Miami University
Contact Info:
Andor Kiss
086 Pearson Hall
700 East High Street
Oxford, OH 45056
http://www.cas.miamioh.edu/cbfg/
Grants and Identifiers:
RRID: RRID:SCR_026415
Instrumentation:
ABI 3100 Capillary Genetic Analyzer
Benchtop capillary genetic analyzer multicolor fluorescence based DNA analysis system with 16 capillaries. It can process 96 or 384 well plates. [Product Link]
cite this instrument
BD FACSAria Aria I Flow Cytometer
BD FACSAria cell sorter incorporates a fixed-alignment cuvette flow cell that can detect up to 13 colors, for a total of 15parameters. [Product Link]
cite this instrument
Bio-Rad CFX96 Real-Time PCR Detection System
The CFX96 Touch System is a real-time PCR detection system that combines optical technology with temperature control. This six-channel (five colors and one FRET channel) real-time PCR instrument combines advanced optical technology with precise temperature control to deliver sensitive, reliable detection for singlexplex or multiplex reactions. Quickly set up runs and monitor amplification traces in real time on the integrated LCD touch screen, or use the included CFX Maestro Software to easily and intuitively design your experiment and analyze results from a connected computer. With up to five-target detection, thermal cycler performance, unrivaled stand-alone functionality, and easy-to-use software, the CFX96 Touch System is designed to advance your qPCR. [Product Link]
cite this instrument
Bio-Rad Chemidoc Gel Imaging System
Gel imaging system that enables visible light,RGB, far red, near infrared, FR, NIR, fluorescence and chemiluminescence detection. It visualizes proteins without gel staining. [Product Link]
cite this instrument
Bio-Rad QXDx AutoDG ddPCR System
Droplet generator and reader that is designed for high-throughput processing of samples in a 96-well format and provides precise and absolute quantification of target DNA and RNA molecules in a wide variety of research applications. [Product Link]
cite this instrument
Covaris ME220 Focused Ultrasonicator
Focused ultrasonicator with compact, easy to use system, formatted for 1 to 8 sample batch processing with integrated chiller and automated water management. [Product Link]
cite this instrument
Eppendorf epMotion 5073m Automated Pipetting
Automated pipetting workstation that is tailored for nucleic acid purification, but can be used for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications. [Product Link]
cite this instrument
General Electric AKTA FPLC System, Protein Purification System
Purification system intended for microgram-scale protein purifications in Tricorn columns up to milligram-scale using HiTrap and HiScreen columns. For fast protein liquid chromatography of tens of grams of protein,can be used with flow rates up to 150 mL/min. This high flow rate is necessary when working with high-flow resins in large columns. Columns can even be packed at flow rates as high as 300 mL/min. System reduces hands-on time so that you can spend less time purifying proteins and more time focusing on your results. Easily switch between different users and applications. To get you up and running quickly, methods are easily created by dragging and dropping predefined templates in UNICORN 7. Purification of protein to sufficiently high yield and purity can be a time- and resource-consuming process. To address fast and efficient protein purification, Can be set up in different ways to handle multistep purification. With an additional column valve up to 10 columns can be connected enabling automation of several samples and steps. [Product Link]
cite this instrument
Illumina MiSeq System
Access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 × 300 bp read lengths. [Product Link]
cite this instrument
Life Technologies QuantStudio 7 Real Time PCR System
Applied Biosystems QuantStudio 7 Flex Real-Time PCR System advances your research further by enabling a broad range of real-time PCR-based applications through its multiplexing capabilities and interchangeable block formats. With a simplified workflow, software, automation capabilities, and touch-screen interface, the QuantStudio 7 Flex system offers reproducibility with minimal well-to-well and instrument-to-instrument variation. [Product Link]
cite this instrument
Maxwell 16 DNA purification system
Nucleic Acid and Protein Purification instrument that provides consistent, automated purification of high-quality DNA, RNA, viral total nucleic acid, or recombinant proteins using paramagnetic particles. There are no Clogs or Drips, Optimal Capture, Washing, and Elution of Target Material, Purifier Can Configure as an SEV or LEV Instrument, Preprogrammed Purification Protocols, For Purification of High-Quality DNA, RNA, and More. It works as a particle processor, not a liquid handler, so there are no clogs or drips, allowing optimal capture, washing, and elution of target material. Purification protocols are preprogrammed into the instrument and can be combined with purification kits containing prefilled reagent cartridges to maximize simplicity and convenience. The purifier can be configured as an SEV Instrument (Standard Elution Volume, 200 400 ?L) for maximum yield or an LEV Instrument (Low Elution Volume, 30 100 ?L) for maximum concentration. Accessories information: Kits are sold separately and contain enough materials to run 48 preps each. [Product Link]
cite this instrument
Molecular Devices SpectraMax M5 Multimode Plate Reader
Microplate Reader delivers single mode reader performance and can be equipped to read volumes as low as 2uL in one multimode reader package. The dual monochromator optics allow the widest range of applications to be utilized for bioresearch and drug discovery applications, all without the need to change filters. For fluorescence intensity, time resolved fluorescence, and fluorescence polarization assays, the SpectraMax M5 Microplate Reader optical design provides the highest level of flexibility. Users can select from top or bottom read modes for improved sensitivity for solution and cell-based assays. Assays can be better optimized by scanning across a range of wavelengths in increments as small as 1 nm. Up to 4 wavelength pairs can be read in one protocol for endpoint and kinetic measurements, allowing for fast setup of FRET and TR-FRET assays. For luminescence, the SpectraMax M5 Microplate Reader utilizes a dedicated luminescence photomultiplier tube (PMT), providing the user the maximum signal and lowest background possible for glow luminescence reporter gene assays. The SpectraMax M5 utilizes a single monochromator design for UV/VIS Absorbance, allowing the user to maximize sensitivity and tunability, and also uses patented PathCheck Pathlength Measurement Technology: the only temperature independent pathlength correction for microplates. The M5 can read volumes down to 2uL with the uMax Low Volume Plate. [Product Link]
cite this instrument
Sage Science BluePippin system
Used for DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp ? 50kb).BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user. Target sizes or ranges of sizes are entered in software, and fractions are collected in buffer. Up to 5 samples/gel cassette may be run, with no possibility of cross contamination. [Product Link]
cite this instrument
Thermo Fisher Attune Nxt Nxt
2020 Attune NxT Flow Cytometer makes multiparametric flow cytometry available to both new and experienced researchers. [Product Link]
cite this instrument
Other Equipment
ABI 3130xl, ABI 3700, Illumina MiSeq, BiomekFX
Services Provided:
Genome/Transcriptome Assembly And Annotation
Relevant Publications:
Description:
The Center for Bioinformatics and Functional Genomics (CBFG) has a full time staff scientist; Dr. Andor Kiss who serves as its Director as well as handling the day-to-day oversight, long-term planning, securing grant funding (intramural and extramural), as well as new protocol development, training new users, performs on-demand sample analysis, routine maintenance of equipment and accounting related to the CBFG. The CBFG main wet laboratory is housed in a 232 m2 suite that serves as an undergraduate, graduate, post-doctoral and principal investigator ‘hands-on’ full service training facility in the main biological science building (Pearson Hall) at Miami University. The CBFG is composed of a main wet laboratory, a flow cytometry core, an A/V & Internet equipped conference room that seats twelve, a computer room that houses eight high-end workstations. Access to the CBFG is on-demand by users via swipe-card after business hours. The CBFG houses a Pacific Biosciences VEGA benchtop long-read system, an Oxford Nanopore Technologies minION and an Illumina® MiSeq™ Next Generation Sequencing instrumentation, an ABI Capillary Electrophoresis Genetic Analyzer (3130xl); an Eppendorf epMotion 5073m NGS liquid handling workstation; a Promega MaxwellRSC Nucleic Acid extraction robot; four real-time qPCR instruments (Rotor-Gene Q with HRM, a Bio-Rad CFX Connect, a QuantStudio 7 Flex [384/96 well interchangeable blocks]), and a Bio-Rad ddPCR QX200 system, a four laser Attune NxT Flow Cytometer for analysis, a three laser BD FACS Melody Flow Cytometer for sorting, two UV NanoDrop spectrophotometers (ND1000, ND2200), and a NanoDrop (ND3300) Fluorospectrophotometer; a Promega Quantus, an Agilent Bioanalyzer 2100; a Covaris M220 Ultrasonic Nucleic Acid Shearer, a Sage BluePippin, seven 96 well gradient capable PCR thermal cyclers, two thermally controlled table top centrifuges capable of accepting 96-well plates used for DNA template preparation; two Eppendorf ThermoMixer C mixing units (384 well PCR to 50 mL tube format), two benchtop micro-centrifuges, Molecular Devices SpectraMax iD5 microplate reader, an ÄKTA-FPLC with UV detector and fractions collector, a UV-1600PC UV-VIS Spectrophotometer with Sipper module, an AlphaInnotechHP Gel Imaging System, Bio-Rad ChemiDoc MP Imaging System, Bio-Rad Dodeca-Cell Criterion PAGE system, several Bio-Rad Mini-Protean Gel Apparatus, Bio-Rad IEF Focusing Cells; numerous power-packs for gel electrophoresis, DNA gel boxes, pipettors, multi-channel pipettors. Eight computers (Linux & Win10), including four powerful Ubuntu O/S based workstations that have (a) a dual socket CPU AMD EPYC (128 logical cores), dual RTX TITAN nVIDIA GPUs, 2 TB DDR4 2666 MHz ECC RAM, 25 TB RAID10 HDD running Ubuntu 18.04 LTS, (b) an AMD Ryzen ThreadRipper PRO 3955WX 16 Cores with 512 GB EEC RAM, a 4090 NVIDIA GPU, 30 TB RAID10 storage array, (c) Opteron 16 Core Processor with 256GB ECC RAM and (d) an Intel CORE Quad CPU with 32GB ECC RAM, (e) Intel Xeon E5620 with 192GB EEC RAM – all for genome assembly and related bioinformatics analyses. The CBFG maintains paid licenses for CLC Genomics Workbench, CLC Main Workbench, BioBam OmicsBox, SnapGene, FlowJo 10, SoftMax 7.1, Biogazelle qBasePLUS, and CANOCO. CBFG staff maintain a direct line of communication (e.g. policy, equipment outages) with users via a LISTSERV <BIOINF@listserv.miamioh.edu>; as well as enables trained users to reserve equipment online using an electronic calendaring software <http://mualwebp01.mcs.miamioh.edu/cgi-bin/cbfg4/Calcium40.pl>. The CBFG is also responsible for implementing communications protocols between the CBFG workstations and Miami University’s High Performance Computing facilities (on-site RedHawk HPC, and Columbus based Ohio Supercomputing Center; OSC) for effective bioinformatics data processing and computation (e.g. NCBI+ Tools, R, IPScans, CANU, HGAP4, FALCON, HiFiASM, HiCanu, Trinity, ntEdit, wtdbg2, Maker2; JASPER; BRAKER3) of large datasets.
