BioMicro Center News
I wanted to bring you up to date on a number of major changes in the BioMicro Center. We've been spending the last several months focused extensively on improving turn around time and on reducing the cost of library preparation significantly. While not all of our efforts are ready for primetime, we do have several significant changes that I hope will be of interest.
The largest change is the addition of a second NextSeq500 and a second MiSeq. We are increadibly grateful to Li-Huei Tsai, Miriam Heiman, Michael Birnbaum and Biological Engineering for these additional instruments. Their addition has significantly reduced our turn around time and we've been able to keep our queue time for both instruments to under a week, which is a dramatic improvement over last year. It also allows us to have instrument redundancy for the inevitable machine failures.
A second change we are rolling out is a modification to our library pooling that can significantly lower the QC costs for an experiment. We have been experimenting using fluorometric measurements of the individual samples before pooling. This cuts out a day in preparing libraries for sequencing and reduces the costs as well. We have been using this internally for a couple of months and the results are on par with what we were observing using qPCR of the individual constituents. We will be making this available to everyone now as a new option "IlluminaQC-Rapid" through iLabs and it can be marked on our latest downloadable forms. This will cost half of a regular quality control reaction but will remove the guarantee of the pooling, as it is a less rigorous check of the quality of the sample. We would discourage using this method if there is signficant variation in the samples within a project, but it is a good method when you are pooling large numbers of libraries prepared in parallel where you have high confidence in the preparation.
Finally, we are rolling out a brand new eukaryotic RNAseq library preparation method that will significantly reduce preparation costs. High throughput 3' digital gene expression (HT-3'DGE) uses a very early indexing step to tag each sample, allowing us to significantly reduce the cost of the experiment - preps will cost $1200 for 24 samples and $4000 for a whole plate. We have been working on this protocol (based on the Soumillon et al.,doi: http://dx.doi.org/10.1101/003236) as part of a new collaboration with the KI High-Throughput Screening Core. It is NOT appropriate for all situations, but can be a huge savings where it is applicable. As with all of our high-throughput methods, samples can drop out and will not be rerun if they do.
Thank you all for your patience as we worked through a number of issues with the sequencers this fall. As a heads up, we will be having a lot of staff turnover this summer as some of our staff are moving on to other positions and graduate school. We are already hiring new staff and we hope to minimize any disruptions.
A couple of updates from the BioMicro Center to let you know about as we begin summer.
- Microarrays: Starting in July, we will be phasing out our Agilent microarray service. The demand for this platform has been very weak and the vendor support has been even weaker. We will continue to maintain the scanner for walkup service but labeling and hybridization services will be done on a custom basis only. Affymetrix services will continue, and will even decrease in price significantly as the company has provided us with very aggressive pricing for the next year. A list of prices for the next year is on our website.
- Bioinformatics: We have begun a monthly training series in informatics for our core researchers. We are still in the pilot phase and definitely have some kinks to work out as we introduce these new classes. The classes will alternate between basic introductions and more advanced topics but will generally be in the afternoon on the second Monday of each month. Duan Ma will be leading this effort. You can find the calendar on our website.
- Sequencing: We are making a few tweaks to the pricing for Illumina sequencing – all in the down direction. The initial reprime for index reads on the HiSeq will now be included in the price of the lane. Additionally, multiplex costs will be removed for all libraries prepped by the BMC.
- We are continuing to work closely with Illumina on the ongoing challenges with read quality for long MiSeq runs. The issues have been traced to the sequencing reagents and we are aware Illumina is working aggressively on a solution. However, there is still no timeline on a fix yet. 250PE and particularly 300PE MiSeq runs should be done cautiously.
Finally, a couple personnel changes to know about. Fangming and Jonathan will be rotating off in a couple weeks. We are bringing their replacements, Rachel and Rob, up to speed now and they’ll be ready by July. We also are welcoming Vidya Subramanian on board as our new technology development specialist. She will be focusing initially on bringing new library preparation methodologies into the BioMicro Center.
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.
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 email@example.com to help keep folks who use Rous regularly up to date. You can sign up for it using Moira.
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.
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.
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 firstname.lastname@example.org 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"
- Chang SC, Fedeles BI, Wu J, Delaney JC, Li D, Zhao L, Christov PP, Yau E, Singh V, Jost M, Drennan CL, Marnett LJ, Rizzo CJ, Levine SS, Guengerich FP, and Essigmann JM. . pmid:25837992.
- O'Meara CC, Wamstad JA, Gladstone RA, Fomovsky GM, Butty VL, Shrikumar A, Gannon JB, Boyer LA, and Lee RT. . pmid:25477501.
- Boutz PL, Bhutkar A, and Sharp PA. . pmid:25561496.
- Naba A, Clauser KR, Ding H, Whittaker CA, Carr SA, and Hynes RO. . pmid:26163349.
- Li CM, Gocheva V, Oudin MJ, Bhutkar A, Wang SY, Date SR, Ng SR, Whittaker CA, Bronson RT, Snyder EL, Gertler FB, and Jacks T. . pmid:26341558.
- Hassan MA, Jensen KD, Butty V, Hu K, Boedec E, Prins P, and Saeij JP. . pmid:26510153.
- Lin X, Ding H, and Zeng Q. . pmid:26522011.
- Penterman J, Abo RP, De Nisco NJ, Arnold MF, Longhi R, Zanda M, and Walker GC. . pmid:24501120.
- De Nisco NJ, Abo RP, Wu CM, Penterman J, and Walker GC. . pmid:24501121.
- Hassan MA, Butty V, Jensen KD, and Saeij JP. . pmid:24249727.
- Nagel ZD, Margulies CM, Chaim IA, McRee SK, Mazzucato P, Ahmad A, Abo RP, Butty VL, Forget AL, and Samson LD. . pmid:24757057.
- 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. . pmid:24763590.
- 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. . pmid:24899568.
- Äijö T, Butty V, Chen Z, Salo V, Tripathi S, Burge CB, Lahesmaa R, and Lähdesmäki H. . pmid:24931974.
- Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, and Fox JG. . pmid:24413286.
- Thornton SR, Butty VL, Levine SS, and Boyer LA. . pmid:25333635.
- Knouse KA, Wu J, Whittaker CA, and Amon A. . pmid:25197050.
- Naba A, Clauser KR, Whittaker CA, Carr SA, Tanabe KK, and Hynes RO. . pmid:25037231.
- Sánchez-Rivera FJ, Papagiannakopoulos T, Romero R, Tammela T, Bauer MR, Bhutkar A, Joshi NS, Subbaraj L, Bronson RT, Xue W, and Jacks T. . pmid:25337879.
- Shao DD, Xue W, Krall EB, Bhutkar A, Piccioni F, Wang X, Schinzel AC, Sood S, Rosenbluh J, Kim JW, Zwang Y, Roberts TM, Root DE, Jacks T, and Hahn WC. . pmid:24954536.
- Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, and Sharp PA. . pmid:24788094.
- McFadden DG, Vernon A, Santiago PM, Martinez-McFaline R, Bhutkar A, Crowley DM, McMahon M, Sadow PM, and Jacks T. . pmid:24711431.
- McFadden DG, Papagiannakopoulos T, Taylor-Weiner A, Stewart C, Carter SL, Cibulskis K, Bhutkar A, McKenna A, Dooley A, Vernon A, Sougnez C, Malstrom S, Heimann M, Park J, Chen F, Farago AF, Dayton T, Shefler E, Gabriel S, Getz G, and Jacks T. . pmid:24630729.
- O'Meara CC, Wamstad JA, Gladstone RA, Fomovsky GM, Butty VL, Shrikumar A, Gannon JB, Boyer LA, and Lee RT. . pmid:25477501.
- Pang YL, Abo R, Levine SS, and Dedon PC. . pmid:25348403.
- Gravina MT, Lin JH, and Levine SS. . pmid:23662897.
- Kelly L, Ding H, Huang KH, Osburne MS, and Chisholm SW. . pmid:23657361.
- 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.
- Gurtan AM, Ravi A, Rahl PB, Bosson AD, JnBaptiste CK, Bhutkar A, Whittaker CA, Young RA, and Sharp PA. . pmid:23630078.
- 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.
- 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.
- 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.
- Li CM, Chen G, Dayton TL, Kim-Kiselak C, Hoersch S, Whittaker CA, Bronson RT, Beer DG, Winslow MM, and Jacks T. . pmid:23873940.
- 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.
- 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.
- Zhen AW, Nguyen NH, Gibert Y, Motola S, Buckett P, Wessling-Resnick M, Fraenkel E, and Fraenkel PG. . pmid:23703590.
- 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.
- Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. . pmid:22847430.
- Kelly L, Huang KH, Ding H, and Chisholm SW. . pmid:22102570.
- 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.
- 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.
- Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. . pmid:20581084.
- Boselli M, Rock J, Unal E, Levine SS, and Amon A. . pmid:19531355.
RECENT CHANGES TO THE WEBSITE
26 September 2016
23 September 2016