BioMicroCenter:News

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BioMicro Center News SUMMER 2025 Sequencing Updates: We are completing an overhaul of the sequencing technologies in the core and will be retiring many of our older sequencers in the very near future. The new offerings we have introduced over the last few years provide significant improvements in quality and price point and support both larger and smaller scale experiments. High Yield Sequencers (>1b reads): The price war on the high-end sequencers has made the NovaSeq6000 in the core all but obsolete, but has also created a glut of capacity in the area. To access these lower prices we have transitioned to an outsourcing model using the NovaSeqX, Illumina's top end sequencer, taking advantage of placements at neighboring academic institutions (DFCI, Broad, Harvard). We have worked closely with these shared resources to provide the best prices we can on each service. All the logistics (from QC to data delivery) will still be handled by the BioMicro Center and it will work just as if you are submitting to the core. As we do have preferential pricing at many of these institutions, we cannot reasonably place the pricing on our website. Instead, you will be able to see the pricing as you submit on ilabs (or by request). Mid Yield Sequencers (250m-1.2b): BMC will continue to support mid-yield sequencing on site with our Element AVITI24. The AVITI provides both a higher quality read than Illumina as well as a dramatically better price than the older NextSeq500. We anticipate a software upgrade in the next few weeks that will also increase the yield per lane from 400m to ~600m reads. Low Yield Sequencers (<250m reads): BMC will also support low yield experiments with both the Singular G4 as well as a new MiSeq i100. The Singular G4 is the lowest cost sequencer we now have with 100m reads available for $300 (50PE). It does require different anchor sequences, but is perfect for pilot experiments. For those needing longer reads or P5/P7 anchors, we are also acquiring a MiSeq i100 to replace the aging MiSeqs in the core. Importantly, the i100 will be available both as an assisted service and as a true walkup sequencer, available to anyone with training. Each run of the i100 is significantly faster than the older MiSeq (600nt runs take only 1 day) with some significant price improvements as well. A huge thank you to the VPR equipment replacement fund, Department of Biology, Gene Li, Michael Birnbaum, and an alumni donor for making the MiSeq i100 possible. UPCOMING TECHNOLOGY SEMINARS: Friday, July 25th Covaris: Covaris R230 in extraction, chromatin assays, protein and NGS library prep. Tuesday, Aug 19th 10X Genomics: Fresh Frozen/polyA based chemistry added to the Visium HD TBD, Sept Illumina: Introduction to the MiSeq i100 SPRING 2025 Spatial Transcriptomics: - The BioMicro Center has recently expanded our spatial 'omics options with the addition of the AVITI24. This upgrade to our existing Element sequencer enables it to do in situ sequencing. For this method, cells are either grown directly onto a flowcell or placed there, fixed and panels of transcripts identified. The system can currently handle up to 350 transcripts and dozens of antibodies with cellular features identified as well (nuclei, cytoskeletin, membrane, etc.). More information is on the Element website. The upgrade was a generous gift from Scott Ritterbush. TO highlight the new capabilities, we have a special seminar upcoming. Molly He, CEO of Element, will be speaking at the KI on May8 (12n). She'll be talking both about the science of the AVITI and the AVITI24, but also about building a company that is competing with the near monopolistic power of Illumina. I hope you can make it to what should be a fantastic seminar. High Output Sequencing: - The BioMicro Center is now supporting sequencing on Illumina's NovaSeqX through collaborations with our sister shared resources in the Boston area. Practically, this will still act like any other sequencing: You will still submit on ilabs and bring the samples to the core. We will preform all the QC and receive the data back, process it, confrim the quality of the data (resolving any technical issues) and place it in your data delivery folders. Since the rates we can share with you are below the published rates, we cannot put these rates on our website, but they are visible in ilabs. Website: - Lastly, the website we have used for well over a decade appears to have failed. Openwetware, a scientific wiki platform, was built at MIT many years ago, starting in Bldg68, and the wiki seemed like a natural fit for the core and worked well for many year. The website failed on us a few weeks ago. We have set up a new page (still reachable at bmcwiki.mit.edu) but our backup was a few months old. We're working to get it back up to date and apologize for any missing information. If you do have questions or see broken links, please do let us know at biomico@mit.edu

NIH ACKNOWLEDGMENT 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 Publications from Stuart Levine PREVIOUS NEWSLETTERS 2017+ 2016 2015 2014 2013 2012 2011 2010 RECENT CHANGES TO THE WEBSITE