All instrumentation in the CMB is available the CMB booking site at the link on the right side of this site or at cmb.scheduling.smith.edu . All instruments are available for use to Smith students, faculty, and staff. If you are a researcher outside of the Smith community and would like access to the CMB, please reach out to the Director at email@example.com.
To access the CMB, all users are required to complete a general training that covers safety and scheduling with the director. After general training is completed, instrument-specific training can be requested on an individual basis. For general or instrument-specific training, please email Riccardo Racicot at firstname.lastname@example.org Please include your lab affiliation, information about your project, if you need general or instrument-specific training, and times that you are available in the upcoming 2 weeks. If you are requesting instrument-specific training, you should also include which instrument you plan to use. General training is brief and typically takes around 30 minutes. Instrument-specific training times are variable and highly depended on individual needs.
Once you have completed general training, you will be provided with access to the booking site. The booking site uses your Smith login and password. Please schedule all instrument use on the booking site. This helps to avoid time conflicts between users, but also helps to document instrument use. This documentation can, and does, help both you and I, as it provides reasoning for instrument upgrades and repairs!
If there is instrumentation that you’d like to see added to the CMB repertoire, please reach out. We can’t always make it happen, but we can always try!
Instruments and resources available for booking:
NanoDrop 8000 Spectrophotometer is a versatile and robust instrument with full-spectrum UV-Vis absorbance analyses (220-750nm) for measuring absorbance of DNA, RNA, dyes, proteins and microbial cell culture OD. Only 0.5-2μl of sample is needed. The Nanodrop 8000 can measure a single sample or up to 8 samples at once and has a large dynamic range: 2-3700 ng/ul for DNA measurements. Multichannel micropipettes are available in the CMB for ease of sample loading when using the 8 sample module. We request that you bring your own pipette tips, but it is not required. Nuclease-free water, 1X TE buffer, and Qiagen buffer EB are all provided. Please make note of what buffer your sample is in prior to using the Nanodrop. You will need to use it to blank the instrument. Failure to do so can impact your results.
SpectraMax M5 is a multi-detection microplate reader with a triple-mode cuvette port and 6-384 microplate reading capability. Detection modalities include absorbance (UV-Vis), fluorescence intensity, fluorescence polarization, time-resolved fluorescence and luminescence. This instrument can be run standalone or through the SoftMax Pro Software.
Genesys 10S UV-Vis Spectrophotometer is a completely modular UV/Vis Spectrophotometer which provides easy sample handling and operation, along with accurate measurement of all your samples. Read modes include single and 6 samples (5 samples+ 1 blank). The Genesys 10S is most commonly used for monitoring culture growth, but is highly versatile with a wavelength range of 190-1100 nm. Features include programmable reads, absorbance ratio and absorbance difference measurements for quick comparisons and quality control, and quantitative analysis with up to 15 standards and five calibration curve fits. A minimum of one ml is required. A variety of cuvette materials are compatible with the instrument. The required cuvette type is dependent on your assay, so please reference the chart below for compatibility. The CMB has some cuvettes available for use, but please check with Riccardo for the most current availability.
Qubit 4 Fluorimeter Fluorimeter specifically designed to quantitate dsDNA, ssDNA, RNA, or protein specifically by measuring fluorescence bound to the specific components, giving more reliable quantitation than traditional spectrophotometry-based quantification, but does not provide indication of contaminants .
Agilent Fragment Analyzer The Agilent Fragment Analyzer 5200 (FA) is a capillary electrophoresis instrument. Capillary electrophoresis provides sizing distribution analysis for DNA or RNA, a critical QC step for many workflows and protocols. The FA provides sizing information similar to running a gel, but is much more accurate, with resolution down to 3 bp, and can provide additional quality and quantity information. Various kits are available for the FA, which are application dependent. The CMB stocks 3 different kits at all times. High Sensitivity dsDNA NGS, 1-6000bp. High Sensitivity dsDNA Large Fragment 1-48,500bp. HS RNA 1-6000 nt. Our instrument can run 11 samples (+ 1 ladder) in parallel and has the capacity to run 3 plates in sequence. Additional kits are available from Agilent. Please reach out to Riccardo if you’re interested in using a kit not stocked by the CMB.
The Agilent 2100 Bioanalyzer Bioanalyzer provides information similar to the Fragment Analyzer, but is a much lower throughput instrument. The Bioanalyzer uses proprietary chips instead of plates or tubes. Only 11 samples (+1 ladder) can be run in parallel, with no expanded ability to run chips in sequence.
The StepOne Plus QRT-PCR System The CMB houses two StepOne Plus quantitative Real Time PCR (SO+) instruments. The SO+ performs a variety of assays include standard curve, relative standard curve, comparative Ct, genotyping and presence/absence. Compatible with SYBR green and TaqMan reagents. Capable of performing standard and fast runs. Mutiplexing capable, with up to 4 dyes. In addition, it features a Veri-Flex block, which allows for 6 different annealing temperatures to be used for highly controlled optimization of reactions.The CMB has 2 of these instruments.
The QuantStudio 3D Digital PCR System extends the performance of existing TaqMan® Assays enabling applications that benefit from higher sensitivity, precision, or absolute quantification by dividing ones sample into 20,000 partitions and then performing an endpoint PCR assay, counting how many partitions contained a particular target. Such high precision applications include rare mutation detection, viral or bacteria quantification and detection, genetically modified organism detection, and reference standard quantification.
Choose from the applications below to learn more:
- Rare allele detection
- Precise copy number variation
- Absolute quantification of viral load
- Absolute quantification of nucleic acid standards
- Absolute quantification of next‐generation sequencing libraries
- Low‐level pathogen detection
- Low‐level fold change of gene expression
BioRad ChemiDoc MP A versatile imaging system that handles chemiluminescence and fluorescence through a large spectrum, in gel sandwiches, agarose and polyacrylamide gels, membranes and microplates.
The Applied Biosystems Veritii Thermal Cycler The Veritii can hold 0.2ml tubes or 96 well plates. It has a Veri-Flex block allowing one to use up to 6 different annealing temperatures, in one run, for reaction optimization.
BioRad C1000 This thermal cycler has dual 48 well blocks. Blocks can hold 0.2ml tubes or 48 well plates. Dual 48/48-well fast module allows 2 independently controlled protocols to be run side by side in a single bay. Features gradient PCR for optimization.
The Pre PCR Prep Room is a bookable space whereby researchers may use the UV hood to set up and aliquot PCR and sequencing master mixes in a close-to-nucleic-acid-free environment.For use with sensitive assays, or any time false positives are of concern. Training must be obtained through Dr. Samantha Torquato prior to use. Please reach out her at email@example.com
Hermle Z 400 K Benchtop Refrigerated Centrifuge allows for spinning and density separation in 15ml / 50ml tubes, and 96-well plates with speeds up to 3500 RPM.
Savant DNA 120 SpeedVac Used for reducing sample volumes, lyophilization, and evaporation of water based buffers, ethanol and isopropanol.
AccuBlock Digital Temp Block.Dry bath with digital temperature control from room temp (no cooling) to 150C. Adjustable to 1/10 of a degree C. Blocks for 1.5-2 mL tubes and thermal beads for other applications.
Applied Biosystems 3500 Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 8 capillaries operating in parallel for a wide range of sequencing and fragment analysis applications. This instrument can only be used with Riccardo or by the CMB intern. Samples can be submitted for running. See the procedure for submission on the Services page of this website.
The Illumina MiSeq Next Generation Sequencer can sequence entire metagenomes, genomes or transcriptomes from multiple samples in a single run. With up to 25 million reads, 2 x 300bp paired-end runs, and automated data storage and analysis in the BaseSpace cloud, sequencing doesn’t get any easier than this:). All runs must be supervised by Riccardo, who is happy to help with any design and technical needs as well.
The Oxford Nanopore MinION can sequence whole genomes or transcriptomes in a single run, sequencing fragments of unlimited length, making this little power house the choice for resolving multiple repeat areas and alternative splicing. Riccardo is happy to help you with any technical needs in planning your Nanopore experiment.