Equipment

Most equipment in the CMB is on the HHMI Scheduler at the link on the right side of this website or at https://www.science.smith.edu/resources/assess/login.php

Users will need to be granted access to use the equipment by the CMB’s ITI, Lou Ann Bierwert, at lbierwer@smith.edu  You need to email her with your lab affiliation and project name and make an appointment for training if needed.  Access is usually granted within 2 days.

Once access is granted, you will be able to sign in to the scheduler with your Smith username and password, and schedule your use of the equipment, from any computer with internet access.

Scheduling is vital in order to avoid conflicts with other researchers and to document use of the equipment to validate requests for future funding and upgrades. Sincerest thanks in advance for your cooperation.

Equipment and resources that require HHMI Scheduling:

The NanoDrop 8000 Spectrophotometer gives full-spectrum UV-Vis absorbance analyses (220-750nm) for measuring absorbance of DNA, RNA, dyes, proteins and microbial cell culture OD; 2ul of sample is needed; Large dynamic range: 2-3700 ng/ul of dsDNA.  Can do Single or up to 8 samples at a time.  Multichannel micropipet available for use. Need to provide your own extended length p10 tips for 8 channel use.                    

 

SpectraMax i3x 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 (FI), fluorescence polarization (FP), time-resolved fluorescence (TRF) and luminescence (Lum).                                                                                   

 

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.  Has both a single and a 6-position cuvette holder.  Used mostly for monitoring bacterial culture growth as a minimum of one ml is required.  Either crystal or plastic cuvettes can be used. Most nucleic acid and protein quantification can be done more economically on the NanoDrop as it only requires 2µl of sample.                                                                                                                                                     

 

Qubit

The Qubit 2.0 Fluorimeter allows you to quantitate dsDNA, ssDNA, RNA, or protein specifically by measuring fluorescence bound to the specific components, giving more reliable quantitation and indication of contaminants than traditional spectrophotometry.   

 

Bioanalyzer

The Agilent 2100 Bioanalyzer allows for in depth detail of quantity and quality of RNA and DNA samples or libraries, with a breakdown of range and average fragment size. This type of information is critical in library prep for Next Generation Sequencing and other downstream applications.                                                                                                                      

 

StepOnePlus QRT-PCR System

The StepOne Plus QRT-PCR System performs a wide variety of applications including gene expression analysis, pathogen quantitation, SNP genotyping, and +/- assays that utilize internal positive controls.  Uses Fast-Plates (30µl maximum reaction volume) and is Fast-chemistry capable, with a few more features for master mix and relative Ct calculations etc. than the 7300 system.  In addition, it features a Veri-Flex block, which allows for 6 different annealing temperatures to be used for highly controlled optimization of reactions.                                                                                                                                               

 

7300 QRT-PCR System

The 7300 QRT-PCR System performs a wide variety of applications including gene expression analysis, pathogen quantitation, SNP genotyping, and +/- assays that utilize internal positive controls.                                                                                                                      

KIMG0052

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 (otherwise known as looking for a needle in a haystack such as in cancer samples), virus & bacteria quantification and detection (getting an absolute count of pathogens detected), genetically modified organism detection (detecting a GMO seed where in places it shouldn’t be), next generation sequencing workflow optimization (accurately quantifying NGS libraries and validating sequencing results), and reference standard quantification (developing a reference for your real‐time experiment when it doesn’t exist).

Choose from the applications below to learn more:

                                                                                                                                                                    

BioChemi Multimode Imager

The EpiChemi 3 Darkroom Transilluminator is a versatile imaging system handles chemiluminescence and fluorescence in gel sandwiches, agarose and polyacrylamide gels, membranes, microplates, and even microarrays. Unlike the Typhoon, gel prep(cutting out bands, etc) can be done with this instrument.                                                                                   

 

 

Typhoon MultiMode Imager

The Typhoon 9200 Multimode Imager is a versatile imaging system that handles chemiluminescence and fluorescence in gel sandwiches, agarose and polyacrylamide gels, membranes, microplates, and even microarrays.                                                                             

 

PrepOneGelImager

The PrepOne Sapphire Gel Imager is our only color imager.  The light source is a blue light (safe for eyes, skin, and sample) that works on SYBR and GelGreen Stains (please no EtBr gels on this platform) and penetrates plexiglass so you can even check the progress of your gel while it is still running.  The light source is from the side, providing a smoother and darker background.  The system comes with several filters to optimize your image.  If the wifi is working, images can be emailed to you straight from the camera, if not, simply hook the camera to the neighboring Nanodrop computer and email from there.  This computer can also be used for charging.                                                                                             

 

MJ PCR Machine

MJ Research PTC-200 Peltier Thermal Cycler can hold 0.2ml and 0.65ml PCR tubes or 96-well plates and can operate two PCR programs simultaneously;
Interchangeable Alpha unit sample blocks are designed for frequent changing.                       

 

Veriti PCR Machine

The Applied Biosystems Veritii Thermal Cycler 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.                                                                       

 

Microarray scanner

Axon Instruments GenePix Personal 4100A Scanner is a microarray scanner for microarrays, tissue and cell arrays, and fluorescence studies.                                                       

Microarray Printer

The Spot Bot Microarray printer spots down oligos or cDNA in determined grid from 96 or 284 well plates.  Capable of printing up to 50,000 spots on a single microarray slide. 

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 Nils Pilotte BEFORE booking or using.___________

Other equipment that does not require HHMI scheduling:

Centrifuge

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 2547xg (note: it lets you set up to 18000xg but will not exceed the 2547).                                               

 

UV Crosslinker and Incubator

BioRad GS Genelinker crosslinker used for linking nucleic acids to membranes and microarray slides

Rotary incubator can be used for still or rotary incubation of tubes, plates and bottles.    

A Savant DNA 120 SpeedVac, an AccuBlock Digital Temp Block and Eppendorf 5417C Microfuge are also available.

The CMB also has two sequencers/genetic analyzers that can be run by request either by, or with the help of, Louie Bierwert: 

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 machine can only be used by or with Louie or the CMB intern.  Samples can be submitted for running.  See the procedure for submission on the “Services” page of this website.

MiSeqonly

The 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 Louie, who is happy to help with any design and technical needs for a well planned experiment.