WHAT’S NEW FOR RU RESOURCE CENTERS – FY20The Rockefeller University Resource Centers continued to support our scientific community with expert staff, cutting edgeequipment and services in fiscal year 2020. The Resource Center staff continued to conduct applied research to improve techniquesand methodologies and fine tune services to meet researchers’ changing needs.In the latter half of FY20, the University dealt with an unprecedented set of circumstances due to the COVID-19 Pandemic.Beginning in mid-March, the University, its laboratories, departments, and Resource Centers went into shutdown, with onlyessential operations and approved COVID-19 related research activities occurring on campus. While the University was able torelatively quickly broaden on-campus activities, we remained in limited operational phase, following NYS and OSHA guidelines,through the end of FY20.As a result, the Resource Centers were challenged to provide service and support at the fullest level possible while upholding socialdistancing requirements, reducing services per capacity, and limiting use by external researchers. Through increased remoteoperations, greater use of videoconferencing, recorded training video sessions, and remote programming of instruments, theCenters found and implemented ways to increase and maintain productivity. Work-from-home activities have increased andinclude design of experiments and interpretation of experimental results. Development of new and expanded remote and virtualtraining has helped the Resource Centers to continue to operate and navigate through these unusual times.NEW METHODS OF TRAINING and CONNECTIVITYThe Structural Biology Resource Center (SBRC), led by Deena Oren, created a Microlearning video to show how to freeze crystalsfor the synchrotrons, an effort initiated and created by Jeff Hennefeld from the IT Creative department to train users virtually. Tocomply with University social distancing requirements, PPMS was used to limit the number of users per room when schedulinginstruments, i.e., for rooms housing more than one system, a reservation on one of the systems blocked access to the other.The High Throughput & Spectroscopy Resource Center (HTSRC), headed by Fraser Glickman, holds weekly group meeting via Zoom. Allmembers of the HTSRC staff are reading, reviewing, and discussing the scientific literature on the specific COVID projects supported bythe HTSRC, training researchers in instrument use remotely, designing experiments, analyzing data and technology horizon scanning.Safe zones were created in the PPMS booking system, to support personal distancing measures and limit room occupancy, and somesystems were relocated to DWB 6th floor to allow for appropriate social distancing.The Bio-Imaging Resource Center (BIRC), headed by Alison North, sent out numerous broadcast e-mails during the shutdown, providingspecific guidance on how to safely access the BIRC, announcing Dr. North’s confocal review article, describing remote assistance methods,and advertising frequent online seminars and workshops including one given by a BIRC staff member on deep learning methods for imageanalysis. COVID-suitable training methods on microscopes involved new user guides written by staff, videos to teach the initial operationof the instruments, and remote trainings via zoom.The Flow Cytometry Resource Center (FCRC), headed by Svetlana Mazel, developed SOPs (Standard Operation Procedures) to keepessential operations going while observing social distancing. A new “satellite” analysis room was set up for efficient operation of fullspectrum analyzers. For user training on the instruments, an innovative hybrid training approach was developed, allowing FCRC Staff totrain users virtually, using an iPad-based Zoom session with a VPN-based Radmin-login session into the instrument’s computer.The Bioinformatics Resource Center (BRC), headed by Thomas Carroll, moved all user meetings to Zoom and operated at full capacitythroughout the extent of the shutdown. The BRC held approximately 200 hours of workshops over Zoom for 140 people in virtualattendance with all sessions video recorded and available to those unable to attend. The BRC released two publicly available, peerreviewed software packages to accelerate the collaborative analysis with users and streamline the installation of software used in trainingmaterial.Genomics Resource Center (GRC), headed by Connie Zhao, has restored all services and resumed normal turnaround time. Specialfreezer space was designated for users to drop off samples any time, 24/7. GRC staff communicated with users by email, phone, and zoomroutinely, and held weekly group meetings via zoom. During the Pandemic, GRC introduced new single cell ATAC-Seq and single cellRNA-Seq/ATAC-Seq combined services.The High Performance Computing Resource Center (HPCRC), headed by Jason Banfelder, operated at full capacity throughout theuniversity shutdown and limited operational phases. Two new software systems were implemented that addressed increased remote andthe increased emphasis on computing and data analysis. (1) Open OnDemand: a web-based portal for accessing HPC resources enabledremote visualization and interaction with scientific imaging and other datasets; and (2) Globus: a system for extramural data transferbetween academic institutions enabled rapid transfer of COVID genomic data.
EQUIPMENTBIO-IMAGINGVISIFRAP/PHOTOACTIVATION MODULE FOR THE ISIM - VisiView acquisition softwareand VisiFRAP module for photo-manipulation of experiments including photobleaching,photoactivation and photoablation.COMPARATIVE BIOSCIENCE CENTERRADPRO OMNERA 50 VETERINARYDIGITAL RADIOGRAPHIC SYSTEMHigh Frequency 30kW Single PhaseGenerator: 125kVp LCD displayprovides two and three-pointoperation for individual control ofexposure parameters.ELECTRON MICROSCOPYWOHLWEND COMPACT HP03 HIGH-PRESSURE FREEZERfor cryofixation of biological samples with superior ultrastructuralpreservationGENOMICSAGILENT TAPE STATION 4200 is anestablished automatedelectrophoresis tool for DNA andRNA sample quality control andincludes analysis of size,concentration, and integrity. Fullyautomated sample processing of anysample number between 1 and 96.FLOW CYTOMETRY:CYTEK AURORA SPECTRAL ANALYZER- was added andupgraded with the UV-laser to accommodate 64fluorescent detectors.SONY MA900 CELL SORTER- 4-laser/12-chanelinstrument in the Biosafety Cabinet was purchased andinstalled to increase capacity and meet the demand in cellsorting.GLASSWASHING: RELIANCE 400XLS- Secondreplacement unit in two years.HIGH THROUGHPUT SPECTROSCOPY:CD SPECTROMETER- An effective tool for measuringprotein quality to high throughput screening.STRUCTURAL BIOLOGY: SEC-MALS- Instrumenttransferred from the Blobel Laboratory.HIGH-PERFORMANCE COMPUTINGFOUR COMPUTE NODES WITH TWIN V100GPUS - added to the HPC cluster to enablerapid analysis of IMAGING DATA and NOVELAI workflows. THE DATA PARK SCIENTIFICDATA ARCHIVE PLATFORM - added toaddress growing volumes of scientific datebeing generated on campus.PRECISION INSTRUMENTATION TECHNOLOGIESCLAUSING KALAMAZOO 20" METAL/WOODVERTICAL BANDSAW- used for woodworking,metalworking or for cutting a variety of othermaterials, and particularly useful for cuttingirregular or curved shapes, while also used toproduce straight cuts.
Acknowledgement of the Resource Centers ensures that the University meets contractual obligations to fundingagencies, strengthens the reputation of the Centers and increases the competitiveness of grant applications thatreference use of the Centers. In the two-year period, 2019-2020, University Resource Centers were acknowledgedand/or Resource Center staff were co-authors on 278 publications by University scientists.EDUCATION AND OUTREACHThe heads of all the Centers participated in the orientationfor first year Graduate Students on September 14, 2019, tointroduce them to the support, services, training, andconsultative services available from the Centers.ON AND OFF CAMPUS LECTURES (Examples)BIRC C. Pyrgaki presented at a workshop on Light SheetMicroscopy at ABRF annual meeting, Palm Springs, CA.,March 2020. EMRC A. Pasolli, presented “New methods inultrastructural analysis applied to cell biology by HighResolution Microscopy”, Electron Microscopy Center (CME),National University of Córdoba, Argentina. Theoretical andpractical course, December 14-20, 2019. GRC C. Zhao,participated in Center for Disorders of the Digestive Systemand Infectious Disease Biology Retreat and presented posterOctober 14-15,2019. PRC H. Molina, presented during Tri-Istudent group visit to the PRC, January 21, 2020. HTSRC F.Glickman, “Introduction to Drug Discovery” for TriInstitutional MD-PhD students, September 24th, 2019.HTSRC User group meeting on new CRISPR/Cas9 mediatedknockout screening and new Hitbit technology fordeveloping endogenous gene reporter assays, December 13th,2019. FCRC S. Mazel, FCS Express Site License - "Lunchand Learn" Flow Cytometry Seminar "The FCS ExpressDifference – Moving Beyond FlowJo” presented by SeanBurke, MS, Senior Product Manager, De Novo Software, July10, 2019. BIRC Zeiss Zen Blue imaging workshop October15, 2019.RU SPONSORED RETREATSEMRC, GRC Center for Basic and Translational Research onDisorders of the Digestive System and Infectious DiseaseBiology Retreat October 14 –15,2019.NEW HIRESBioinformatics Resource Center: CLASSES AND TRAINING ( Limited listin g)BIRC hosted a 1-day Imaris image processing workshop,January 15, 2020 FCRC “Beyond the Basics Flow CytometryClasses” and “Pre-Sort Consultations” regularly scheduledon-demand through request forms placed in FCRC-PPMS,July-June 2020 PIT “User Training” conducted twiceweekly, Sept.- Nov. 2019 BRC conducted the “Introductionto High-Throughput Sequencing” open workshop, MayAugust, 2020, Graduate School training “Introduction toBioinformatics,” June-September, 2020.KEY METHODOLOGYPUBLICATIONS/PRESENTATIONS (A few)BIRC “Tutorial: guidance for quantitative confocalmicroscopy” James Jonkman, Claire Brown, Kurt Anderson,Graham D. Wright, Alison North, Nat Protoc. 2020 May;15(5):1585-1611. FCRC "Spectral Flow and Panel DesignDay at the Rockefeller University" February 26, 2020.SOME RU TECHNOLOGY AND VENDORPRESENTATIONSDoug BarrowsBioinformatics Analyst Wei WangBioinformatics AnalystHigh Throughput & SpectroscopyResource Center: Chloe LarsonResearch Support AssistantProteomics Resource Center: Alexandra PaganoResearch Support Assistant
OPERATING FUNDS FOR THE RESOURCE CENTERS ARE D RAWN FROM THE UNIVERSITY’S ANNUALOPERATING BUDGET AND A RE OFFSET, TO VARYING LE VELS, BY USER FEES. USER FEES FOR CENTERSERVICES AND PRODUCTS ARE SET TO OFFSET ONLY DIR ECT OPERA TING COSTS, E.G., CONSUMABLES,SERVICE CONTRACTS AND L ABOR. USER FEES DO NOT INCLUDE CAPITAL EQUIPMEN T COSTS.User fees for services and products are established by the University administration with input from the Centers’Scientific Advisory Committees, and with review by University Finance.FY18FY19FY20FY21 (budgeted)Resource CenterOperatingCostRecoveryAntibody & ,491189,121697,279234,208BioinformaticsOperating Cost 19,303,49611,950,3689,690,979CRISPR & Genome 22,393189,919Cryo 340487,500Electron 478,474135,000Flow 3,032498,616280,000High Performance 864High Throughput & 811862,0051,175,490850,000Precision Instr. 6740,4721,214,535787,7911,228,630826,200Reference 661,132,7561,130,923Structural 326,500Transgenic & ERUSAGE FY2013,813,656 24,678,28839%30%NUMBER OF LABS USING THE RESOURCE CENTERSBio-ImagingBioinformaticsCBCCryo EMElectron MicroscopyFlow CytometryGenomicsCRISPR & Genome EditingGlasswashingHigh Throughput & SpectroscopyHigh Performance ComputingAntibody & BioresourcePrecision Instrumentation TechnologiesLaboratory of Comparative PathologyProteomicsStructural BiologyTransgenic & Reproductive Technologies36%24,746,569 XTERNAL3002011221222 1001—3711
BY THE NUMBERS - OPERATIONAL & CAPITAL INVESTMENTSFY20 Cost Recoveryby Funding Source 1,103,436.009% 5,533,580.0031% 2,297,643.0013%RUGrantsHHMINon-RU 8,248,688.0047%BY THE NUMBERSOPERATIONAL &CAPITOL INVESTMENTSBY THE NUMBERS – OPERATIONAL & CAPITAL INVESTMENFY20 Capital Equipment ( 70K) FY03-FY20University FundsHOL Contribution or Start UpGifts/Grants 7,000,000Annual Average 2.45M 6,000,000Millions 5,000,000 4,000,000 3,000,000 2,000,000 1,000,000 FY03 FY04 FY05 FY06 FY07 FY08 FY09 FY10 FY11 FY12 FY13 FY14 FY15 FY16 FY17 FY18 FY19 FY20
CYTEK AURORA SPECTRAL ANALYZER - was added and upgraded with the UV-laser to accommodate 64 fluorescent detectors. SONY MA900 CELL SORTER-4 -laser/12 chanel instrument in the Biosafety Cabinet was purchased and installed to increase capacity and meet the demand in cell sorting.