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| == BioMicro Center News == | | == BioMicro Center News == |
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| === OCTOBER 2014 ===
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| A number of very important announcements from BioMicro Center this month. More details are on our website.<BR>
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| * We have added our newest sequencer: The [[BioMicroCenter:Sequencing#NextSeq|Illumina NextSeq500.]] The NextSeq is built as a very powerful MiSeq; using a single sample flowcell and processing a base every 5 minutes, but produces 400m reads per run. The system can produce 30x mammalian genomes in a couple days with read lengths up to 150 paired end. The NextSeq was funded by Doug Laufenburger, Penny Chisholm, the KI and the Dept of Biology. Note: Long single and paired end reads will be given priority on the NextSeq.
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| * This month we are rolling out our newest library prep service – [[BioMicroCenter:Nextera|automated NexteraXT.]] Available in batches of 16 samples, prep includes quantification, library preparation, indexing, quality control and pooling.
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| * '''November 1st''' we will be beginning our [https://mit-ki.ilabsolutions.com iLabs roll out.] On that day all walk up service calendars will be moved from openwetware and google calendar to iLabs. Please take the next few weeks to visit the lab and learn about the system.
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| * [[BioMicroCenter:PacBio|Pacific Biosciences]] will be presenting the Technology Seminar Series on '''October 22nd''' . We now provide PacBIo Service in the BioMicro Center using the RSII located at U.Mass Medical Center in Worcester.
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| * On this Friday, '''October 17th''', The BioMicro Center will be closed for a lab clean up. We will be making available consumables and equipment that are no longer useful for the core at 3PM. Please stop by and take anything useful before we dispose it.
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| === AUGUST 2014 ===
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| We have set up a collaboration with the University of Massachusetts Medical Center Deep Sequencing Core Facility to provide Pacific Biosciences seqeucning to MIT users. We will be providing initial library preparation and quality control before sending the samples out to Worcester for sequencing. Completed sequence data will be returned through your BioMicro Center public folders. More details about PacBio sequencing can be found on our website.<BR><BR>
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| The Illumina pipeline has been upgraded to version 1.3. This upgrade includes quality control metrics for RNAseq and paired end reads as well as some changes under the hood to speed up data delivery. These quality control metrics are dependant on genome alignment, so will not be produced for samples aligned to phiX.<BR><BR>
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| Most of the price increases scheduled for the next fiscal year have been cancelled. We will be re-evaluating the rates in 6 month increments to ensure we remain within our mandated budget constraints.<BR><BR>
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| Our new co-op students, Austin Hendricks and Adam Perez have joined us and will be working in the Center through December.
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| The following packages have been added or updated on ROUS in the past few months:
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| * trinityrnaseq: r20140413p1
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| * bedtools: 2.20.1
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| * bowtie2: 2.2.3
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| * tophat: 2.0.12
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| * rsem: 1.2.15
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| * fastqc: 0.11.2
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| * bwa: 0.7.10
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| * pear: 0.9.4
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| * perl: 5.20.0
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| * samtools: 1.0
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| Older versions can still be selected using the module function. We’ve also created a new mailing list rous_active_users@mit.edu to help keep folks who use Rous regularly up to date. You can sign up for it using Moira.
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| === MAY 2014 ===
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| Some quick bullet pointed updates from BioMicro. We’re in the middle of rolling out several new initiatives right now that will hopefully be in the July newsletter.
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| * We are now offering sample prep using the [[BioMicroCenter:Nextera|Nextera XT]] system from Illumina. This modification of the Nextera uses only 1ng of input DNA (instead of the typical 50ng) and is significantly less expensive. Tuning it for insert size is somewhat more challenging than standard Nextera and so it should not be used where insert size is critical.
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| * [[BioMicroCenter:PricingFY2015|Pricing for 2015]] is up on our website. There is a link at the bottom of the pricing page.
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| * The Wafergen system is no longer available in the BioMicro Center. There is a system at Children’s Hospital if you absolutely need the Wafergen system. Most applications can also be done on the [[BioMicroCenter:RTPCR|Fluidigm BioMark]], which we still have in the lab.
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| * This month, we say goodbye to Scott Morin who will be leaving for medical school. Leigh Manley, who has transferred over from the Biopolymer core, will be taking over Illumina processing.
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| * Finally, the BioMicro Center will be shifting over to iLabs in the coming months. We are still early in the process but we would encourage everyone to [https://mit-ki.ilabsolutions.com/account/login register for iLabs] to help smooth the transition.
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| === MARCH 2014 ===
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| A couple highlights of things going on in the center.
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| * 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).
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| * 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]].
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| * 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.]]
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| * 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.]]
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| === JANUARY, 2014 ===
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| 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.
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| * 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.
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| * New Co-op students - [[BioMicroCenter:People|Ani Webb and Sam Kaplan]] started this week.
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| * 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.
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| * 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).
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| * Testing out a [[BioMicroCenter:Forms|new sample submission form]] based on Excel instead of Word. We’re piloting it with the BioAnalyzer form.
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| * 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.
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| * Data storage costs have gone down significantly to [[BioMicroCenter:Pricing|$280/TB/y]]
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| * 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]
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| == ABOUT THE BIOMICRO CENTER == | | == ABOUT THE BIOMICRO CENTER == |
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| 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> | | 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 provides MIT faculty members with integrated facilities for high-throughput data-intensive genomics, bioinformatic analysis, as well as large-scale database storage, management, data mining and data modeling required to fully implement systems approaches to investigate a broad spectrum of biological problems. The BioMicro Center is designed to maximize the likelihood of successfully designing, implementing, and analyzing systems biology data. With an expert staff available for consultation and collaboration, including several full time bioinformatics scientists and experimentalist with significant experience in systems biology, ample resources exist to assist MIT researchers in any aspect of the research project. This unique cross-disciplinary collaboration leverages resources, spreading institutional commitment, and providing an environment that strongly encourages intellectual rapport between scientists that contributes to the success of projects. This collaborative environment creates a unique opportunity for interactions of biologists and biological engineers who study a broad range of problems. Investigators are able to adopt novel techniques to address their topics of interest as well as develop new collaborations throughout the institute. <BR><BR> |
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| 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. | | 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. |
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| == PUBLICATIONS == | | == PUBLICATIONS == |
| '''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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| #Paper6 pmid=24899568 <!- VB.SL Dedon->
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| #Paper7 pmid=24931974 <!- VB Burge->
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| #Paper8 pmid=24413286 <!- RPA.SL Tannenbaum Fox->
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| | | Publications from [https://www.ncbi.nlm.nih.gov/sites/myncbi/stuart.levine.1/bibliography/47165401/public/?sortby=pubDate&sdirection=descending Stuart Levine] |
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| </biblio>
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| '''2013'''<BR><BR>
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| <biblio>
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| #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>
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| '''2011'''<BR><BR>
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| <biblio>
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| #Paper1 pmid=21892155 <!-SL Sur->
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| </biblio>
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| '''2010'''<BR><BR>
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| <biblio>
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| #Paper1 pmid=20720539 <!-SL Young->
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| #Paper2 pmid=20581084 <!-SL Zwaka->
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| </biblio>
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| '''2009'''<BR><BR>
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| <biblio>
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| #Paper1 pmid=19531355 <!-SL Amon->
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| </biblio>
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| == PREVIOUS NEWSLETTERS == | | == PREVIOUS NEWSLETTERS == |
| | | '''[[BioMicroCenter:News2017+|2017+]]'''<BR> |
| | '''[[BioMicroCenter:News2016|2016]]'''<BR> |
| | '''[[BioMicroCenter:News2015|2015]]'''<BR> |
| '''[[BioMicroCenter:News2014|2014]]'''<BR> | | '''[[BioMicroCenter:News2014|2014]]'''<BR> |
| '''[[BioMicroCenter:News2013|2013]]'''<BR> | | '''[[BioMicroCenter:News2013|2013]]'''<BR> |
