixture of samples, instead of only phiX.  As I mentioned in our [[BioMicroCenter:News#APRIL_20.2C_2013|April newsletter]], if you have reason to believe your data was compromised by this issue, please come talk to us so we can help get replacement kits to get your samples rerun as soon as possible. The new control lane is in early beta but is being included on all HiSeq flowcells now. We do want to thank the Laub, Niles and Walker labs for DNA to help us in this effort.<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)].
+
-
== SEPTEMBER 19, 2012 ==
+
Finally, the [[BioMicroCenter:Technology_Seminar_Series|Technology Seminar Series]] will return this year. We begin next Wednesday with Wafergen talking about the Smartchip system. The seminar will be at noon in 68-180 and lunch will be provided. We’re hoping to have seminars every month throughout the year so be sure to look for them on our website.
-
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>
+
=== JUNE 17, 2013 ===
-
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>
+
First, we have a number of [[BioMicroCenter:People staffing changes]] to tell you about. The end of June will see three members of the core moving on. Ryan Abo, one of our informatics scientists, will be heading to the Dana Farber and Paraj Patel and Pierrick Millet will be returning to Northeastern. Our new co-op students, Ashley Machado and Alexander Soltoff will be starting July 1st. We are currently undertaking a job search to look for Ryan’s replacement. If you have any concerns about the personnel changes, please feel free to contact me. <BR><BR>
-
Couple of other quick notes:
+
In a piece of good news, the root cause of the critical failures we have had with our MiSeq for the last month plus with homopolymer samples appear to have been identified and should be fixed today. A recent software upgrade that was supposed to improve the handling of homopolymeric samples apparently failed to install properly, resulting in a mix of pipeline versions that was unable to handle the sequences at all. I do want to thank everyone for their patience as we have struggled with this problem and assure everyone we will move through our backlog on the MiSeq as fast as we possibly can. I also want to thank the techs in the lab, especially Scott Morin, who have been working weekends to try to get as many samples through the MiSeq as possible. <BR><BR>
-
- 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.
+
 +
Finally, with the end of the fiscal year, our annual price adjustments are due to take effect on July 1st. You can find a complete list of the [[BioMicroCenter:PricingFY2014|new prices here]] . The largest change is a reduction in cost for HiSeq sequencing, especially for longer reads. This is associated with a significant decrease in the amount of time we will be holding data on our servers and with the recent switch from fastq + SAM file formats to retaining only BAM files. (see January 2013 notes).
-
== 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>
 
-
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>
+
=== APRIL 20, 2013 ===
-
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!
+
 +
We have noticed a number of technical issues with some Illumina runs. We want to share with you to make sure you are aware of some changes and newly identified technical issues with the platform and what we are doing to correct them where we can. All of these changes are from the Illumina side and none were especially well documented (some not at all). These issues are unlikely to be limited to the BMC, so samples from elsewhere on campus or around the country may also have these issues. Please read this as it may have some impact on your analyses.  <BR><BR>
 +
 +
Just to begin, all of these changes are subtle and not obvious in most cases directly from the sequencers. It was the rare cases that had dramatic effects that caused us to notice them. If you decide you need to have samples rerun, we will work with you to try to get Illumina to replace the reagents and to get the samples rerun. Unfortunately, there is no way we can possibly do bulk reruns of several months’ worth of studies.  <BR><BR>
 +
 +
The most concerning issue is a dropout of GC rich regions in clustering. This has been an on-again off-again issue with Illumina that we have addressed over a year ago by improvements in amplification cycling conditions and enzyme selection. Some time, several months ago (we do not have a precise window), Illumina appears to have changed the chemistry of one of their clustering components and that caused a major change in performance on GC rich areas. This can be seen as an absence of reads from very GC rich areas but, because these areas are rare in most genomes, they cannot be seen on the flowcell wide metrics. This issue is found on current HiSeq and MiSeqV2 kits but not on MiSeqV1 kits nor, we suspect, on the GAII. We have been able to address this problem by adding a brief boiling step during NaOH denaturation of the samples and have implemented this as SOP starting about two weeks ago. This drop out of regions can cause significant issues for several studies – most notably ChIP analyses – when you are comparing data from different chemistries.  <BR><BR>
 +
 +
A second concern is one that has been reported in the community but we have not identified on our machines – yet – where samples from a run are being observed in the following run as minor contaminants. This issue is limited to the MiSeq and HiSeq2500 (we do not have the latter) where the tubes that add sample to the flowcell are not changed. This contamination is reported to be <1% and so would not show up on our quality metrics. However, if your MiSeq analyses are being based on finding a few reads in a large pool of discarded data or you are doing a number of sequential runs, you may wish to validate your data more carefully using an alternative technique such as qPCR or sanger sequencing. There is currently no technical fix to this problem.  <BR><BR>
 +
 +
A third issue has been around for a while though we had not appreciated the implications. Illumina’s newer versions of basecalling software have become less capable of handling uniform sequence (all A’s for example). In earlier versions, only 5 basepairs of variability were needed and intensities could be determined by the control lane we run on all HiSeq flowcells. Now, it appears that nt 1-25 all must have representation of all 4 bases at all positions, even with a control lane. This has always been an issue on the MISeq and we have solved it by spiking in 30%PhiX in the lane (as opposed to our normal 0.1% spike in). Similar solutions can be used on the HiSeq. Given this change, we are re-evaluating whether there is value in using the 8th lane as a control. The latest version of MiSeq software (only a couple days old) supposedly allows us to lower the fraction to 5%, but how successful this is remains to be seen. Base rearrangement with the GAII allows the GAII to avoid this issue.  <BR><BR>
 +
 +
Finally, it appears that custom priming on the MiSeq is not the same as custom priming on the HiSeq and GAII. It can still be done, but the Tm requirement is much higher. Primers that work on the HiSeq may fail on the MiSeq. As long as your Tm matches or exceeds the Tm used for Illumina primers, the MiSeq should work, but the MiSeq’s different chemistry (formamide instead of heat denaturation) is less forgiving.  <BR><BR>
 +
 +
In summary, we have a number of technical challenges that may (or may not) effect you and we want to make sure you have all the information we can give you. I want to thank the researchers and labs that have been very patient as we have struggled running their samples which led us to identify these problems. If you believe these issues have effected your data, please do not hesitate to contact me and we can discuss how to move forward.  <BR><BR>
 +
 +
 +
=== MARCH 11, 2013 ===
 +
Quick update from BioMicro: <BR><BR>
 +
The [[BioMicroCenter:Wafergen|Wafergen qPCR system]] is now operational. We have done a couple pilot experiments so far and it does seem to work, if there are a few more limitations than we anticipated. We are working with Wafergen to see how many of these can be alleviated but you are more than welcome to try it out and see if it would be useful to you. They have given us quite competitive pricing that is a lot lower than the cost for the [[BioMicroCenter:Fluidigm|Fluidigm BioMark]] . Please email us if you are interested in training.
 +
 +
 +
 +
=== JANUARY 9, 2013 ===
 +
Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
 +
First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.  <BR><BR>
 +
During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.  <BR><BR>
 +
Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting  how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week.
 +
If you have any concerns, please do not hesitate to contact me.
-
== 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.
 
|valign="top"|
|valign="top"|
-
== PREVIOUS NEWSLETTERS ==
+
== 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 ==
 +
'''2014'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=24501120 <!- RPA Walker->
 +
#Paper2 pmid=24501121 <!- RPA Walker->
 +
#Paper3 pmid=24249727 <!- VB Saeij->
 +
</biblio>
 +
 +
'''2013'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=23662897 <!- BMC Paper->
 +
#Paper2 pmid=23657361 <!- HD Chisholm->
 +
#Paper3 pmid=23352431 <!- HD.VB Boyer->
 +
#Paper4 pmid=23630078 <!- CW.AJ Sharp->
 +
#Paper5 pmid=23523371 <!- CW Jacks->
 +
#Paper6 pmid=23990805 <!- SL.VB Boyer->
 +
#Paper7 pmid=24009526 <!- CW Lees->
 +
#Paper8 pmid=23873940 <!- CW Jacks2->
 +
#Paper10 pmid=24134150 <!- SL.RPA Tannenbaum->
 +
#Paper11 pmid=24367253 <!- VB Saeij->
 +
 +
</biblio>
 +
'''2012'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=22981692 <!-SL Boyer: Heart->
 +
#Paper2 pmid=22847430 <!-SL Saeij->
 +
#Paper3 pmid=22102570 <!-HD Chisholm->
 +
</biblio>
 +
'''2011'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=21892155 <!-SL Sur->
 +
</biblio>
 +
'''2010'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=20720539 <!-SL Young->
 +
#Paper2 pmid=20581084 <!-SL Zwaka->
 +
</biblio>
 +
'''2009'''<BR><BR>
 +
<biblio>
 +
#Paper1 pmid=19531355 <!-SL Amon->
 +
</biblio>
 +
 +
== PREVIOUS NEWSLETTERS ==
 +
'''[[BioMicroCenter:News2012|2012]]'''<BR>
'''[[BioMicroCenter:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2011|2011]]'''<BR>
'''[[BioMicroCenter:News2010|2010]]'''
'''[[BioMicroCenter:News2010|2010]]'''

Revision as of 22:26, 16 March 2014

Image:BioMicroCenter-header6.jpg

.

Contents

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

MARCH 2014

A couple highlights of things going on in the center.

  • We are resuming the Technology Seminar Series this week with Roche speaking on Wednesday at lunch. The talk will focus on non-standard applications of the Light Cycler (SNP detection, etc).
  • The Fraenkel lab has very kindly donated their Covaris sonicator to the core and we will be putting it under a service contract. We will need to put in place a small fee to cover the cost of the contract - likely starting in July. Training for new users will be available through Shmulik.
  • We’ve generally had positive feedback about our new AA/BioA form and we’re expanding the new excel forms to include Illumina sequencing. This new form will cover most types of sample preparation.
  • Illumina is raising the prices on all of their sequencing reagents starting April 1. We lowered our prices very aggressively last year so, in order to break even, we will have adjust our prices slightly higher.

JANUARY, 2014

I hope everyone had a fantastic holiday. We have several updates to let you know about. Since there are a few more than usual, I’m just going to give you the bullet list which you can check out on our website.

  • Upgrade the basic analysis pipeline for Illumina – corrects some bugs, mostly with data overwrite problems, improves speed and provides more QC data, including GC bias checks on all HiSeq runs.
  • New Co-op students - Ani Webb and Sam Kaplan started this week.
  • New protocol for the Advanced Analytical allows us to do picoRNA samples on the machine. This cuts the cost of the analysis in half. We can still do the analysis on the BioAnalyzer if you prefer.
  • If you run a lot of AA samples, you can lower your cost significantly by submitting the samples preloaded in a plate for the machine (contact us at biomicro@mit.edu if you are interested in this).
  • Testing out a new sample submission form based on Excel instead of Word. We’re piloting it with the BioAnalyzer form.
  • We’re also trying to improve communication by sending database snapshots to users doing Illumina sequencing to make sure we have all the data entered correctly.
  • Data storage costs have gone down significantly to $280/TB/y
  • There are several IAP sessions highlighting software packages available from the MIT libraries. These include [ http://student.mit.edu/searchiap/iap-BD6D0CF8E096B284E0400312852F4A61.html Ingenuity Pathway Analysis,] GeneGO, and our own training session on using Rous


SEPTEMBER 12, 2013

I hope everyone had a great summer. A couple new things to tell you about with the start of the academic year. First, we have two new bioinformatics scientists on board. Dr. Duan Ma comes to us from the Dept of Biostatistics at Washington University as well as several years in industry where she worked on a broad variety of bioinformatics problems as well as cloud computing solutions. Dr. Jie Wu did his PhD in computational biology Cold Spring Harbor where he focused on developing algorithms for RNAseq. Both Jie and Duan are located in 68-317, so please stop by and say hello.

One new product to tell you about is new MiSeq v3 kits which just came out. These kits increase read counts to 25m from the current 15m maximum. The kits only come in 150 and 600 nt sizes and are somewhat more expensive than the current reagents. The changes to the MiSeq do not help v2 kits and they cannot reach the 25m threshold. We will be offering both the v2 and v3 kits for a short while, but our expectation is the v2 kits will be discontinued by Illumina in the not so distant future. New pricing for the v3 kits is up on our BioMicroCenter:Pricing pricing site.

Also on the sequencing front, we have some evidence that the CG bias issues we were seeing on the HiSeq may not have been totally resolved. We are in the middle of implementing some significant changes in our control lane chemistry in collaboration with Illumina. These will at least allow us to monitor the situation very aggressively and detect any changes in GC bias by using a more complex mixture of samples, instead of only phiX. As I mentioned in our April newsletter, if you have reason to believe your data was compromised by this issue, please come talk to us so we can help get replacement kits to get your samples rerun as soon as possible. The new control lane is in early beta but is being included on all HiSeq flowcells now. We do want to thank the Laub, Niles and Walker labs for DNA to help us in this effort.

Finally, the Technology Seminar Series will return this year. We begin next Wednesday with Wafergen talking about the Smartchip system. The seminar will be at noon in 68-180 and lunch will be provided. We’re hoping to have seminars every month throughout the year so be sure to look for them on our website.

JUNE 17, 2013

First, we have a number of BioMicroCenter:People staffing changes to tell you about. The end of June will see three members of the core moving on. Ryan Abo, one of our informatics scientists, will be heading to the Dana Farber and Paraj Patel and Pierrick Millet will be returning to Northeastern. Our new co-op students, Ashley Machado and Alexander Soltoff will be starting July 1st. We are currently undertaking a job search to look for Ryan’s replacement. If you have any concerns about the personnel changes, please feel free to contact me.

In a piece of good news, the root cause of the critical failures we have had with our MiSeq for the last month plus with homopolymer samples appear to have been identified and should be fixed today. A recent software upgrade that was supposed to improve the handling of homopolymeric samples apparently failed to install properly, resulting in a mix of pipeline versions that was unable to handle the sequences at all. I do want to thank everyone for their patience as we have struggled with this problem and assure everyone we will move through our backlog on the MiSeq as fast as we possibly can. I also want to thank the techs in the lab, especially Scott Morin, who have been working weekends to try to get as many samples through the MiSeq as possible.

Finally, with the end of the fiscal year, our annual price adjustments are due to take effect on July 1st. You can find a complete list of the new prices here . The largest change is a reduction in cost for HiSeq sequencing, especially for longer reads. This is associated with a significant decrease in the amount of time we will be holding data on our servers and with the recent switch from fastq + SAM file formats to retaining only BAM files. (see January 2013 notes).


APRIL 20, 2013

We have noticed a number of technical issues with some Illumina runs. We want to share with you to make sure you are aware of some changes and newly identified technical issues with the platform and what we are doing to correct them where we can. All of these changes are from the Illumina side and none were especially well documented (some not at all). These issues are unlikely to be limited to the BMC, so samples from elsewhere on campus or around the country may also have these issues. Please read this as it may have some impact on your analyses.

Just to begin, all of these changes are subtle and not obvious in most cases directly from the sequencers. It was the rare cases that had dramatic effects that caused us to notice them. If you decide you need to have samples rerun, we will work with you to try to get Illumina to replace the reagents and to get the samples rerun. Unfortunately, there is no way we can possibly do bulk reruns of several months’ worth of studies.

The most concerning issue is a dropout of GC rich regions in clustering. This has been an on-again off-again issue with Illumina that we have addressed over a year ago by improvements in amplification cycling conditions and enzyme selection. Some time, several months ago (we do not have a precise window), Illumina appears to have changed the chemistry of one of their clustering components and that caused a major change in performance on GC rich areas. This can be seen as an absence of reads from very GC rich areas but, because these areas are rare in most genomes, they cannot be seen on the flowcell wide metrics. This issue is found on current HiSeq and MiSeqV2 kits but not on MiSeqV1 kits nor, we suspect, on the GAII. We have been able to address this problem by adding a brief boiling step during NaOH denaturation of the samples and have implemented this as SOP starting about two weeks ago. This drop out of regions can cause significant issues for several studies – most notably ChIP analyses – when you are comparing data from different chemistries.

A second concern is one that has been reported in the community but we have not identified on our machines – yet – where samples from a run are being observed in the following run as minor contaminants. This issue is limited to the MiSeq and HiSeq2500 (we do not have the latter) where the tubes that add sample to the flowcell are not changed. This contamination is reported to be <1% and so would not show up on our quality metrics. However, if your MiSeq analyses are being based on finding a few reads in a large pool of discarded data or you are doing a number of sequential runs, you may wish to validate your data more carefully using an alternative technique such as qPCR or sanger sequencing. There is currently no technical fix to this problem.

A third issue has been around for a while though we had not appreciated the implications. Illumina’s newer versions of basecalling software have become less capable of handling uniform sequence (all A’s for example). In earlier versions, only 5 basepairs of variability were needed and intensities could be determined by the control lane we run on all HiSeq flowcells. Now, it appears that nt 1-25 all must have representation of all 4 bases at all positions, even with a control lane. This has always been an issue on the MISeq and we have solved it by spiking in 30%PhiX in the lane (as opposed to our normal 0.1% spike in). Similar solutions can be used on the HiSeq. Given this change, we are re-evaluating whether there is value in using the 8th lane as a control. The latest version of MiSeq software (only a couple days old) supposedly allows us to lower the fraction to 5%, but how successful this is remains to be seen. Base rearrangement with the GAII allows the GAII to avoid this issue.

Finally, it appears that custom priming on the MiSeq is not the same as custom priming on the HiSeq and GAII. It can still be done, but the Tm requirement is much higher. Primers that work on the HiSeq may fail on the MiSeq. As long as your Tm matches or exceeds the Tm used for Illumina primers, the MiSeq should work, but the MiSeq’s different chemistry (formamide instead of heat denaturation) is less forgiving.

In summary, we have a number of technical challenges that may (or may not) effect you and we want to make sure you have all the information we can give you. I want to thank the researchers and labs that have been very patient as we have struggled running their samples which led us to identify these problems. If you believe these issues have effected your data, please do not hesitate to contact me and we can discuss how to move forward.


MARCH 11, 2013

Quick update from BioMicro:

The Wafergen qPCR system is now operational. We have done a couple pilot experiments so far and it does seem to work, if there are a few more limitations than we anticipated. We are working with Wafergen to see how many of these can be alleviated but you are more than welcome to try it out and see if it would be useful to you. They have given us quite competitive pricing that is a lot lower than the cost for the Fluidigm BioMark . Please email us if you are interested in training.


JANUARY 9, 2013

Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.

First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.

During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.

Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week. If you have any concerns, please do not hesitate to contact me.



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

2014

  1. Penterman J, Abo RP, De Nisco NJ, Arnold MF, Longhi R, Zanda M, and Walker GC. . pmid:24501120. PubMed HubMed [Paper1]
  2. De Nisco NJ, Abo RP, Wu CM, Penterman J, and Walker GC. . pmid:24501121. PubMed HubMed [Paper2]
  3. Hassan MA, Butty V, Jensen KD, and Saeij JP. . pmid:24249727. PubMed HubMed [Paper3]
All Medline abstracts: PubMed HubMed

2013

  1. Gravina MT, Lin JH, and Levine SS. . pmid:23662897. PubMed HubMed [Paper1]
  2. Kelly L, Ding H, Huang KH, Osburne MS, and Chisholm SW. . pmid:23657361. PubMed HubMed [Paper2]
  3. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, and Boyer LA. . pmid:23352431. PubMed HubMed [Paper3]
  4. Gurtan AM, Ravi A, Rahl PB, Bosson AD, JnBaptiste CK, Bhutkar A, Whittaker CA, Young RA, and Sharp PA. . pmid:23630078. PubMed HubMed [Paper4]
  5. Snyder EL, Watanabe H, Magendantz M, Hoersch S, Chen TA, Wang DG, Crowley D, Whittaker CA, Meyerson M, Kimura S, and Jacks T. . pmid:23523371. PubMed HubMed [Paper5]
  6. Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, and Boyer LA. . pmid:23990805. PubMed HubMed [Paper6]
  7. Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM, Farrington S, Postlethwait JH, Legius E, Hopkins N, and Lees JA. . pmid:24009526. PubMed HubMed [Paper7]
  8. Li CM, Chen G, Dayton TL, Kim-Kiselak C, Hoersch S, Whittaker CA, Bronson RT, Beer DG, Winslow MM, and Jacks T. . pmid:23873940. PubMed HubMed [Paper8]
  9. Lu K, Cable PH, Abo RP, Ru H, Graffam ME, Schlieper KA, Parry NM, Levine S, Bodnar WM, Wishnok JS, Styblo M, Swenberg JA, Fox JG, and Tannenbaum SR. . pmid:24134150. PubMed HubMed [Paper10]
  10. Melo MB, Nguyen QP, Cordeiro C, Hassan MA, Yang N, McKell R, Rosowski EE, Julien L, Butty V, Dardé ML, Ajzenberg D, Fitzgerald K, Young LH, and Saeij JP. . pmid:24367253. PubMed HubMed [Paper11]
All Medline abstracts: PubMed HubMed

2012

  1. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. . pmid:22981692. PubMed HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. . pmid:22847430. PubMed HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. . pmid:22102570. PubMed HubMed [Paper3]
All Medline abstracts: PubMed HubMed

2011

  1. Mellios N, Sugihara H, Castro J, Banerjee A, Le C, Kumar A, Crawford B, Strathmann J, Tropea D, Levine SS, Edbauer D, and Sur M. . pmid:21892155. PubMed HubMed [Paper1]

2010

  1. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, and Young RA. . pmid:20720539. PubMed HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. . pmid:20581084. PubMed HubMed [Paper2]
All Medline abstracts: PubMed HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. . pmid:19531355. PubMed HubMed [Paper1]

PREVIOUS NEWSLETTERS

2012
2011
2010

RECENT CHANGES TO THE WEBSITE

19 December 2014

       13:11 (Upload log) . . Michael Gravina (Talk | contribs) uploaded "Image:BioMicroCenter Seq Request Form v13.xlsx"
       13:10 BioMicroCenter:Forms (diff; hist) . .  (0) . . Michael Gravina (Talk | contribs) (SUBMISSION FORMS: )
       11:36 BioMicroCenter:People (diff; hist) . .  (+5) . . Jonathan Olson (Talk | contribs) (WET LAB: )

17 December 2014

+      15:53 BioMicroCenter:People‎ (2 changes) . . (+399) . . (Page history) [Fangming Zheng‎ (2×)]

16 December 2014

+      16:27 BioMicroCenter:Sequencing‎ (3 changes) . . (+250) . . (Page history) [Leigh J Manley‎ (3×)]
Personal tools