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BioMicro Center News OCTOBER 2014 A number of very important announcements from BioMicro Center this month. More details are on our website. We have added our newest sequencer: The 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. This month we are rolling out our newest library prep service – automated NexteraXT. Available in batches of 16 samples, prep includes quantification, library preparation, indexing, quality control and pooling. November 1st we will be beginning our 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. 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. 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. AUGUST 2014 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. 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. 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. Our new co-op students, Austin Hendricks and Adam Perez have joined us and will be working in the Center through December. The following packages have been added or updated on ROUS in the past few months: trinityrnaseq: r20140413p1 bedtools: 2.20.1 bowtie2: 2.2.3 tophat: 2.0.12 rsem: 1.2.15 fastqc: 0.11.2 bwa: 0.7.10 pear: 0.9.4 perl: 5.20.0 samtools: 1.0 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. MAY 2014 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. We are now offering sample prep using the 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. Pricing for 2015 is up on our website. There is a link at the bottom of the pricing page. 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 Fluidigm BioMark, which we still have in the lab. 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. 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 register for iLabs to help smooth the transition. 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

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 Penterman J, Abo RP, De Nisco NJ, Arnold MF, Longhi R, Zanda M, and Walker GC. Host plant peptides elicit a transcriptional response to control the Sinorhizobium meliloti cell cycle during symbiosis. Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3561-6. DOI:10.1073/pnas.1400450111 | De Nisco NJ, Abo RP, Wu CM, Penterman J, and Walker GC. Global analysis of cell cycle gene expression of the legume symbiont Sinorhizobium meliloti. Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3217-24. DOI:10.1073/pnas.1400421111 | Hassan MA, Butty V, Jensen KD, and Saeij JP. The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages. Genome Res. 2014 Mar;24(3):377-89. DOI:10.1101/gr.166033.113 | Nagel ZD, Margulies CM, Chaim IA, McRee SK, Mazzucato P, Ahmad A, Abo RP, Butty VL, Forget AL, and Samson LD. Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis. Proc Natl Acad Sci U S A. 2014 May 6;111(18):E1823-32. DOI:10.1073/pnas.1401182111 | Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, Ding H, Marttinen P, Malmstrom RR, Stocker R, Follows MJ, Stepanauskas R, and Chisholm SW. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014 Apr 25;344(6182):416-20. DOI:10.1126/science.1248575 | Cao B, Chen C, DeMott MS, Cheng Q, Clark TA, Xiong X, Zheng X, Butty V, Levine SS, Yuan G, Boitano M, Luong K, Song Y, Zhou X, Deng Z, Turner SW, Korlach J, You D, Wang L, Chen S, and Dedon PC. Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences. Nat Commun. 2014 Jun 5;5:3951. DOI:10.1038/ncomms4951 | Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, and Lähdesmäki H. Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. Bioinformatics. 2014 Jun 15;30(12):i113-20. DOI:10.1093/bioinformatics/btu274 | Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, and Fox JG. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect. 2014 Mar;122(3):284-91. DOI:10.1289/ehp.1307429 | Thornton SR, Butty VL, Levine SS, and Boyer LA. Polycomb Repressive Complex 2 regulates lineage fidelity during embryonic stem cell differentiation. PLoS One. 2014;9(10):e110498. DOI:10.1371/journal.pone.0110498 | 2013 Gravina MT, Lin JH, and Levine SS. Lane-by-lane sequencing using Illumina's Genome Analyzer II. Biotechniques. 2013 May;54(5):265-9. DOI:10.2144/000114032 | Kelly L, Ding H, Huang KH, Osburne MS, and Chisholm SW. Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent. ISME J. 2013 Sep;7(9):1827-41. DOI:10.1038/ismej.2013.58 | 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. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell. 2013 Jan 31;152(3):570-83. DOI:10.1016/j.cell.2013.01.003 | Gurtan AM, Ravi A, Rahl PB, Bosson AD, JnBaptiste CK, Bhutkar A, Whittaker CA, Young RA, and Sharp PA. Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts. Genes Dev. 2013 Apr 15;27(8):941-54. DOI:10.1101/gad.215376.113 | Snyder EL, Watanabe H, Magendantz M, Hoersch S, Chen TA, Wang DG, Crowley D, Whittaker CA, Meyerson M, Kimura S, and Jacks T. Nkx2-1 represses a latent gastric differentiation program in lung adenocarcinoma. Mol Cell. 2013 Apr 25;50(2):185-99. DOI:10.1016/j.molcel.2013.02.018 | Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, and Boyer LA. H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation. PLoS Genet. 2013;9(8):e1003725. DOI:10.1371/journal.pgen.1003725 | Zhang G, Hoersch S, Amsterdam A, Whittaker CA, Beert E, Catchen JM, Farrington S, Postlethwait JH, Legius E, Hopkins N, and Lees JA. Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery. PLoS Genet. 2013 Aug;9(8):e1003734. DOI:10.1371/journal.pgen.1003734 | Li CM, Chen G, Dayton TL, Kim-Kiselak C, Hoersch S, Whittaker CA, Bronson RT, Beer DG, Winslow MM, and Jacks T. Differential Tks5 isoform expression contributes to metastatic invasion of lung adenocarcinoma. Genes Dev. 2013 Jul 15;27(14):1557-67. DOI:10.1101/gad.222745.113 | 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. Gut microbiome perturbations induced by bacterial infection affect arsenic biotransformation. Chem Res Toxicol. 2013 Dec 16;26(12):1893-903. DOI:10.1021/tx4002868 | 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. Transcriptional analysis of murine macrophages infected with different Toxoplasma strains identifies novel regulation of host signaling pathways. PLoS Pathog. 2013;9(12):e1003779. DOI:10.1371/journal.ppat.1003779 | Zhen AW, Nguyen NH, Gibert Y, Motola S, Buckett P, Wessling-Resnick M, Fraenkel E, and Fraenkel PG. The small molecule, genistein, increases hepcidin expression in human hepatocytes. Hepatology. 2013 Oct;58(4):1315-25. DOI:10.1002/hep.26490 | 2012 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 | 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 | 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 | 2011 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 | 2010 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 | 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 | 2009 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 | PREVIOUS NEWSLETTERS 2014 2013 2012 2011 2010 RECENT CHANGES TO THE WEBSITE List of abbreviations: N This edit created a new page (also see list of new pages) m This is a minor edit b This edit was performed by a bot (±123) The page size changed by this number of bytes 18 April 2024      15:01  Pan:Who we are‎ diffhist +14‎ Taopan talk contribs      15:00  Pan:Methods‎‎ 2 changes history +456‎ [Taopan‎ (2×)]       15:00 (cur | prev) +2‎ Taopan talk contribs       14:59 (cur | prev) +454‎ Taopan talk contribs      14:56  Pan:Publications‎‎ 2 changes history +396‎ [Taopan‎ (2×)]       14:56 (cur | prev) +74‎ Taopan talk contribs       14:54 (cur | prev) +322‎ Taopan talk contribs      13:03  BioMicroCenter:Pricing‎ diffhist +166‎ Challee talk contribs      12:58  BioMicroCenter:Singular Sequencing‎‎ 2 changes history +124‎ [Challee‎ (2×)]       12:58 (cur | prev) +14‎ Challee talk contribs (→‎Things to Consider)       12:57 (cur | prev) +110‎ Challee talk contribs      12:12  BioMicroCenter:Tecan Freedom Evo‎‎ 7 changes history +1,746‎ [Noelani Kamelamela‎ (7×)]       12:12 (cur | prev) +4‎ Noelani Kamelamela talk contribs       12:12 (cur | prev) +3‎ Noelani Kamelamela talk contribs       10:13 (cur | prev) +7‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)       10:08 (cur | prev) −42‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)       10:08 (cur | prev) +86‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)       09:34 (cur | prev) +23‎ Noelani Kamelamela talk contribs (→‎verrity Chemagic 360)       09:32 (cur | prev) +1,665‎ Noelani Kamelamela talk contribs      11:42  3D Cell Culture - McLean Taggart, Emma Villares, Maximillian Marek, Scott LeBlanc, Adam Lyons and Jacob Belden‎ diffhist −3‎ Sarah L. 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