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=== September 16, 2011 ===
+
== 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.
  
Dear users,
 
  
I hope everyone had a great summer. I have a few updates for on recent changes in the BioMicro Center.
 
  
First, we will be running the Technology Seminar Series again this year. This seminar series is designed to showcase a different technology in the facility each month and to bring you up to date on the latest advances and future directions of the technology in the BioMicro Center. The seminar is on Tuesdays at noon in 68-181 and lunch will be provided.  We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly. The first session will be in just under two weeks with Tecan presenting on the robotics systems we have in the core. The full schedule is being maintained on our website at http://openwetware.org/wiki/BioMicroCenter:Technology_Seminar_Series.
 
 
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.
 
 
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.
 
 
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.
 
 
Best regards,
 
-Stuart Levine
 
 
--
 
--
 
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/
 
 
 
 
=== 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.
 
 
First, by popular demand we are announcing that our RNA seq sample preparation service is officially accepting samples. This service requires 100ng of high quality eukaryotic RNA as input and is based on the Illumina TruSeq RNAseq kits coupled with the SPRIworks sample preparation robot. The initial price is $350/sample, which is a little more than then price of a microarray preparation. While the service is open, we are still in the tweaking stage and we are evaluating a number of different protocols that could reduce the total RNA amount or lower the quality of the RNA needed. We do hope to have these questions resolved in the very near future, but the quality of the data we have been getting has been sufficient that we wanted to open the service up to everyone.<BR><BR>
 
 
Second, prices for all of our services were updated on July 1st. Many prices are decreasing. A few key things to notice:
 
* Agilent microarray prices are dropping to be significantly lower than Affymentrix. A full experiment can cost $350/array.
 
* HiSeq lane prices have decreased – particularly for paired end samples. GAII prices have also dropped a little.
 
* Robotics usage prices are now set in two hour blocks instead of on a “per session” basis.
 
* Fluidigm usage prices will be rising to help defray repair costs.
 
The full list can be found '''[[BioMicroCenter:Pricing|on our pricing page]]<BR><BR>
 
 
Finally, this month we have a number of personnel changes. Katie Sullivan and Justin Elliot will be returning to Northeastern with our thanks for six months of hard work, and our new co-ops Jessica Lebowitz and Kaitlyn Sanders, will be starting on July 5th. Jessica and Kaitlyn will be taking over operation of the BioAnalyzer/LabChip and other sample quality control services. In addition, we will be adding a new bioinformaticist, Dr. Huming Ding, to the Center in early July. Dr. Ding comes to us from the University of Toronto where he worked extensively with Dr. Charlie Boone on high throughput screening of genetic interactions and will be helping us establish pipelines for analyzing Illumina data. Please say hello and make them feel welcome the next time you stop by!<BR><BR>
 
Best regards and have a happy Fourth of July!<BR>
 
-Stuart Levine
 
 
=== May 24, 2011 ===
 
 
 
Dear users,
 
 
We have a number of updates to let you all know about that have happened in the last few months.
 
 
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>
 
  
 +
|valign="top"|
  
 
+
== PUBLICATIONS ==
 
+
'''2013'''<BR><BR>
|valign="top"|
+
'''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 ==
 
== PREVIOUS NEWSLETTERS ==
  
 
+
'''[[BioMicroCenter:News2012|2012]]'''<BR>
 
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 
'''[[BioMicroCenter:News2011|2011]]'''<BR>
 
'''[[BioMicroCenter:News2010|2010]]'''
 
'''[[BioMicroCenter:News2010|2010]]'''

Revision as of 19:16, 11 January 2013

BioMicroCenter-header6.jpg

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

BioMicro Center News

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.



PUBLICATIONS

2013

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. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28;151(1):206-20. DOI:10.1016/j.cell.2012.07.035 | PubMed ID:22981692 | HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity. Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13458-63. DOI:10.1073/pnas.1117047109 | PubMed ID:22847430 | HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage. Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40. DOI:10.1093/nar/gkr1022 | PubMed ID:22102570 | 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. miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity. Nat Neurosci. 2011 Sep 4;14(10):1240-2. DOI:10.1038/nn.2909 | PubMed ID:21892155 | 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. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010 Sep 23;467(7314):430-5. DOI:10.1038/nature09380 | PubMed ID:20720539 | HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev. 2010 Jul 15;24(14):1479-84. DOI:10.1101/gad.1935210 | PubMed ID:20581084 | HubMed [Paper2]
All Medline abstracts: PubMed | HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. Effects of age on meiosis in budding yeast. Dev Cell. 2009 Jun;16(6):844-55. DOI:10.1016/j.devcel.2009.05.013 | PubMed ID:19531355 | HubMed [Paper1]

PREVIOUS NEWSLETTERS

2012
2011
2010

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