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Protein Localization, Identification and Folding Core

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Molecular Biology Core

Facilities and Resources

Overview

The four Molecular Biology Core Programs take advantage of state-of-the-art research laboratories and equipment to execute the wide array of services. Members have ready access to each of the four Programs. The Transgenic Rodent Program laboratories are clustered in 2,500 square feet of central space in Medical Science Research Building (MSRB) I and MSRB II, which are adjacent to the animal facility. There are separate laboratories for ES cell culture and embryo microinjection. The Genome Editing Program is housed in 250 sq. ft. of laboratory space on the 6th floor of the Brehm Tower. Although only a 12 min walk from the Central Medical Campus, a frequent shuttle bus facilitates access. The Viral Vector Program occupies 1,225 sq. ft. of wet laboratory space on the third floor of MSRB II near the Transgenic Rodent Program. The Viral Vector space is divided into three separate wet laboratory modules. One 750 sq. ft. module is split between a virus-free section and a section configured specifically for the construction, isolation and purification of recombinant viral vectors. Access to the Integrated Genomics Program occurs in office space in Palmer Commons on the Central Medical Campus to facilitate face-to-face discussions with Center members. A medical school drop-off site with multiple daily pick up facilitates submission of samples to the UM DNA Sequencing Core located in the North Campus Research Complex 4 miles away where microarray and NextGen sequencing is performed. Research laboratory space for sample preparation and sequencing equipment are in separate rooms, which together total 10,000 sq. ft. High-capacity computer space totaling 3500 sq. ft. is located within the same complex facilitating rapid access to sequencing data for bioinformatics analysis.

Transgenic Rodent Program

Please be sure to submit this core services request form and submit to the appropriate Core Director to be eligible to receive the subsidies.

The Transgenic Rodent Program has a large collection of state-of-the-art equipment for mouse embryo collection and microinjection, tissue culture facilities for ES cell growth and manipulation and molecular biology equipment for DNA cloning. Program laboratories include an embryo microinjection laboratory of 993 sq. ft. in Medical Science Research Building I, ES cell culture laboratories of 194 sq. ft. and 566 sq. ft. in Medical Science Research Building II, and a molecular biology/DNA cloning laboratory of 900 sq. ft. for BAC recombineering, plasmid cloning, and genotyping in MSRBII. These laboratories are in close proximity to each other in the University of Michigan Biomedical Core Laboratory space adjacent to the animal housing area where the Transgenic Program has a dedicated specific pathogen free mouse room with a capacity up to 700 mouse cages and a dedicated room for transgenic rat production colonies (up to 75 cages). These laboratories are in central Medical School space, nearby UMCGR member research laboratories. Dr. Saunders’ office is down the hall from the Program laboratories, and Drs. Samuelson and Merchant offices are nearby in the Biomedical Sciences Research Building. The specialized equipment in the Transgenic Program is listed below.

Mouse Embryo Lab Equipment:  Five microinjection work-stations with Nikon microscope and Narishige micromanipulators are set up for DNA injection into fertilized eggs and ES cell injection into blastocysts. One workstation includes a video monitor and camera to view micromanipulations for training and educational purposes. Three mouse embryo retrieval and surgery workstations are in the same room, which include laminar flow benches, microscopes, and surgical equipment. Support equipment for the microinjections includes pipet pullers, microfuges, incubators, and a Prime Tech PMM1 150 FU Piezo drill. A programmable embryo cryopreservation cooler is available to freeze embryos for storage in liquid nitrogen.

Tissue Culture Equipment:  Cell culture workstations are available for up to 7 people to work with ES cells. Equipment includes biological safety cabinets, incubators, centrifuges, Bio-Rad Gene Pulser electroporator, microscopes for cell culture and chromosome analysis, Milli-Q PF water purification system, autoclaves, -80oC freezers, and liquid nitrogen storage containers. A Forma 1535 alarm/monitor of the type used in blood banks is used to continuously monitor the incubators and freezers.

Molecular Biology Equipment: A laboratory bay with support equipment for molecular cloning and BAC analysis includes a BioRad CHEF DRIII pulsed field gel system, a Mupid Exu submarine agarose gel system, a Sorvall RC6 Plus centrifuge, an I26 New Brunswick Scientific incubator shaker, a C76 New Brunswick Scientific water bath shaker, a Labconco Filtered PCR, Thermomixer - Eppendorf tube mixers, Ovens and Incubators, 2 Veriti 96-well Thermal Cyclers, Mikro 22R - Hettich refrigerated microcentrifuge.

 

Genome Editing Program

Please be sure to submit this core services request form and submit to the appropriate Core Director to be eligible to receive the subsidies.

The Genome Editing Program occupies 250 sq. ft. of laboratory space on the 6th floor of the Brehm Tower for the Michigan Diabetes Research Center Molecular Genetics Core. The space is positioned between the laboratories of the Program Manager Dr. David Olson and the Diabetes Center Director Dr. Martin Myers, who is also a UMGRC member. Thus this program represents collaboration between two University of Michigan NIDDK-supported Centers. Along with bench space, the Program space contains desks for two personnel, each equipped with their own PC desktop computer. The Genome Editing Program has designated refrigerator, -20°C freezer and -80°C freezer. Other laboratory equipment includes two BioRad thermocyclers, shaking incubator, electrophoresis equipment, microfuges, and other common laboratory equipment. The facilities share access to a gel imager, a spectrophotometric plate reader, a laminar flow hood, and several fluorescent and confocal microscopes. The Genome Editing Program has ready access to services of the University of Michigan DNA Sequencing Core used to validate constructs and screen for nucleotide sequence changes in addition to Transgenic Rodent and the Viral Vector Programs where constructs are submitted for use in various in vivo and in vitro experiments.

Viral Vector Program

Please be sure to submit this core services request form and submit to the appropriate Core Director to be eligible to receive the subsidies.

The Vector Core occupies 1,225 sq. ft. of wet laboratory space on the third floor of Medical Science Research Building II. This space is centrally located near the Transgenic Rodent Program laboratories and is near laboratory space occupied by UMCGR members. The Vector Core space is divided into three physically separate wet laboratory modules. One 750 sq. ft. module is configured specifically for the construction, isolation and purification of recombinant adenovirus. This module contains 2 tissue culture hoods, 3 dual and 2 single chamber CO2 incubators, ultracentrifuge, 2 super speed centrifuges and allows 4 researchers to work simultaneously. One hood and 3 incubator stacks have been reserved for core staff use. A second 250 sq. ft. module is configured for the construction and production of recombinant retrovirus/lentivirus. This module is equipped with one laminar flow hood and 2 single chamber CO2 incubator stacks and a fluorescent microscope. A third 225 sq. ft. module has been configured to allow for the construction, isolation and purification of plasmid vectors and related molecular biological analyses. In addition, an adjacent common equipment area is equipped with an ultracentrifuge, an environmental shaker for growth of bacterial cultures, as well as 2 ultracold -80°C freezers and liquid nitrogen freezer for storage of viral stocks and cell banks.  Together these modules provide the Vector Core with the space necessary to comply with biosafety requirements (BL2) for the use and production of these vectors as established by OSEH and the NIH. It establishes an easy access Core facility that can provide investigators with a variety of vector systems for use as in vitro and in vivo reagents. Dr. Lanigan has an office adjacent to the laboratory space.

An itemized list of the major equipment present within the Vector Core follows.


1 Baker SG-400 Class II type A/B3 biological safety cabinet

1 Thermolyne Locator 4 liquid nitrogen freezer

1 Forma 1184 Class II type A/B3 biological safety cabinet

1 Revco ULT 1786 -80°C freezer

1 Nuaire 440-400 Class II type A/B3 biological safety cabinet

1 Forma 993 -86°C ULT freezer

3 Forma water-jacketed, CO2 incubator stacks (dual chamber)

1 Forma 907 -86°C ULT freezer

4 ThermoForma Steri-Cult Incubators

1 Milton Roy Spectronic 601 spectrophotometer

1 Beckman model J2-21 centrifuge

1 Thermo Sci Nanodrop 2000 spectrophotometer

1 Beckman Avanti J-E centrifuge

1 New Brunswick Scientific Innova 4300 environmental shaker

1 Beckman XL-90 ultracentrifuge equipped with SW28 and SW41 swinging bucket rotors

1 E-C Apparatus EC-600-90 power supply

1 Beckman-Coulter Optima LE-80K ultracentrifuge with 2 SW28 and 1 SW41 rotors

1 Mettler AE200 semimicro analytical balance

2 Eppendorf 5810R refrigerated centrifuges

1 Mettler PM4000 top loading balance

1 Eppendorf  5415 R microcentrifuge

1 Thermolyne rotating platform shaker

3 Nikon TMS inverted microscopes with 4X, 10X and 20X phase objectives

2 –20°C freezers

1 Olympus IX73 Inverted Phase Contrast/Ultra-Violet Microscope plus camera

2 Refrigerators

5 Dell Optiplex 755 computers connected to the University of Michigan computer network, equipped with MS Office, Internet software and DNA analysis software.

 

Integrated Genomics Program

Please be sure to submit this core services request form and submit to the appropriate Core Director to be eligible to receive the subsidies.

Bioinformatics Anaylsis: The Bioinformatics Core at the University of Michigan School of Medicine serves as a collaborative unit for researchers as well as providing service using a recharge model for cost-recovery. The Core occupies 3,519 sq. ft. of office space in Building 22 at the North Campus Research Complex, near the Sequencing Core. The Bioinformatics Core utilizes open community software tools such as BWA, Bowtie2, Tophat2, Velvet, Oases, Trinity and many other software applications for diverse bioinformatics analysis. The compute environment includes access to programming languages such as Perl, Python and R as well as all the libraries necessary for developing novel applications and algorithms. In addition the Core (with support from the UMMS Office of Research) licenses Genomatix, GeneGo, and DNAStar Lasergene NGS commercial software, which are shared licenses for researchers across campus. The Bioinformatics Core operates on a cost-recovery model, with charges for the various analyses performed. For example, analysis and reporting for RNA-Seq is charged on a per-sample basis. In addition, more custom analysis can be arranged on a project-by-project basis with cost dependent on the time and resources necessary for the analysis. Dr. McEachin’s office and dedicated laboratory space are near the bioinformatics core. Dr. McEachin also has office space in central Medical School space to facilitate meeting with UMCGR investigators to design and implement the project.

Computational resources:  Individuals have their own laptops and access to shared printers and other office equipment. The researchers all have Gigabit network connections to the desktop.  The Bioinformatics Core has 3 main servers which range from 8-40 cores and 64-512 GB RAM for the majority of computational analysis. In addition, we have direct access to 100 cores (each with 4 GB RAM) in the UM Flux cluster (an 8,000 core cluster) for large batch processing. This allocation can be expanded as needed and is leased on a CPU/month basis. The Core has significant storage capacity with a 2 tiered system: Fast I/O storage for processing and analysis in a 150 TB array (Isilon) dedicated for Core use, and a slower archive tier (NetApp) of expandable storage currently 100 TB, with ability to grow to 1.2 PB. The computing infrastructure is divided between three sites: the Palmer Commons building (PC), the Michigan Academic Computing Center (MACC), and the North Campus Data Center (NCDC). These sites are geographically separated on the University of Michigan campus in Ann Arbor, Michigan. Battery backup, fault monitoring, data snapshots, site-distinct mirroring and off-site backups, are part of our comprehensive backup/recovery strategy. The computing sites are connected by a campus network backbone consisting of a mixture of Gigabit and, increasingly, 10-Gigabit Ethernet. The researchers all have Gigabit connections to the desktop. The campus network is connected to the Internet and Internet2. University of Michigan researchers are also affiliated with several computing consortia, such as Blue Water Petascale computing initiative, TeraGrid, BIRN, and other grid computing and computational infrastructure initiatives.

The Vertebrate Genome Sequencing Core provides access to automated DNA sequencing, genotyping, epigenomics and gene expression analysis technologies on a recharge basis. The Core occupies about 10,000 sq. ft. of pre- and post-PCR laboratory space, with 30 FTE to provide DNA/RNA analysis services, including gene expression profiling (via Affymetrix, OpenArray, Illumina iScan, NextGen sequencing), epigenetic analyses (Sequenom EpiTyper, Qiagen PyroMark) and genome-scale sequencing (Illumina HiSeq 2000/2500 [nine such instruments, a tenth on order]; Pacific Biosciences ‘RS II’, Ion Torrent PGM, Ion Proton). Computation and informatics is provided by numerous Linux systems, with 500 TB of available storage. These systems are supported by our comprehensive Laboratory Information Management System (LIMS), providing sample tracking, data Q/C, data processing and automated data distribution. Ancillary equipment is available to purify DNA (two QiaRobots, a Sage BluePippin), test DNA/RNA quality and concentration (three Agilent 2100/2200 instruments; many fluorimeters and spectrophotometers), and fragment nucleic acids (two Covaris S2 AFA Systems, two Hydroshear systems).

Major Sequencing Core equipment:

ABI Model 3730XL DNA Analyzers (3)
ABI Model 7900HT RT-PCR Systems (2)
ABI QuantStudio system (1)
ABI StepOne qPCR systems (2)
Funded for a digital PCR system, most likely the LifeTech QuantStudio 3D
Affymetrix GeneAtlas scanner
Affymetrix GeneTitan system
Affymetrix GeneChip 3000 7G scanners (2)
Affymetrix FS450 Fluidics Stations (5)
Agilent Bioanalyzer 2100 (2)
Agilent 2200 TapeStation
Illumina BeadStation 500GX
Illumina iScan system with Autoloader 2X
Illumina HiSeq (Models 2000, 2500, qty 9; funded for a tenth sequencer)
Illumina cBOT systems (5)
Ion Torrent Personal Genome Machine
Ion OneTouch Template Prep System (2)
Ion Proton sequencing system
Pacific Biosciences RS II DNA sequencer
Sequenom MassARRAY Compact system
Sequenom RoboDispenser spotting system
Sequenom Nanodispenser spotting robot
Qiagen PyroMark 96 MD
Hydroshear DNA fragmentation system (2)
Covaris S2 DNA fragmentation system (2)
Molecular Dynamics 96-well Fluorimeter
Nanodrop ND1000 spectrophotometer (2)
Nanodrop 1-channel fluorimeter
Qubit 2.0 fluorimetric system
Coulter Z1 Particle Counter
EpMotion 5075 robotic workstation (2)
IntegenX Apollo 324 robotic workstation
Tecan Freedom EVO robotic workstation
Beckman Biomek FX robotic workstation
Beckman Multimek robotic workstations (2)
QiaCube robotic DNA prep system (2)
Robbins Hydra 96-channel pipettor
Low-speed tabletop centrifuges (numerous)
Tabletop microfuges (numerous)
Thermal Cyclers, ~24 heads (MJR, G-Storm, ABI, Qiagen)
Hybridization ovens (numerous)
Savant speed-evaporator (2)
Abgene 96 well plate heat sealers (4)
Site-licensed software for Core/client use (Sequencher [3 copies], GeneMarker [3 copies], Mutation Survey

 

 

 

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