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Bauer Core Laboratory (FAS)

Location: Harvard FAS Center for Systems Biology, Northwest Lab Building, 52 Oxford Street, B227.80, Cambridge MA 02138

Summary:

Our goal is to advance research efforts in the life sciences that cannot readily be accomplished in the traditional academic laboratory because of a need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise.

To promote cutting-edge research and to foster scientific collaborations, we make our extensive laboratory and computational resources available to scientists at Harvard. Our technical staff provide expertise and hands-on training in protocols and the use of instrumentation for a nominal fee. Researchers can sign up to use the instrumentation through an on-line scheduling system and conduct their experiments independently.

Affiliations:

People:

    Resources:

    Instruments

    • ABI 3730xl DNA analyzer ( DNA sequencer )

      "The 96-capillary 3730xl DNA Analyzer is the Gold Standard for high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample." Two of these available: "Sanger" and "Watson." Used for traditional capillary-based dye terminator sequencing.

    • ABI PRISM 6100 nucleic acid prepstation ( Nucleic acid preparation station )

      "The ABI 6100 purifies total RNA or genomic DNA from a variety of biological sources using a vacuum system. It handles up to 96 samples at a time."

    • ABI PRISM 7900HT sequence detection system ( Real-time PCR machine )

      "This system is used for real-time quantitative PCR in 96-well plates and TaqMan Low Density Array cards. Features include a fast cycling mode and a linear dynamic range of nine orders of magnitude. The system is capable of detecting the following probes: SYBRGreen I, FAM, VIC, JOE, NED, ROX, TAMRA, and TET."

    • Agilent 2100 Bioanalyzer ( Microfluidics platform )

      "The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells on a single platform. Results are delivered within 30-40 minutes in automated, high quality digital data.

      The BioAnalyzer can be used for rapidly analyzing RNA, DNA, and proteins. This instrument uses lab-on-a-chip technology to perform automated quality control, quantification, and sizing of samples. Applications include: Microarray sample quality control, PCR optimization, Analysis of protein purifications."

    • Agilent TapeStation ( Electrophoresis system )

      "The TapeStation rapidly analyzes the size and quantity of RNA and DNA samples. Tapes allow for small-scale gel electrophoresis using very little sample. Each tape can analyze up to 16 samples which may be run all together or at different times over the course of a week."

    • Alpha Innotech ChemiImager ( Gel imaging system )

      "This digital imaging system is used for chemiluminescent and fluorescence applications, including gel documentation, imaging western blots, colony counting, and viewing high-density arrays. Advantages include a high-resolution cooled CCD camera, digital documentation, and data analysis software."

    • AutoGenPrep 965 ( Nucleic acid preparation station )

      "The AutoGenPrep 965 provides completely automated DNA extraction from up to four 96-well plates at a time. The FAS Center has protocols for tissue, blood, and plasmids/BACs."

    • Axon GenePix 4000A Scanner ( Slide scanner )

      "These confocal laser scanners are used to analyze standard two-color (Cy3 and Cy5) microarrays. GenePix software allows for adjustable scan area and resolution, as well as automated spot finding."

    • BD FACSAria Cell Sorter ( Flow cytometer sorter )

      "The FACS Aria cell sorter is equipped with three lasers (488, 405, and 635nm), 12 colors, and 4 way sorting capability. It also contains a Photo Multiplier Tube (PMT) for Forward Scatter (FSC) for greater dynamic range among smaller particles. The Aria can sort into a variety of collection devices including: microscope slides, micro-tubes, 12 x 75ml test tubes, 15 or 50ml falcon tubes, as well as multi-well plates (6, 24, 96, or 384). The fixed nozzle eliminates the need for alignment with every run, and makes this instrument easier to use than the MoFlo. For this reason, people who anticipate heavy use of the instrument can be trained to use it independently. Users who needed it less frequently can have their samples run by the facility."

    • BD Fortessa analyzer ( Flow cytometer analyzer )

    • BD LSR II analyzer ( Flow cytometer )

      "This analyzer has 4 lasers (405, 488, 561, and 633 nm) and can be used to analyze cells stained with many different fluorophores (fluorescent proteins, DsRed, mCherry, APC, and phycoerythrin, among others). Like the FACSARIA, the LSRII has a PMT option to allow a greater dynamic range for FSC. The high throughput sampler (HTS) allows cells to be taken from a 96 or 384 well plate. Researchers can be trained to use this instrument independently."

    • Beckman Coulter Biomek FX laboratory automation workstation ( Liquid handler )

      "This 96-channel pipetting instrument is used for high-throughput liquid-handling applications in microtiter plates. Applications include: Plasmid purifications, PCR Purification, PCR setup, Plate-to-plate transfers or replications, Compression or expansion of samples in 96- or 384-well plates."

    • Beckman Coulter MoFlo Astrios cell sorter ( Flow cytometer sorter )

      "The MoFlo Astrios EQ is a high speed cell sorter with 7 lasers, 34 detectors, and 6 way sorting capability. It is equipped with a 355nm, 405nm, 488nm, 532nm, 561nm, 592nm, and 640nm lasers. The instrument is also equipped with a dual forward scatter PMT small particle detector that allows for the measurement of submicron particles. Common nozzle sizes used on the instrument are the 70 micron and the 100 micron. The sorter is inside a Baker bio safety cabinet for sorting bio safety level two samples. A variety of collection devices can be used including: microscope slides, micro tubes, 12x75 test tubes, 15ml or 50ml falcon tubes, as well as multi well plates (6, 24, 96, 384, 1536, or custom). The collection device as well as the sample chamber can be cooled or warmed during sorting. The Astrios is capable of sorting into plates with the sort stream straight down instead of at an angle like most traditional sorters. Index sorting is also available for single cell plate sorting. This instrument is operated by staff on a fee for service basis."

    • Beckman Coulter MoFlo Legacy Cell Sorter ( Flow cytometer sorter )

      "The MoFlo is a high speed cell sorter with three lasers, 9 colors, and two way sorting capability. It is equipped with a solid state 488nm laser, an I90 argon ion multiline UV laser, and an I70C spectrum tunable laser (providing wavelengths from 440nm to 568nm). A variety of collection devices may be used including: microscope slides, micro-tubes, 12 x 75ml test tubes, 15 or 50ml falcon tubes, as well as multi-well plates (6, 24, 96, or 384). This instrument is operated by staff on a fee for service basis."

    • Beckman Coulter MoFlo XDP cell sorter ( Flow cytometer sorter )

      "The XDP is a high speed cell sorter with 2 lasers, 7 colors, and 4 way sorting capability. It is equipped with a 488nm solid state laser and a 635nm diode laser. The XDP uses complete digital processing and can sort a high yield of cells at a greater efficiency. A variety of collection devices may be used including: microscope slides, micro-tubes, 12 x 75ml test tubes, 15 or 50ml falcon tubes, as well as multi-well plates (6, 24, 96, 384, or 1536). The machine is also capable of cooling or warming the sort collection device while sorting. This instrument is operated by staff on a fee for service basis."

    • Beckman Coulter Multisizer 3 ( Automatic cytometer )

      The Multisizer™ 3 Coulter Counter is a particle sizing and counting analyzer. The coulter counter uses an Electrical Sensing Zone Method to generate data on number, volume, mass, and surface area size distributions of particles. Apertures of 50 µM and 100 µM are currently available to measure particles ranging from 1-60 µM in diameter. Researchers can be trained to use this instrument independently.

    • Biacore 3000 analyzer ( Surface plasmon resonance instrument )

      "This fully automated instrument detects molecular interactions in real time using surface plasmon resonance (SPR)."

    • BioRad CFX384 Touch Real Time PCR instrument ( Real-time PCR machine )

      This system is used for real-time quantitative PCR in 384-well plates. Features include rapid cycling, a gradient capability for protocol optimization, and a linear dynamic range of ten orders of magnitude. The system is capable of four-color detection with the following excitation/detection wavelengths:

      - 450-490nm/510-530nm (FAM, SYBR)
      - 515-535nm/560-580nm (HEX)
      - 560-590nm/610-650nm (Texas Red)
      - 620-650nm/675-690nm (Cy5)

    • BioRad CFX96 Touch Real Time PCR instrument ( Real-time PCR machine )

      This system is used for real-time quantitative PCR in 96-well plates. Features include rapid cycling, a gradient capability for protocol optimization, and a linear dynamic range of ten orders of magnitude. The system is capable of five-color detection with the following excitation/detection wavelengths:

      - 450-490nm/510-530nm (FAM, SYBR)
      - 515-535nm/560-580nm (HEX)
      - 560-590nm/610-650nm (Texas Red)
      - 620-650nm/675-690nm (Cy5)
      - 672-684nm/705-730nm (Quasar 705)

    • Bioscreen-C growth curves analysis system ( Microplate reader )

      "Use this instrument to generate growth curves in yeast or bacteria. The instrument will incubate samples while shaking at a designated temperature and will take periodic OD measurements to determine the growth rate."

    • Biotek Epoch 2 ( Microplate spectrophotometer )

      "Epoch 2 Microplate Spectrophotometer offers excellent performance for UV-Vis measurements in microplates, cuvettes and in micro-volume samples with the available Take3 plate. Full function Gen5 Software is onboard, ready to read and analyze data at the touch of the screen! Endpoint, kinetic, spectral scanning are well area scanning modes, plus incubation and shaking keep your application options open! Epoch 2 is a fully contained microplate spectrophotometer workstation with available WiFi, Bluetooth and USB flash drive."

    • BioTek µFill dispensing device ( Liquid handler )

      "This dispensing device is used to rapidly fill the wells of 24, 96, or 384-well standard-height or deep-well microtiter plates. The instrument uses a syringe pump to dispense in 1µl increments down to a minimum volume of 5 µl."

    • Covaris S220 Ultrasonicator ( Sonicator )

    • Fisher Scientific 550 (Misonix XL2020) sonicator ( Sonicator )

      "Used for DNA fragmentation and cell disruption."

    • Fluidigm Biomark HD ( Real-time PCR machine )

    • Fluidigm C1 Single Cell Autoprep ( Cell assay platform )

      "The world’s first automated solution for single-cell genomics research continues to break new ground, now offering more capabilities than ever before. C1 lets you prepare single-cell templates for mRNA sequencing, DNA sequencing, epigenetics or miRNA expression. Reflected in over 100 published studies, the breadth of C1 applications empowers users to survey cell diversity, identify rare cell types and characterize cellular functions, all on the same single-cell biology platform. Investigate tissue heterogeneity with transcript end counting. Use T cell receptor sequencing and other full-length mRNA-seq protocols to recognize isoform- and receptor-specific expression. Examine gene-specific and microRNA expression. Perform epigenetic analysis and identify genomic variants. The C1 system delivers power and flexibility to support you all along your path to discovery."

    • GE Amersham Typhoon imager ( Variable mode imager )

      "This multifunction scanner can be used for storage phosphor autoradiography, fluorescence, and chemiluminescence. The scanner has 3 lasers (488, 532, and 633nm) and multiple filters for fluorescent imaging. It can be used to take images of gels, membranes, phosphor screens, microtiter plates and more. Advantages include an adjustable focal plane and resolutions down to 25 microns."

    • GeneMachines (DigiLab) Hydroshear ( Sonicator )

      The Hydroshear is used for fragmenting DNA to sizes larger than 1KB.

    • Illumina HiSeq 2000 ( DNA sequencer )

      These systems generate up to 200 million reads per sample and can be configured to meet researcher's individual needs.

      - Reads from 50 to 150 bp long
      - Single Read or Paired End
      - Standard Run or Rapid Run
      - Indexing/barcoding supported

    • Illumina HiSeq 2500 ( DNA sequencer )

      These systems generate up to 200 million reads per sample and can be configured to meet researcher's individual needs.

      - Reads from 50 to 150 bp long
      - Single Read or Paired End
      - Standard Run or Rapid Run
      - Indexing/barcoding supported

    • Illumina NextSeq 500 ( Next generation sequencer )

    • IntegenX Apollo324 Automated NGS Library Preparation System ( Liquid handler )

    • MJ Tetrad thermal cycler ( Thermal cycler )

      "These thermal cyclers can be used for high-throughput PCR and cycle sequencing applications. Each instrument has a capacity of four 96-well or 384-well PCR plates." Four copies available.

    • Molecular Devices FlexStation multi-mode plate reader ( Microplate reader )

      The FlexStation 3 is a multi-mode plate reader with 8 integrated liquid dispensers capable of the following applications:

      - Absorbance (200-1000 nm)
      - Fluorescence (top or bottom read, 250-850 nm)
      - Fluorescence Polarization (top read, 400-750 nm)
      - Luminescence (top or bottom read, 250-850 nm)
      - Time-Resolved Fluorescence

    • Molecular Devices SpectraMax Gemini XS Plate Reader ( Microplate reader )

      "The Spectramax Gemini XS is used for fluorescence measurements in microtiter plates. It can be used for emission and excitation wavelengths between 250 and 850 nm."

    • Molecular Devices Spectramax i3 multi-mode plate reader ( Microplate reader )

      "The Spectramax i3 is a muti-mode plate reader used for measuring absorbance and fluorescence in microtiter plates. It can measure absorbance from 230 -1000 nm. It can measure fluorecence from the top or bottom of a plate with a range of 250 - 850 nm."

    • Molecular Devices Spectramax L luminescent reader ( Microplate reader )

      "The Spectramax L is a highly sensitive luminescent plate reader with dual injectors to enable rapid measurement after adding a reagents to an assay plate."

    • Molecular Devices SpectraMax Plus384 Plate Reader ( Microplate reader )

      "The Spectramax Plus 384 is a UV-visible absorbance spectrophotometer used for sample analysis in microtiter wells or cuvettes. The instrument has a pathlength correction feature."

    • NanoDrop ND-1000 Spectrophotometer ( Spectrophotometer )

      "The Nanodrop is a UV-Visible Spectrophotometer designed to read 1-2 microlitre samples without a cuvette. Most samples can be run without dilution. It has a wavelength range of 220-750nm."

    • Qubit Fluorometer ( Fluorometer )

      "The Qubit enables precise quantification of dsDNA, ssDNA, RNA and protein using a fluorescent dye."

    • Tecan Evo robotic workstation ( Liquid handler )

      This robot has eight independent pipetting tips for automated liquid handling in a variety of vessels including microtiter plates, tubes, and slides. Applications include:

      - PCR setup
      - Reagent dispensing
      - Sample dilution and reconfiguration
      - In situ hybridization of up to 48 slides using the Genepaint system

    • Tecan Safire2 plate reader ( Microplate reader )

      "The Safire2 is multimode tunable plate reader capable of reading fluorescense and absorbance. Plates can be read multiple times with shaking between each read."

    • Thermo MultiDrop ( Liquid handler )

      "This dispensing device is used to rapidly fill the wells of 96-well or 384-well standard-height microtiter plates."

    • Thermo MultiDrop Micro ( Liquid handler )

      "This dispensing device is used to rapidly fill the wells of 96-well or 384-well standard-height microtiter plates."

    Protocols

    • ABI 6100 extraction protocol ( Protocol )

      "This protocol describes how to use the ABI6100 to extract RNA and/or DNA from cultured cells, yeast, blood, and animal or plant tissue. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core?s instrumentation."

    • Amersham/GE Typhoon Imager protocol ( Protocol )

      "This protocol provides instructions for using the GE (Amersham) Typhoon Trio Imager for storage phosphor autoradiography, and fluorescent or chemiluminescent imaging. Three excitation wavelengths are available for fluorescent imaging: red (633), green (532) and blue (488). The Typhoon can acquire images from phosphor screens, gels, and microtiter plates, and it has an adjustable focal plane to allow for imaging gels between glass plates. The resolution can be adjusted down to 25 micron pixels."

    • AutoGenprep 965 plasmid protocol ( Protocol )

      "This protocol describes how to run the Plasmid/BAC DNA isolation protocol on the AutoGenprep 965. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core?s instrumentation."

    • AutoGenprep 965 tissue protocol ( Protocol )

      "This protocol describes to extract genomic DNA from tissue using the Mouse Tail DNA protocol on the AutoGenprep 965. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core's instrumentation."

    • Axon Scanner and GenePix software to scan and analyze microarrays protocol ( Protocol )

      "This protocol provides instructions for scanning microarrays on the Bauer Core's Axon 4000A or 4000B scanner. It also explains how to use the GenePix Software to do the initial analysis that extracts raw data from the features on the array."

    • Biacore protocol ( Protocol )

      Protocol dealing with protein-molecule interaction.

    • Bioanalyzer RNA Nano protocol ( Protocol )

      This protocol provides instructions for running RNA samples on the Agilent 2100 Bioanalyzer using one of the RNA Nano Protocols.

    • Capillary-based sequencing sample preparation protocol ( Protocol )

    • ChemiImager protocol ( Protocol )

      "This protocol describes how to acquire images using the AlphaInnotech ChemiImager. The ChemiImager can be used for gel documentation of ethdium bromide or SYBR green stained gels using UV transillumination and Coomassie stained gels using white light. The instrument can also acquire chemiluminescent data without a light source. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core?s instrumentation."

    • Creating and Running Scripts on the Tecan Evo ( Protocol )

      This protocol provides instructions for creating and running scripts on the Tecan Evo, including a section on how to define labware. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    • Dispensing into plates with the BioTek µFill protocol ( Protocol )

      This protocol provides instructions for using the Biotek μFill to dispense liquid into microtiter plates (96 or 384 well plates, including deep well plates). The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any Bauer Core instrumentation.

    • Filling plates with the MultiDrop or MultiDrop Micro protocol ( Protocol )

      This protocol provides instructions for using the MultiDrop or MultiDrop Micro to fill microtiter plates (96 or 384 well plates). Both systems use peristaltic pumps to deliver liquid to the plates. The MultiDrop can dispense in increments of 5μl and the MultiDrop Micro can dispense in increments of 1μl.

    • Gemini protocol ( Protocol )

      This protocol provides instructions for using the Spectramax Gemini XS Fluorescent Plate Reader to capture fluorescent or luminescent data from microtiter plates at wavelengths between 250 and 850 nm. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    • Hydroshear protocol ( Protocol )

    • NanoDrop protocol ( Protocol )

      This protocol provides instructions for using the NanoDrop ND-1000 Spectrophotometer to read absorbance between 220 – 750 nm in as little as 1μl. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    • Operating the MJ Tetrad or DNA Engine Thermal Cyclers ( Protocol )

      This protocol describes how to use MJ Research Tetrad or MJ DNA Engine thermal cyclers. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    • Plus 384 Protocol ( Protocol )

      This protocol provides instructions for using the Spectramax Plus 384 UV-Visible Plate Reader to read absorbance between 190 – 1000 nm. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    • Protocol for scanning microarrays with the Agilent scanner ( Protocol )

      "This protocol provides instructions for scanning microarrays on the Bauer Core Agilent scanner and analyzing the data using the Feature Extraction software. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core instruments."

    • Qubit Protocol ( Protocol )

      This protocol provides instructions for using the Qubit to measure concentrations of DNA, RNA or protein. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    • Real Time PCR using the M X3000 ( Protocol )

      This protocol provides instructions for setting up and analyzing
      a real-time PCR reaction on Stratagene’s MX3000p but does not provide advice on how to design your experiment. Please contact Christian Daly if you have questions about experimental
      design. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instruments.

    • Real Time PCR using the MJ Opticon ( Protocol )

      This protocol provides instructions for setting up and anal
      yzing a real-time PCR reactionon the MJ Opticon but it does not provide advice on how to design your experiment. Please contact Christian Daly if you have questions about experimental design. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instruments.

    • Setting up a print on the OmniGrid ( Protocol )

      "This protocol provides instructions for setting up the OmniGrid for printing custom microarrays. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core arrayers."

    • Sonicator protocol ( Protocol )

      Protocol describes how to use the Fisher (Misonix) sonicator to fragment DNA or disrupt cell samples. The protocol is designed as a reference and is not a substitute for training. Users must complete a training session before using any of the Bauer Core’s instrumentation.

    Services

    • Cell analysis service ( Material analysis service )

    • Cell sorting service ( Material processing service )

    • DNA, RNA and protein sample analysis service ( Material analysis service )

    • Fragment analysis ( Material analysis service )

    • Genotyping service ( Material analysis service )

    • Illumina Sequencing Service ( Material analysis service )

      The Center supports massively parallel high throughput sequencing using two Illumina HiSeq 2000 systems. These sequencers can generate billions of bases of data per run and enable a wide variety of applications including

      * DNA sequencing
      * Gene Expression
      * Small RNA
      * ChIP-Seq

      Researchers can choose read lengths of 50 or 100 bp. Paired end reads make sequence mapping easier. Multiple samples can be indexed (barcoded) and be combined in order to make the most of the system's output.

      Each flow cell contains 8 channels, enough for 7 samples and 1 control. All the channels on a flow cell must be used at the same time, but they may be shared by different groups. If you are interested in sharing a flow cell, please talk to us and we'll try to help match you with someone.

    • Library prep for Illumina sequencing service ( Material processing service )

      The Center supports automated Illumina library preparation with the Apollo 324 system. The system generates libraries for DNA sequencing, RNA-seq or ChIP-seq starting from as little as 200 ng of DNA or 2ng of total RNA (even smaller starting amounts may be used if necessary). The system uses standard enzymes for library creation and magnetic beads for purification. Researchers may be trained to use the system independently. We are currently piloting full-service library preparation performed on the Apollo system by our core staff. If you are interested in full-service library prep, please email illumina_submission-list@lists.fas.harvard.edu.

    • Nucleic acid shearing service ( Material modification service )

    • Sanger sequencing service ( Material analysis service )

    Software

    • GeneMapper ( Software )

      "GeneMapper® Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. This software specializes in multiapplication functionality, including amplified fragment length polymorphism (AFLP®), loss of heterozygosity (LOH), microsatellite, and SNP genotyping analysis. GeneMapper® Software can help users increase data processing efficiency with remote auto-analysis and command line operation, and allows for multiuser, client-server deployment. The software uses Process Quality Values (PQVs) for automated identification that reduces data review time for high throughput genotyping. In addition, the security and audit features help users meet 21 CFR 11 requirements."

    • Sequencher ( Software )

      DNA sequence assembly software.


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    Last updated: 2015-02-04T13:23:13.891-06:00

    Copyright © 2016 by the President and Fellows of Harvard College
    The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016