This is a listing of SOM Cores which have not yet implemented iLab. The roll out of the non-iLab cores will occur over a period of two years. As cores implement the iLab management program they will move from this listing to the cores active in iLabs.
The core service listing includes contact information for each core. Click on the core website to access the core.
Leadership
To update or edit information please contact Shawn Franckowiak (sfrancko@jhmi.edu).
Contacts
Name
Role
Phone
Email
Location
Shawn Franckowiak, MBA
Director, OFRR
2-0484
sfrancko@jhmi.edu
JHU School of Medicine, Non-iLabs Cores' Service Listing
The Angle2 stereotaxic system (Leica) consists of a software-assisted stereotaxic instrument which facilitates the accurate targeting of brain regions by using software combined with transponders that detect the position of the pipette carrier. Advantages include an on-screen atlas to facilitate identification of targets, the ability to use an angled approach without the need for path-of-approach calculation, and the ability to automatically correct for head tilt.
To facilitate research involving small molecules, the Department maintains a Bruker Avance III 500 MHz NMR spectrometer equipped with an autosampler. The automation is configured for a convenient queue up of common 1D (1H, 13C, 31P, DEPT, 1H with solvent suppression) and 2D (COSY, TOCSY, HSQC, HMBC, and NOESY) experiments.
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Center for Image-Guided Animal Therapy - Non-iLab Service (see description below for details)
The Center for Image-Guided Animal Therapy (CIGAT) is an internationally-recognized advanced diagnostic imaging facility designed specifically for the veterinary patient.
CIGAT offers the advantage of having experts in radiology and interventional radiology overseeing advanced imaging techniques on leading edge equipment. A veterinary anesthesiologist is involved with every procedure to ensure that each patient is provided optimal care. In addition to veterinary imaging, MRI-, CT- and ultrasound-guided biopsies may be performed, as well as interventional radiology procedures.
The Center for Interdisciplinary Sleep Research and Education (CISRE) is an interdisciplinary program that supports clinical research and education related to Sleep Medicine at Johns Hopkins Medical Institutions and off-site multi-centered clinical trials.
The CISRE leverages the expertise and resources of sleep specialists and their colleagues in a wide range of medical disciplines to facilitate state-of-the-art interdisciplinary initiatives in research and education in Sleep Medicine.
The CISRE integrates a variety of programs in Sleep Medicine including a 10-bed sleep research center with an on-site chronobiology suite, the Johns Hopkins Hospital and Johns Hopkins Bayview Medical Center clinical sleep facilities, an ACGME fellowship program, an NIH-funded T32 training program in multidisciplinary sleep medicine, dedicated sleep IT infrastructure, and a multifaceted AASM-accredited scoring hub.
The Center faculty includes specialists in pulmonary medicine, neurology, psychiatry, endocrinology, cardiology, physical medicine, radiology, gastroenterology, behavioral medicine, pediatrics, geriatrics, otorhinolaryngology, general surgery, neuroscience, nuclear medicine, behavioral pharmacology, internal medicine, and anesthesia.
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Computational Medicine Core - Non-iLab Service (see description below for details)
The CMC offers services and consulting for investigators interested in mathematical modeling of complex biological systems in health and disease. We will work as a consultancy group, offering specific experience in modeling of a variety of biological systems. We can provide free consulting on: selecting the class of models that are most appropriate given the data and scientific questions at hand; guidance on how to formulate and test models; advice on implementation of computational models using different programming languages and environments, hardware considerations, and data visualization methods.
We are the proper entity to activate network jacks in all the Basic Science occupied buildings. We help with static IP requests, static device connection and coordinating moving devices with static IPs as the destination network often is on a different IP subnet. We work with folks with computer viruses that trigger the Hopkins firewall to block their connection to the internet, a way of informing them that something serious is wrong. We help ensure devices are configured correctly for the location they are in. We help with DNS requests as well.
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Computer Support - Non-iLab Service (see description below for details)
We do complete support of PC and Mac computers and network support for Linux based systems. We are an Apple Authorized Provider and can handle warranty claims and get next day parts. There are no hourly rates but parts are billable. We do software configuration, operating system install and data migration to new computers. We sell external hard drives and will work to get automated backups going. We do some crashed hard drive recovery but will send out the extreme cases. We assist with new computer recommendations and purchases when requested.
We support a single home machine for faculty or administrators as the home office is often as important as the East Baltimore one.
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Confocal Microscopy - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core please email: Yuan Cai
The ICE Confocal Service Center is established to provide JHU research Community with imaging needs on confocal microscopy, digital image processing and analysis. Our Center comprises Zeiss LSM710, LSM5 live and LSM510 meta with two photon laser, and one Zeiss LCM (laser cut microscope). These microscopes enables a wide variety of applications in cell and developmental biology.
Consultation is available from MMC directors and staff members on the entire procedures of generating gene knock-out mice. Consultation on generation of BAC transgenic lines
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Coordinated Services for Metabolism Research - Non-iLab Service (see description below for details)
Coordinated Services for Metabolism Research (CSMR) features a 600-square-foot laboratory with ventilated housing for mice, CLAMS and Oxymax open-flow indirect calorimeters, and associated or additional services to measure food and fluid intake, physical activity, glucose homeostasis and behavioral outcomes. CSMR also offers indirect calorimetry during treadmill exercise, with alternative ambient temperatures and photoperiods. The service core is managed by Susan Aja, Ph.D., who provides project management, conducts studies, provides expertise for in vivo approaches to metabolism and obesity research, and refers researchers to CSMR and other facilities and personnel with appropriate equipment and expertise to support metabolic research. CSMR has been supporting projects in energy balance and metabolism since 2008. A downloadable menu of services and pricing is available at the core website.
Please contact the core, for further information and a downloadable menu of services:
The third confocal system is a custom-built two-photon imaging platform based on a design developed by Dr. Karel Svoboda at HHMI/Janelia Farm that is specialized for in vivo imaging. This system also uses a Chameleon Ultra II two-photon laser for excitation and is equipped with a blue LED for epifluorescence imaging. This system offers capabilities beyond that of the commercial Zeiss microscopes in the Core, including simultaneous two-color imaging, more rapid scanning (improved by a factor of two), and greater flexibility due to the open source MATLAB code used to control the instrument. In addition to a standard stereotaxic frame, the system includes a platform for in vivo imaging of both the dorsal horn and dorsal root ganglia of intact spinal cord.
The Johns Hopkins DNA Diagnostic Lab is a CLIA/CAP accredited and NY State licensed clinical genetic testing laboratory that has been in operation since 1979. The lab currently offers clinical grade testing for over 40 germline disorders using NGS, Sanger sequencing, multiple probe ligation assay, DNA fragment analysis, MassARRAY genotyping and bisulfite sequencing. All testing is performed using in-process quality controls and lab performance (accuracy, turn-around time (TAT), client satisfaction) is closely monitored with a quality assurance program and a comprehensive proficiency testing program.
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DNA Synthesis and Purification - Non-iLab Service (see description below for details)
The Synthesis and Sequencing Facility uses five 394 DNA synthesizers. We offer synthesis in four scales at the following rates:
Scale
Price per Base
Approximate Purified Yield
40 nmol
$0.50
NOT AVAILABLE
0.2 umol
$1.00
200-500 ug
1.0 umol
$5.00
1-2 mg
10 umol
$24.00
10 mg
Turnaround time is usually the next day for crude oligos. Oligos that need HPLC purification will take 2 days normally. Longer oligos that require trityl-on purifications may take longer so please inquire when dropping these orders off.
Oligo orders delivered with a template will be cycle sequenced and subsequently loaded on our automated DNA sequencer as soon as the oligo is ready.
For whole exome sequencing projects, we pretest all samples using a high-density SNP array (>200,000 markers). For custom targeted sequencing, we pretest all samples using a 96 SNP GoldenGate assay and 10% using a high-density SNP array (>200,000 markers). For genotyping, we pretest samples using a 96 SNP GoldenGate assay. This extensive pretesting allows us to unambiguously tie DNA samples to production sequencing or genotyping data and to verify sample quality, gender, family relationships and unexpected duplicates.
Investigators have an option to resolve problems found during the pretesting phase. This service is not available for VeraCode custom, focused content arrays or methylation studies.
We include bisulfite conversion for methylation studies using the Zymo EZ-96 DNA Methylation™ Kit. Conversion efficiency is generally >99%.
Statistical genetics consultation is available to interested investigators. This collaboration must be requested well in advance. Appropriate letters of commitment will also be required. These services are not available for methylation or mouse studies.
Graphic Arts in the School of Medicine provides in-house creative design and art production services to the Johns Hopkins community. If you have a project that requires printed materials, please call us for a consultation. We will work with you to create the best possible solution to suit your goals, timeframe and budget.
DESIGN SERVICES
Brochures / Books / Booklets / Newsletters For print and e-distribution
Mailing Packets Fund-raising or information packages may contain a cover letter or small brochure, envelope, return card, return envelope
Posters / Flyers / Exhibits We design a wide range of posters, signs and flyers. We produce up to 2' x 3' prints in-house, and can mount your prints on foam board for easel display. Let us design something for you, or send us a pdf file of your own design. We also design banners, free-standing exhibits, table-top exhibits, and permanent installations.
Certificates
Certificates of completion
Awards
Special Recognition
STATIONERY
You can order a full range of stationery items from us in either Johns Hopkins University style or Johns Hopkins Medicine Style: letterhead, envelopes, business cards, mailing labels, memos, routing slips, note pads, etc.
To order, select the appropriate style link below to download a pdf order form. The completed form can be submitted by clicking on the submit order button or, if you prefer, you can print the completed form and fax the order to us.
Graphics - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: PathPhoto
The requirement of professionally created graphics is a necessity for an institute the caliber of Johns Hopkins. Often, bringing cutting-edge technological breakthroughs means being able to graphically display information that can be both extremely detailed and complex.
PathPhoto can provide a professional and talented resource to convey any type of graphic information, whether statistical, or just artistic. Our staff of highly trained graphic people is available to assist in any form of visual communications. If you’re not positive how to proceed with your visual requirements, talk to us, and we can provide suggestions and ideas.
Some of the major aspects of Graphics found at PathPhoto are:
The facility has two dedicated image analysis workstations each running Imaris software (Bitplane) for performing 3D reconstruction, isosurface rendering, filament tracing/particle tracking, and quantitative co-localization. The Imaris suite of programs has been designed to accept images in many different formats, include Tiff series, BMP series, and images collected with Leica, Olympus, and Zeiss acquisition software. The available modules are Imaris suite, ImarisXT, Filament tracer, and AutoDeblur. AutoDeblur is a deconvolution software package that produces extremely high-quality results through image restoration. ImarisXT allows users to develop their own task-oriented algorithms for Imaris, or use analysis modules developed by others.
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Informatics - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: CIDR
CIDR has a multi-disciplinary informatics team led by Lee Watkins Jr., Director of BioInformatics & IT, Janet L. Goldstein, Assistant Director Bioinformatics, and Elvin Hsu, IT Systems & Support Manager. In addition to bioinformatics, database, systems, and user support professionals, our software development group designs custom solutions for internal clients. Using a team-based, flexible development methodology, the software development team -- fluent in Java, Python, hibernate, JDBC, Django, Perl, JavaScript, SQL and shell scripting -- works collaboratively with colleagues to build and maintain a variety of essential tools to support CIDR's genotyping and next-generation sequencing services:
Laboratory information management system (LIMS)
Automated data analysis pipeline
QC diagnostics
Tailor-made reporting tools
Integration and customization of third-party products
Currently we have an opening for a LAN Administrator III. If you have IT systems and network administration experience and an interest in science, please apply at the JHU Jobs website for requisition #301749.
Because of CIDR's high throughput, quality control standards, and customized services, off-the-shelf software products do not always meet our needs. When it is not possible to integrate a third-party software into our workflows, CIDR's in-house software development team creates solutions for our lab, data analysts, project managers and statistical geneticists. Read about some of them here.
Informatics Infrastructure
To meet the enormous computational and data management challenges created by genotyping and sequencing over 100,000 samples per year, we have continuously expanded and improved our informatics infrastructure, described in detail here. We also have access to the new Maryland Advanced Research Computing Center (MARCC) on the Hopkins Bayview campus. This HPC facility opened in May 2015 with over 19,000 cores (including large-memory and GPU nodes), 20 petabytes of storage and 100 gigabits/second network connectivety, with a CLIA-certifiable platform to be available to us in mid-2016.
Scientific Posters CIDR informatics staff have presented more than 20 posters at scientific conferences. You can find most of them here.
Technical Reports
CIDR informatics staff, working closely with laboratory and scientific colleagues, regularly conduct technology evaluation projects that, if successful, may result in new production processes or systems. When appropriate and time permits, a project technical report is produced to share what we've learned:
Please feel free to contact us if you are a CIDR project investigator with any questions or concerns, are interested in our informatics tools or services or in pursuing potential collaborations. We can most easily be reached at cidr_informatics@lists.johnshopkins.edu
Laboratory Reagents - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: Core Store
Shop Now __________________________________________________________________________________________________
The Core Store is a division of the Genetic Resources Core Facility of the Johns Hopkins University School of Medicine. In operation since 1989, the Core Store is a non-profit resource that offers appreciable savings and fast delivery of a wide variety of research products. The Core Store provides one-stop shopping, saving researchers both time and money. In addition to its product offering, the store charges no shipping and handling fees and has free delivery to three JHU campuses.
A MakerBot Replicator 2x allows individuals to use software to generate a 3D model of their desired product; this is then converted into a file formats which the MakerWare software can output to the 3D printer. This equipment permits inexpensive and efficient production of a wide variety of research components.
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Metabolomics Program
This core is not active in iLabs.
Core Summary
Dr. Le is one of the first investigators to apply metabolomics technologies to the field of cancer metabolism and metabolic aspects of other diseases, demonstrated by her lab’s publication record as a pioneer in the field. Dr. Le’s laboratory developed and brought metabolomics technologies to Johns Hopkins and has been providing metabolomics assessments to researchers from several Johns Hopkins campuses (main medical campus, Bayview medical campus, Applied Physics Laboratory and JHU Homewood campus) as well as researchers outside Johns Hopkins (University of Maryland, NIH, Memorial Sloan-Kettering Cancer Center, George Washington University, Washington State University, Oregon Health & Science University, Kaohsiung Medical University in Taiwan, United Arab Emirates University in UAE, Scientific Centre of Monaco in Monaco; and the University of São Paulo in Brazil…). Their facility is equipped with mass spectrometer-UPLC systems obtained through a shared instrument grant (S10 grant). They are also part of The Johns Hopkins Institute for Clinical and Translational Research (ICTR)-supported facility
What They Offer:
o Provides consultation to basic, clinical, and translational research teams regarding the feasibility, design, and costs of projects using metabolomics technologies (including mass spec and NMR-based metabolomics);
o Metabolomics assessments based on specific research projects/questions: ranging from simple assays to high-throughput approaches such as global metabolic profiling and stable isotope-13C, 15N-labeling on a wide variety of sample types;
o Provides extensive data analysis and identification of options for subsequent steps towards clinical implementation.
Examples of Metabolomics-Based Discovery of Metabolic Aspects of Cancer and Other Diseases
Nikon TU2000 Inverted Microscope This PC has a CD burner, a shared directory on the network, and a USB port for either external hard drives or flash (memory) keys.
Zeiss LSM 510 Meta Confocal The LSM has both CD and DVD burners available. The USB port may be used with an external hard drive or flash key. This PC is not networked to protect it from viruses, spyware, and mis-use.
MRI Research Service Center - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: MRI Research Center
Research MRI facilities -
The MRI Service Center, run by the Division of MR Research in the Department of Radiology and directed by Dr Paul Bottomley, operates four MRI scanners for research. It leases 1-2 scanners back to the hospital for clinical use, leaving 2 full-time scanners for 100% research use. The available scanners are: {1} a GE 1.5T 8-channel Signa Horizon (research upon request), {2} a Philips 16-channel 3T Achieva equipped with an X-ray C-arm (100% research); plus 100% research split between {3} a Siemens 3T Trio and {4} a 1.5T Espree. The Espree is also equipped with a full angiographic floor-mounted X-ray fluoroscopic suite and miyabi table transfer system for the purpose of developing interventional MRI. The scanners are supported by hourly machine rates, and have Radiology Technologist (RT) support by 3 RTs during normal working hours, supported by the MRI Service Center.
The FM Kirby fMRI center in the Kennedy Krieger Institute located near the main hospital has two Philips 3T MRI systems, {5} and {6} available for 100% research for use in the neurosciences. The Kirby Center is supported by an NIH resource grant and is directed by Dr Peter van Zijl in the Division of MR Research. The Kirby center, with support from the Department of Radiology, the NIH and other sources, also has a new 7T Philips whole body MRI system as of 2009.
Small-bore NMR/MRI systems -The Division of MR Research manages 2 other smaller bore NMR/MRI Service Centers suitable for studies of animal models, cell systems, and in vitro studies. -The NMR Service Center - has 400 MHz and 500 MHz Bruker NMR spectrometers, and a Bruker 4.7T 40 cm-horizontal bore spectrometer/imager equipped with rapid-switching gradient coils. -The Molecular Imaging Center – is located in the Broadway Research Building and is primarily geared to animal genetic models in a closed environment. It has a Bruker horizontal bore 9.4T animal system, in addition to an eXplore Vista small animal PET scanner, a SPECT-CT system, an IVIS Xenogen 200 optical imaging system for mice and rats, a VisualSonics small animal ultrasound unit, and a Faxitron MX-20 specimen radiography system.
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nanoACQUITY UPLC system from Waters - Non-iLab Service (see description below for details)
The MS Facility comprises a Triple Quadrupole Mass Spectrometer, TSQ Vantage from Thermo Scientific and a nanoACQUITY UPLC system from Waters. The TSQ bears a HESI-II electrospray ionization source and this UPLC/MS system is well-suited for quantification and identification of small molecules as well as biomolecules.
These services are open to members of the JHU community. For training and further assistance, please contact the NMR/MS Facility Manager.
Shridhar Bhat, Ph.D. NMR/MS Facility Manager Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine 725 North Wolfe Street / WBSB-322 shri@jhu.edu
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Neurolucida Neuron Tracing system (Microbrightfield) - Non-iLab Service (see description below for details)
Additional image analysis capabilities are provided by our Neurolucida Neuron Tracing system (Microbrightfield). This system offers a variety of drawing/analysis options, including cell tracing/morphology quantification, 3D brain mapping, and serial section reconstruction. The software is paired with a Zeiss AxioImager microscope equipped with transmitted light and a motorized stage, for tracing directly from slides. Alternatively, image files collected on another system can be imported into Neurolucida. The analysis capabilities of Neurolucida complement those which can be achieved using the Imaris suite of programs, because the latter is geared almost entirely toward analysis of fluorescent images, whereas Neurolucida excels at reconstruction and analysis of brightfield images (e.g. DAB labeled cells). Because this system includes a color camera, it also provides a route for obtaining color images of brightfield samples, such as LacZ.
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Next Generation Sequencing - Non-iLab Service (see description below for details)
Next Generation Sequencing is now being offered at our facility using Illumina's MiSeq platform.
The MiSeq uses a "Sequencing by Synthesis" concept whereby prepared libraries are loaded onto the MiSeq flow cell, cluster generation is performed and sequencing by synthesis (SBS) occurs.
There are four different reagent kits available: 50 cycles, 150 cycles, 300 cycles, and 600 cycles.
Dual index sequencing is available with the capacity to multiplex up to 96 samples in one run. The coverage you require will determine how many samples can be multiplexed and run at one time.
Cost: Costs vary depending on the number of cycles you need and the type of library prep needed. Please inquire about pricing for individual projects with Jodie.
We will break down the individual cost of each project for you rather than just giving you a generic library prep cost.
As an example, we ran 24 bacterial genomes using a 2 x 300 sequencing kit and Illumina's Nextera Library prep kit at the cost of approximately $188/library.
We partner with the Genomic Analysis and Sequencing Core Facility located in the SOPH. Please visit their website to see a list of their services.
Applications include:
Targeted Resequencing
Amplicon Sequencing
Hybrid Capture
Clone Checking
Small Genome Sequencing
De novo
Resequencing - includes alignment to your reference genome
Plasmids
RNA Sequencing
16S Metagenomics
Small RNA Sequencing
Quality Control
Library QC
Regulation
ChIP-Seq usually for QC before scaling up to a HiSeq run
The steps to generating sequence include the following:
Consultation. We need to sit down and discuss your particular project.
Building a Library. Illumina has sample prep kits for each of their applications. A lot of labs like to save money by doing their own library prep and we are happy to run these samples but please consult with the sequencing staff as to the requirements. Low diversity libraries will require a 5 to 10% PhiX control spike-in to normalize the library and enable better sequencing results.
Each Illumina sample prep kit requires a different amount of starting material and we will advise you as to how much we need depending on your project and library generation needs.
Sequencing run times vary depending on the application but are usually done within 2-3 days.
Data is typically stored in Illumina's BaseSpace Cloud and subsequently be shared with you via email invite. However, we do have a dedicated server where data can be stored as well.
Data analysis - The analysis strategy should be discussed during consultation. You will receive the following files depending on the application.
Raw data in the form of compressed fastq data files.
Aligned reads will provide bam formatted files (.bam) which can be viewed using a Genome Browser such as the Broad's Integrated Genome Viewer (IGV).
Variant calling identifies SNPs and short indels and are generated in a Variant Call Format (.vcf) file.
Further analysis can be performed by a bioinformatician. We do not have a bioinformatics person on staff but rather have someone we can refer you to who is an independent contractor. His contact information is James White, PhD at james.dna.white@gmail.com or http://jameswhitephd.com. James has extensive experience and references can be supplied.
Instrumentation consists of an Aapptec Focus Synthesizer. The synthesis is run utilizing Fmoc chemistry. Purification is performed by Reverse-phase HPLC. Molecular weights are checked by Maldi TOF. All peptides made in the facility are for research purposes only.
The Aapptec Focus Synthesizer allows me to synthesize multiple peptides at once.
Also for those of you that only need a few mgs of peptide, we are offering some "ready-made and purified" peptides. The cost per mg is much lower than what you will find outside. Please click on the following link for a list of peptides that are available.
If you need a lot of peptide, it is cheaper to get a custom synthesis done. Also, if you have suggestions for peptides that we should stock, please send Jodie an email at jfrankl1@jhmi.edu. Thanks.
Large Scale Synthesis:
Expected yields are 300-450 mg of crude peptide and approximately 20-50 mg of purified peptide per each HPLC run consisting of a 150 mg injection. You can have the entire synthesis purified or half of it and receive the remaining crude for any future experiments. Crude peptides can be brought back to us at a later date for purification.
Cost:
$30.00 for each amino acid $150.00 for each preparative HPLC run
Small Scale Synthesis:
Expected yields are 150-200 mg of crude peptide and approximately 5 to 20 mg of purified peptide.
Cost:
$20.00 for each amino acid $150.00 for each preparative HPLC run
We will routinely accept peptides of 30 amino acids or less. Anything greater than 30 will be accepted only after consultation. For longer peptides, please consult with Jodie to see if there are any anticipated problems with your chosen sequence.
Purification of peptides NOT synthesized by the SSF:
Cost: $200 for each preparative HPLC Run
Peptide Modifications:
There are many modifications available including, phosphorylated amino acids, N-terminal acetylation, N-terminal biotinylation, N-terminal myristolation, and N-terminal flourescent dyes. Please inquire about pricing. For any other unusual modifications, please see Jodie.
Peptides for Antibody Production:
The range of purity for peptides used for antibody production is 70% or greater. If your peptide is less than 70% pure, you can expect approximately 20-50 mg after purification
PET Service Center - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: Michelle Willett
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Photography - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: PathPhoto
Our photographers offer a wide range of services to meet your needs for publication, teaching and scientific documentation. From photography in the Operating Room to same day digital color printing, our goal is to provide fast top quality service. The philosophy of the department is to serve the faculty, staff and students with the best service available in the field of medicine.
We setup network printers and do common repairs such as pickup rollers and fuser replacements. We will coordinate an outside technician if it involves a formatter board replacement or major gear damage.
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Protein/Peptide Analysis - Non-iLab Service (see description below for details)
Instrumentation consists of a state-of-the-art Perkin-Elmer/Applied Biosystems Procise Protein Sequencing System. This is a highly sensitive system that can detect quantities as low as 1 picomole. It is also compatible with samples that have been electroblotted onto PVDF.
Cost:
$200.00 set-up and first three cycles (3 amino acids) $20.00 each additional amino acid
$5.00 Prosorb sample clean up (optional)
Chemistry:
The Edman chemistry cycle consists of three stages:
1. Coupling
The N-terminus of the protein couples with PITC under basic conditions to form a phenylthiocarbamyl (PTC)-polypeptide.
2. Cleavage
The peptide bond of the N-terminal PTC-residue undergoes acid cleavage from the polypeptide chain. This results in the release of an unstable anilinothiazolinone (ATZ) derivative of the amino acid.
3. Conversion
The unstable ATZ-amino acid is converted into the corresponding phenylthiohydantoin (PTH) derivative. The PTH-amino acid is stable.
At the end of each cycle of Edman degradation, the PTH-amino acid is separated from reaction by-products and identified, by HPLC chromatography and UV absorbance. Although not part of the Edman degradation cycle per se, PTH-amino acid analysis, like Edman degradation, is an essential step in the protein sequencing process.
Sample Purity -- What to Avoid:
Sample purity is one of the most critical factors for successful protein sequencing. Samples should:
Contain one protein component only.
Be free of reagents which interfere with Edman degradation and the sequencing process (e.g., Tris, glycine, guanidine, glycerol, sucrose, ethanolamine, SDS, Triton X-100, Tween,, ammonium sulfate and other ammonium salts)
The two basic approaches that can be used to purify samples for protein sequencing are:
SDS-PAGE and electroblotting
ProSorb sample preparation cartridges (available in our lab)
SDS-PAGE and electroblotting should be used if the protein of interest is in a complex mixture of proteins. For proteins isolated in solution which are free of contaminating proteins but contain salts, buffers and/or detergents, use ProSorb cartridges.
Sample Preparation: Proteins/Peptides in solution:
For best results an optimal amount of to load on the sequencer is 200 pmole of peptide or protein.
Samples should be as homogeneous as possible and free of salts, detergents, lipids and other non-volatile ingredients (SDS, TRIS, etc.). Solutions used in dissolving samples should, therefore, contain only volatile components such as water, acetonitrile, etc. and be concentrated in a volume of no more than 60 ul. If your sample is supplied dried, it will be brought up in a 1:1:1 mixture of acetonitrile, water and acetic acid unless otherwise specified.
If your sample contains these non-volatile ingredients, we can pass it through a Prosorb column which will clean up your sample while at the same time deposit it onto a piece of PVDF. The fee for this service will be $5.00.
For proteins/peptides adsorbed onto PVDF, again the optimal amount protein/peptide to load on the sequencer is 200 pmole. The piece of PVDF should be no larger than 3 x 7 mm and the number of pieces no more than five. Keep in mind that transfer is not 100% efficient so load an adequate amount of protein or peptide onto the gel prior to electrophoresis. Remember that the intensity of the stain is not indicative of sample amount and that the presence of a single band does not always indicate that there is only one species present.
Please note that nitrocellulose cannot be used in our automated sequencer.
If you would like to have a more detailed description of sample preparation, please look at the Perkin-Elmer/Applied Biosystems Guide to Sample Preparation.
The research radiology lab has 3 spacious rooms to perform a variety of research projects involving animals. The lab has two fluoroscopy suites (Toshiba Infinix-I and Philips Allura Xper FD) with fixed table c-arms and a 1-slice CT. An additional room is available to perform procedures that do not require fluoroscopy, such as endoscopy or surgery. All rooms are equipped with physiological monitoring equipment (end tidal CO2, invasive blood pressure, ECG), gas anesthesia machines, and defibrillators. There is also a portable x-ray machine available for radiographs. The lab has technicians available to help prepare the animals, monitor anesthesia and assist with the fluoroscopy equipment. The lab also has a veterinarian available to help with developing animal models, writing protocols, and other animal issues.
Service Areas
Animal, Imaging
Building
Traylor 312, 319 and 322
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Sanger Sequencing - Non-iLab Service (see description below for details)
Instrumentation consists of an Applied Biosystems 3730xl DNA Analyzer.
NEWS:
DNA Sequencing $6.00/reaction
PeakTrace is now being used to give you longer reads of around 1020 good bases.
We are offering Ampure PCR clean-up using our robot for $1.00 a sample.
If you drop your sample off by 1:00 p.m., you can expect your data to be ready the next day. Please look at the white board when you drop off your samples for the date your data will be ready. The date listed is the worse case scenario, it is always a good idea to check the server the next day in the afternoon anyway no matter what time you drop your samples off.
We also offer Saturday delivery of your data to the server.
Sequencing Cost: $6.00 per reaction (includes universal primer -- see universal primer link below for a complete list of our free primers. We can add to the list if there is a primer that you think we should stock.)
Note: For samples with an RNAi insert, we charge 50 cents more per sample so $6.50. Large templates such as BACS are $20.00 per sample.
Campus Sample Drop-Off Locations:
We have three drop-off locations located on campus.
WBSB: Outside of Room 418 for after hours.
BRB: Outside of room 372
SOPH: Inside the Monument street entrance where the FedEx box is located. Look for the black "mailbox" on the wall. Instructions are on the box.
Requested Concentrations:
Custom Primers Supplied by You:4.0 uM in water with a total of 7 ul per reaction
Plasmid Templates:0.1 to 0.2 ug/ul for (ds) plasmids with 7 ul per reaction in water.
ShRNAi Templates: 0.2 ug/ul with 10 ul per reaction in water. DO NOT MIX WITH PRIMER, please provide template and primer separately if using custom primers.
PCR Products: 10 to 15 ng/ul (with an average length of 500 bp) adjust amount accordingly for longer PCR products. If your PCR products are large, i.e., 4 Kb or something like that, then use the amounts requested under Plasmid Template.
BACs and COSMIDs: 0.5 ug/ul with 12 ul per reaction in water. Must be very clean. The charge for this is $20.00 per reaction. DO NOT MIX WITH PRIMER.
---------------------------------------------------------------------- The benefits of using YOUR JHMI Sequencing Facility:
First and foremost, we are here for YOU. This is the sole reason the facility exists. So please make use of your Hopkins facility.
Template and Primer can be mixed by you or we can do it here in the lab. There is no extra charge if we mix it. If mixing, use equal amounts.
We also offer other discounted pricing for samples that are already cycle sequenced by you. Ask the staff for more details.
All samples will be stored for a month. We will store your samples longer if you request this. We also will hold on to primers that you use frequently as well.
Every chromatogram is analyzed by hand after printing. We will repeat samples, at our discretion, should we see that something failed when everything else worked.
We are available to talk with you from 7:30 a.m. to 5:00 p.m. Monday through Friday regarding your sequencing. Email is checked over the weekend as well; and if possible, we will try to resolve any problems you may have.
For whole exome sequencing projects, we pretest all samples using a high-density SNP array (>200,000 markers). For custom targeted sequencing, we pretest all samples using a 96 SNP GoldenGate assay and 10% using a high-density SNP array (>200,000 markers). For genotyping, we pretest samples using a 96 SNP GoldenGate assay. This extensive pretesting allows us to unambiguously tie DNA samples to production sequencing or genotyping data and to verify sample quality, gender, family relationships and unexpected duplicates.
Investigators have an option to resolve problems found during the pretesting phase. This service is not available for VeraCode custom, focused content arrays or methylation studies.
We include bisulfite conversion for methylation studies using the Zymo EZ-96 DNA Methylation™ Kit. Conversion efficiency is generally >99%.
Statistical genetics consultation is available to interested investigators. This collaboration must be requested well in advance. Appropriate letters of commitment will also be required. These services are not available for methylation or mouse studies.
For Windows, Mac and NAS servers under support, we provide initial setup, secure location, daily backups (not for NAS), account maintenance, gigabit Ethernet connection, hardware and software support. All NAS devices are setup with disk redundancy at the minimum and striping for speed when possible.
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Small Animal Imaging - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: Small Animal Imaging
Small animal imaging is increasingly recognized as an important facet of preclinical and translational cancer research. Perhaps most significant among the clear advantages of imaging experimental animals is that physiology, pathology and novel phenotypes can be understood in the most relevant milieu — in an intact, living system. Less obvious is the fact that often the most significant leap forward an already important biological study takes is when its results can be extended to the in vivo case — a necessary and often sufficient precondition for success in the clinic.
The Johns Hopkins Small Animal Imaging Resource Program (SAIRP) labors to provide that translational step, generating the confidence necessary to move new cancer therapies to patients. Our ultimate goal is to move small animal imaging science forward to the point that the incorporation of these imaging techniques is second nature to the daily practice of cancer researchers.
The MS Facility comprises a Triple Quadrupole Mass Spectrometer, TSQ Vantage from Thermo Scientific and a nanoACQUITY UPLC system from Waters. The TSQ bears a HESI-II electrospray ionization source and this UPLC/MS system is well-suited for quantification and identification of small molecules as well as biomolecules.
These services are open to members of the JHU community. For training and further assistance, please contact the NMR/MS Facility Manager.
Shridhar Bhat, Ph.D. NMR/MS Facility Manager Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine 725 North Wolfe Street / WBSB-322 shri@jhu.edu 410-502-4803
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TSQ Vantage from Thermo Scientific - Non-iLab Service (see description below for details)
The MS Facility comprises a Triple Quadrupole Mass Spectrometer, TSQ Vantage from Thermo Scientific and a nanoACQUITY UPLC system from Waters. The TSQ bears a HESI-II electrospray ionization source and this UPLC/MS system is well-suited for quantification and identification of small molecules as well as biomolecules.
These services are open to members of the JHU community. For training and further assistance, please contact the NMR/MS Facility Manager.
Shridhar Bhat, Ph.D. NMR/MS Facility Manager Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine 725 North Wolfe Street / WBSB-322 shri@jhu.edu
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Veterinary Medical Care and Research Animal Support - Non-iLab Service (see description below for details)
Research Animal Resources (RAR) is Johns Hopkins’ centralized provider of veterinary medical care and research animal support. Visit these pages for information regarding all aspects of animal care and veterinary assistance for your animal research.
This is not the animal care and use committee (ACUC) website. For regulatory (ACUC) issues please visit the IACUC Website or call (443) 287 3738; acuc@jhmi.edu
Clinical calls: Unexpected mortality? Colony problems? Could it be related to an infectious or environmental cause? Call a vet for help on 410-955-3273
The Welch Library’s Informationists provide consultation, collaboration, and training on information tools and questions that arise throughout the research lifecycle. This includes consulting or engaging with teams on systematic reviews and other expert searching; data management planning and sharing; bibliographic citation management; grants and funding; publication of findings; research impact; clinical evidence; and bioinformatics resources.
Welch Informationists services range from simple consultation on best practices and training to full collaboration as members of a research team.
Service Areas
Systematic reviews; expert literature searching; bibliographic citation management; grants and scholarly output; clinical evidence; bioinformatics tools.
Location
Multiple locations: 2024 East Monument St., Welch Medical Library building, staffed locations in Zayed, BSPH, SON, or your office/lab
FINZ is the Institute of Genetic Medicine Center for Functional INvestigation in Zebrafish
"FINZ center construction was funded by a generous gift from Joel J. and Lillian Cohen"
FINZ is your entry point for all things zebrafish. Whether you want to rapidly determine the function of a candidate gene identified in the human population or other systems or assay the regulatory potential of selected sequences – we are here to help.
Location:
FINZ is located in the Edward D. Miller Research Building (452) on the East Baltimore Campus. Services: We provide specialized services that include, microinjection of zebrafish embryos, establishment of transgenic lines, morpholino-based gene knockdown strategies, whole mount in situ hybridizations, and in vitro fertilization. Other services comprise adult fish and embryo sales, and transgenic line screenings. Training courses are also available at times to be advertised during the year.
The second system is a Zeiss AxioExaminer upright microscope with an LSM 710 scan head. Due to refinements of the light path within the scan head, the system has better detection capabilities that improve the signal-to-noise ratio of fluorescent images. In addition, the filter-free spectral detection allows the user to define emission collection parameters, rather than being limited to a particular set of installed emission filters. Furthermore, this instrument has a number of distinct advantages for multiphoton imaging, including a redesigned microscope stand that has increased objective travel, allowing the use of a new 20x high numerical aperture objective with increased transmission in the infrared. An important feature of this microscope is the addition of a low noise photomultiplier tube placed immediately adjacent to the objective for optimal light capture. The 710 can also be used with a highly sensitive GaAsP detector, which excels at collecting images of fluorescently labeled cells deep within tissue. This improvement has been particularly critical for in vivo applications, and has allowed users to monitor cell motility in intact preparations. Because the GaAsP detector is extremely sensitive to ambient light, we have constructed a light-tight enclosure around this system, so that both microscopes can be used simultaneously.
Inquire
Zeiss Cell Observer, Inverted Epifluorescence Imaging - Non-iLab Service (see description below for details)
The Zeiss Cell Observer system consists of an AxioObserver inverted microscope equipped with fluorescent and transmitted light, an Axiocam MRm, and filter sets compatible with DAPI, GFP, Cy3 and Cy5. An environmental chamber to facilitate control of temperature, humidity, and CO2 is mounted on the microscope, allowing maintenance and imaging of live cells over long periods of time. A motorized stage facilitates the identification and imaging of multiple regions of interest. Zen for Widefield software permits flexible design of experiments and provides various post-processing capabilities. The system can also be used to image fixed slides. One feature that is useful to many labs is the motorized stage, which supports acquisition of tiled images and allows users to capture large regions of interest at high magnification. Post-processing features are available to remove line artifacts that are often apparent in such tiled images.
Inquire
Zeiss LSM 510 Confocal Microscope - Non-iLab Service (see description below for details)
The facility contains three confocal microscope systems that allow high resolution imaging of labeled cell components in three dimensional space. The first system consists of a Zeiss LSM 510 motorized upright microscope, equipped with a META scanning module, two non-descanned detectors for multi-photon work, and a motorized stage for time lapse imaging. The LSM 510 can be configured with the META detector plus two traditional detectors for fluorescent or reflected light imaging. The META detector can also be used as a unique spectral detector or a conventional "band-pass" detector. All three detectors can be recorded and displayed simultaneously. This system employs a PC-based user interface to control the microscope, laser excitation, scanning and image acquisition, and is capable of digitally capturing up to 12 bit 2K x 2K pixel images, while the AIM LSM software controls image data acquisition and processing. The system can perform Fluorescent Recovery after Photobleaching (FRAP), Fluorescence Resonance Energy Transfer (FRET), and quantitative co-localization.
We are the proper entity to activate network jacks in all the Basic Science occupied buildings. We help with static IP requests, static device connection and coordinating moving devices with static IPs as the destination network often is on a different IP subnet. We work with folks with computer viruses that trigger the Hopkins firewall to block their connection to the internet, a way of informing them that something serious is wrong. We help ensure devices are configured correctly for the location they are in. We help with DNS requests as well.
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Computer Support - Non-iLab Service (see description below for details)
We do complete support of PC and Mac computers and network support for Linux based systems. We are an Apple Authorized Provider and can handle warranty claims and get next day parts. There are no hourly rates but parts are billable. We do software configuration, operating system install and data migration to new computers. We sell external hard drives and will work to get automated backups going. We do some crashed hard drive recovery but will send out the extreme cases. We assist with new computer recommendations and purchases when requested.
We support a single home machine for faculty or administrators as the home office is often as important as the East Baltimore one.
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Printer Support - Non-iLab Service (see description below for details)
We setup network printers and do common repairs such as pickup rollers and fuser replacements. We will coordinate an outside technician if it involves a formatter board replacement or major gear damage.
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Server and NAS Support - Non-iLab Service (see description below for details)
For Windows, Mac and NAS servers under support, we provide initial setup, secure location, daily backups (not for NAS), account maintenance, gigabit Ethernet connection, hardware and software support. All NAS devices are setup with disk redundancy at the minimum and striping for speed when possible.
The Center for Image-Guided Animal Therapy (CIGAT) is an internationally-recognized advanced diagnostic imaging facility designed specifically for the veterinary patient.
CIGAT offers the advantage of having experts in radiology and interventional radiology overseeing advanced imaging techniques on leading edge equipment. A veterinary anesthesiologist is involved with every procedure to ensure that each patient is provided optimal care. In addition to veterinary imaging, MRI-, CT- and ultrasound-guided biopsies may be performed, as well as interventional radiology procedures.
For whole exome sequencing projects, we pretest all samples using a high-density SNP array (>200,000 markers). For custom targeted sequencing, we pretest all samples using a 96 SNP GoldenGate assay and 10% using a high-density SNP array (>200,000 markers). For genotyping, we pretest samples using a 96 SNP GoldenGate assay. This extensive pretesting allows us to unambiguously tie DNA samples to production sequencing or genotyping data and to verify sample quality, gender, family relationships and unexpected duplicates.
Investigators have an option to resolve problems found during the pretesting phase. This service is not available for VeraCode custom, focused content arrays or methylation studies.
We include bisulfite conversion for methylation studies using the Zymo EZ-96 DNA Methylation™ Kit. Conversion efficiency is generally >99%.
Statistical genetics consultation is available to interested investigators. This collaboration must be requested well in advance. Appropriate letters of commitment will also be required. These services are not available for methylation or mouse studies.
Informatics - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: CIDR
CIDR has a multi-disciplinary informatics team led by Lee Watkins Jr., Director of BioInformatics & IT, Janet L. Goldstein, Assistant Director Bioinformatics, and Elvin Hsu, IT Systems & Support Manager. In addition to bioinformatics, database, systems, and user support professionals, our software development group designs custom solutions for internal clients. Using a team-based, flexible development methodology, the software development team -- fluent in Java, Python, hibernate, JDBC, Django, Perl, JavaScript, SQL and shell scripting -- works collaboratively with colleagues to build and maintain a variety of essential tools to support CIDR's genotyping and next-generation sequencing services:
Laboratory information management system (LIMS)
Automated data analysis pipeline
QC diagnostics
Tailor-made reporting tools
Integration and customization of third-party products
Currently we have an opening for a LAN Administrator III. If you have IT systems and network administration experience and an interest in science, please apply at the JHU Jobs website for requisition #301749.
Because of CIDR's high throughput, quality control standards, and customized services, off-the-shelf software products do not always meet our needs. When it is not possible to integrate a third-party software into our workflows, CIDR's in-house software development team creates solutions for our lab, data analysts, project managers and statistical geneticists. Read about some of them here.
Informatics Infrastructure
To meet the enormous computational and data management challenges created by genotyping and sequencing over 100,000 samples per year, we have continuously expanded and improved our informatics infrastructure, described in detail here. We also have access to the new Maryland Advanced Research Computing Center (MARCC) on the Hopkins Bayview campus. This HPC facility opened in May 2015 with over 19,000 cores (including large-memory and GPU nodes), 20 petabytes of storage and 100 gigabits/second network connectivety, with a CLIA-certifiable platform to be available to us in mid-2016.
Scientific Posters CIDR informatics staff have presented more than 20 posters at scientific conferences. You can find most of them here.
Technical Reports
CIDR informatics staff, working closely with laboratory and scientific colleagues, regularly conduct technology evaluation projects that, if successful, may result in new production processes or systems. When appropriate and time permits, a project technical report is produced to share what we've learned:
Please feel free to contact us if you are a CIDR project investigator with any questions or concerns, are interested in our informatics tools or services or in pursuing potential collaborations. We can most easily be reached at cidr_informatics@lists.johnshopkins.edu
For whole exome sequencing projects, we pretest all samples using a high-density SNP array (>200,000 markers). For custom targeted sequencing, we pretest all samples using a 96 SNP GoldenGate assay and 10% using a high-density SNP array (>200,000 markers). For genotyping, we pretest samples using a 96 SNP GoldenGate assay. This extensive pretesting allows us to unambiguously tie DNA samples to production sequencing or genotyping data and to verify sample quality, gender, family relationships and unexpected duplicates.
Investigators have an option to resolve problems found during the pretesting phase. This service is not available for VeraCode custom, focused content arrays or methylation studies.
We include bisulfite conversion for methylation studies using the Zymo EZ-96 DNA Methylation™ Kit. Conversion efficiency is generally >99%.
Statistical genetics consultation is available to interested investigators. This collaboration must be requested well in advance. Appropriate letters of commitment will also be required. These services are not available for methylation or mouse studies.
The Center for Interdisciplinary Sleep Research and Education (CISRE) is an interdisciplinary program that supports clinical research and education related to Sleep Medicine at Johns Hopkins Medical Institutions and off-site multi-centered clinical trials.
The CISRE leverages the expertise and resources of sleep specialists and their colleagues in a wide range of medical disciplines to facilitate state-of-the-art interdisciplinary initiatives in research and education in Sleep Medicine.
The CISRE integrates a variety of programs in Sleep Medicine including a 10-bed sleep research center with an on-site chronobiology suite, the Johns Hopkins Hospital and Johns Hopkins Bayview Medical Center clinical sleep facilities, an ACGME fellowship program, an NIH-funded T32 training program in multidisciplinary sleep medicine, dedicated sleep IT infrastructure, and a multifaceted AASM-accredited scoring hub.
The Center faculty includes specialists in pulmonary medicine, neurology, psychiatry, endocrinology, cardiology, physical medicine, radiology, gastroenterology, behavioral medicine, pediatrics, geriatrics, otorhinolaryngology, general surgery, neuroscience, nuclear medicine, behavioral pharmacology, internal medicine, and anesthesia.
The CMC offers services and consulting for investigators interested in mathematical modeling of complex biological systems in health and disease. We will work as a consultancy group, offering specific experience in modeling of a variety of biological systems. We can provide free consulting on: selecting the class of models that are most appropriate given the data and scientific questions at hand; guidance on how to formulate and test models; advice on implementation of computational models using different programming languages and environments, hardware considerations, and data visualization methods.
Coordinated Services for Metabolism Research (CSMR) features a 600-square-foot laboratory with ventilated housing for mice, CLAMS and Oxymax open-flow indirect calorimeters, and associated or additional services to measure food and fluid intake, physical activity, glucose homeostasis and behavioral outcomes. CSMR also offers indirect calorimetry during treadmill exercise, with alternative ambient temperatures and photoperiods. The service core is managed by Susan Aja, Ph.D., who provides project management, conducts studies, provides expertise for in vivo approaches to metabolism and obesity research, and refers researchers to CSMR and other facilities and personnel with appropriate equipment and expertise to support metabolic research. CSMR has been supporting projects in energy balance and metabolism since 2008. A downloadable menu of services and pricing is available at the core website.
Please contact the core, for further information and a downloadable menu of services:
The Johns Hopkins DNA Diagnostic Lab is a CLIA/CAP accredited and NY State licensed clinical genetic testing laboratory that has been in operation since 1979. The lab currently offers clinical grade testing for over 40 germline disorders using NGS, Sanger sequencing, multiple probe ligation assay, DNA fragment analysis, MassARRAY genotyping and bisulfite sequencing. All testing is performed using in-process quality controls and lab performance (accuracy, turn-around time (TAT), client satisfaction) is closely monitored with a quality assurance program and a comprehensive proficiency testing program.
Laboratory Reagents - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: Core Store
Shop Now __________________________________________________________________________________________________
The Core Store is a division of the Genetic Resources Core Facility of the Johns Hopkins University School of Medicine. In operation since 1989, the Core Store is a non-profit resource that offers appreciable savings and fast delivery of a wide variety of research products. The Core Store provides one-stop shopping, saving researchers both time and money. In addition to its product offering, the store charges no shipping and handling fees and has free delivery to three JHU campuses.
Graphic Arts in the School of Medicine provides in-house creative design and art production services to the Johns Hopkins community. If you have a project that requires printed materials, please call us for a consultation. We will work with you to create the best possible solution to suit your goals, timeframe and budget.
DESIGN SERVICES
Brochures / Books / Booklets / Newsletters For print and e-distribution
Mailing Packets Fund-raising or information packages may contain a cover letter or small brochure, envelope, return card, return envelope
Posters / Flyers / Exhibits We design a wide range of posters, signs and flyers. We produce up to 2' x 3' prints in-house, and can mount your prints on foam board for easel display. Let us design something for you, or send us a pdf file of your own design. We also design banners, free-standing exhibits, table-top exhibits, and permanent installations.
Certificates
Certificates of completion
Awards
Special Recognition
STATIONERY
You can order a full range of stationery items from us in either Johns Hopkins University style or Johns Hopkins Medicine Style: letterhead, envelopes, business cards, mailing labels, memos, routing slips, note pads, etc.
To order, select the appropriate style link below to download a pdf order form. The completed form can be submitted by clicking on the submit order button or, if you prefer, you can print the completed form and fax the order to us.
Confocal Microscopy - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core please email: Yuan Cai
The ICE Confocal Service Center is established to provide JHU research Community with imaging needs on confocal microscopy, digital image processing and analysis. Our Center comprises Zeiss LSM710, LSM5 live and LSM510 meta with two photon laser, and one Zeiss LCM (laser cut microscope). These microscopes enables a wide variety of applications in cell and developmental biology.
MRI Research Service Center - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: MRI Research Center
Research MRI facilities -
The MRI Service Center, run by the Division of MR Research in the Department of Radiology and directed by Dr Paul Bottomley, operates four MRI scanners for research. It leases 1-2 scanners back to the hospital for clinical use, leaving 2 full-time scanners for 100% research use. The available scanners are: {1} a GE 1.5T 8-channel Signa Horizon (research upon request), {2} a Philips 16-channel 3T Achieva equipped with an X-ray C-arm (100% research); plus 100% research split between {3} a Siemens 3T Trio and {4} a 1.5T Espree. The Espree is also equipped with a full angiographic floor-mounted X-ray fluoroscopic suite and miyabi table transfer system for the purpose of developing interventional MRI. The scanners are supported by hourly machine rates, and have Radiology Technologist (RT) support by 3 RTs during normal working hours, supported by the MRI Service Center.
The FM Kirby fMRI center in the Kennedy Krieger Institute located near the main hospital has two Philips 3T MRI systems, {5} and {6} available for 100% research for use in the neurosciences. The Kirby Center is supported by an NIH resource grant and is directed by Dr Peter van Zijl in the Division of MR Research. The Kirby center, with support from the Department of Radiology, the NIH and other sources, also has a new 7T Philips whole body MRI system as of 2009.
Small-bore NMR/MRI systems -The Division of MR Research manages 2 other smaller bore NMR/MRI Service Centers suitable for studies of animal models, cell systems, and in vitro studies. -The NMR Service Center - has 400 MHz and 500 MHz Bruker NMR spectrometers, and a Bruker 4.7T 40 cm-horizontal bore spectrometer/imager equipped with rapid-switching gradient coils. -The Molecular Imaging Center – is located in the Broadway Research Building and is primarily geared to animal genetic models in a closed environment. It has a Bruker horizontal bore 9.4T animal system, in addition to an eXplore Vista small animal PET scanner, a SPECT-CT system, an IVIS Xenogen 200 optical imaging system for mice and rats, a VisualSonics small animal ultrasound unit, and a Faxitron MX-20 specimen radiography system.
Dr. Le is one of the first investigators to apply metabolomics technologies to the field of cancer metabolism and metabolic aspects of other diseases, demonstrated by her lab’s publication record as a pioneer in the field. Dr. Le’s laboratory developed and brought metabolomics technologies to Johns Hopkins and has been providing metabolomics assessments to researchers from several Johns Hopkins campuses (main medical campus, Bayview medical campus, Applied Physics Laboratory and JHU Homewood campus) as well as researchers outside Johns Hopkins (University of Maryland, NIH, Memorial Sloan-Kettering Cancer Center, George Washington University, Washington State University, Oregon Health & Science University, Kaohsiung Medical University in Taiwan, United Arab Emirates University in UAE, Scientific Centre of Monaco in Monaco; and the University of São Paulo in Brazil…). Their facility is equipped with mass spectrometer-UPLC systems obtained through a shared instrument grant (S10 grant). They are also part of The Johns Hopkins Institute for Clinical and Translational Research (ICTR)-supported facility
What They Offer:
o Provides consultation to basic, clinical, and translational research teams regarding the feasibility, design, and costs of projects using metabolomics technologies (including mass spec and NMR-based metabolomics);
o Metabolomics assessments based on specific research projects/questions: ranging from simple assays to high-throughput approaches such as global metabolic profiling and stable isotope-13C, 15N-labeling on a wide variety of sample types;
o Provides extensive data analysis and identification of options for subsequent steps towards clinical implementation.
Examples of Metabolomics-Based Discovery of Metabolic Aspects of Cancer and Other Diseases
The Angle2 stereotaxic system (Leica) consists of a software-assisted stereotaxic instrument which facilitates the accurate targeting of brain regions by using software combined with transponders that detect the position of the pipette carrier. Advantages include an on-screen atlas to facilitate identification of targets, the ability to use an angled approach without the need for path-of-approach calculation, and the ability to automatically correct for head tilt.
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Custom-Built Two-Photon Imaging Platform - Non-iLab Service (see description below for details)
The third confocal system is a custom-built two-photon imaging platform based on a design developed by Dr. Karel Svoboda at HHMI/Janelia Farm that is specialized for in vivo imaging. This system also uses a Chameleon Ultra II two-photon laser for excitation and is equipped with a blue LED for epifluorescence imaging. This system offers capabilities beyond that of the commercial Zeiss microscopes in the Core, including simultaneous two-color imaging, more rapid scanning (improved by a factor of two), and greater flexibility due to the open source MATLAB code used to control the instrument. In addition to a standard stereotaxic frame, the system includes a platform for in vivo imaging of both the dorsal horn and dorsal root ganglia of intact spinal cord.
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Image Analysis Workstation - Non-iLab Service (see description below for details)
The facility has two dedicated image analysis workstations each running Imaris software (Bitplane) for performing 3D reconstruction, isosurface rendering, filament tracing/particle tracking, and quantitative co-localization. The Imaris suite of programs has been designed to accept images in many different formats, include Tiff series, BMP series, and images collected with Leica, Olympus, and Zeiss acquisition software. The available modules are Imaris suite, ImarisXT, Filament tracer, and AutoDeblur. AutoDeblur is a deconvolution software package that produces extremely high-quality results through image restoration. ImarisXT allows users to develop their own task-oriented algorithms for Imaris, or use analysis modules developed by others.
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MakerBot Replicator 2x - 3D Printer - Non-iLab Service (see description below for details)
A MakerBot Replicator 2x allows individuals to use software to generate a 3D model of their desired product; this is then converted into a file formats which the MakerWare software can output to the 3D printer. This equipment permits inexpensive and efficient production of a wide variety of research components.
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Neurolucida Neuron Tracing system (Microbrightfield) - Non-iLab Service (see description below for details)
Additional image analysis capabilities are provided by our Neurolucida Neuron Tracing system (Microbrightfield). This system offers a variety of drawing/analysis options, including cell tracing/morphology quantification, 3D brain mapping, and serial section reconstruction. The software is paired with a Zeiss AxioImager microscope equipped with transmitted light and a motorized stage, for tracing directly from slides. Alternatively, image files collected on another system can be imported into Neurolucida. The analysis capabilities of Neurolucida complement those which can be achieved using the Imaris suite of programs, because the latter is geared almost entirely toward analysis of fluorescent images, whereas Neurolucida excels at reconstruction and analysis of brightfield images (e.g. DAB labeled cells). Because this system includes a color camera, it also provides a route for obtaining color images of brightfield samples, such as LacZ.
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Zeiss AxioExaminer LSM 710 Confocal Microscope - Non-iLab Service (see description below for details)
The second system is a Zeiss AxioExaminer upright microscope with an LSM 710 scan head. Due to refinements of the light path within the scan head, the system has better detection capabilities that improve the signal-to-noise ratio of fluorescent images. In addition, the filter-free spectral detection allows the user to define emission collection parameters, rather than being limited to a particular set of installed emission filters. Furthermore, this instrument has a number of distinct advantages for multiphoton imaging, including a redesigned microscope stand that has increased objective travel, allowing the use of a new 20x high numerical aperture objective with increased transmission in the infrared. An important feature of this microscope is the addition of a low noise photomultiplier tube placed immediately adjacent to the objective for optimal light capture. The 710 can also be used with a highly sensitive GaAsP detector, which excels at collecting images of fluorescently labeled cells deep within tissue. This improvement has been particularly critical for in vivo applications, and has allowed users to monitor cell motility in intact preparations. Because the GaAsP detector is extremely sensitive to ambient light, we have constructed a light-tight enclosure around this system, so that both microscopes can be used simultaneously.
Inquire
Zeiss Cell Observer, Inverted Epifluorescence Imaging - Non-iLab Service (see description below for details)
The Zeiss Cell Observer system consists of an AxioObserver inverted microscope equipped with fluorescent and transmitted light, an Axiocam MRm, and filter sets compatible with DAPI, GFP, Cy3 and Cy5. An environmental chamber to facilitate control of temperature, humidity, and CO2 is mounted on the microscope, allowing maintenance and imaging of live cells over long periods of time. A motorized stage facilitates the identification and imaging of multiple regions of interest. Zen for Widefield software permits flexible design of experiments and provides various post-processing capabilities. The system can also be used to image fixed slides. One feature that is useful to many labs is the motorized stage, which supports acquisition of tiled images and allows users to capture large regions of interest at high magnification. Post-processing features are available to remove line artifacts that are often apparent in such tiled images.
Inquire
Zeiss LSM 510 Confocal Microscope - Non-iLab Service (see description below for details)
The facility contains three confocal microscope systems that allow high resolution imaging of labeled cell components in three dimensional space. The first system consists of a Zeiss LSM 510 motorized upright microscope, equipped with a META scanning module, two non-descanned detectors for multi-photon work, and a motorized stage for time lapse imaging. The LSM 510 can be configured with the META detector plus two traditional detectors for fluorescent or reflected light imaging. The META detector can also be used as a unique spectral detector or a conventional "band-pass" detector. All three detectors can be recorded and displayed simultaneously. This system employs a PC-based user interface to control the microscope, laser excitation, scanning and image acquisition, and is capable of digitally capturing up to 12 bit 2K x 2K pixel images, while the AIM LSM software controls image data acquisition and processing. The system can perform Fluorescent Recovery after Photobleaching (FRAP), Fluorescence Resonance Energy Transfer (FRET), and quantitative co-localization.
Consultation is available from MMC directors and staff members on the entire procedures of generating gene knock-out mice. Consultation on generation of BAC transgenic lines
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Cryopreservation of ES Cell Line and Embryos - Non-iLab Service (see description below for details)
Graphics - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: PathPhoto
The requirement of professionally created graphics is a necessity for an institute the caliber of Johns Hopkins. Often, bringing cutting-edge technological breakthroughs means being able to graphically display information that can be both extremely detailed and complex.
PathPhoto can provide a professional and talented resource to convey any type of graphic information, whether statistical, or just artistic. Our staff of highly trained graphic people is available to assist in any form of visual communications. If you’re not positive how to proceed with your visual requirements, talk to us, and we can provide suggestions and ideas.
Some of the major aspects of Graphics found at PathPhoto are:
Photography - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: PathPhoto
Our photographers offer a wide range of services to meet your needs for publication, teaching and scientific documentation. From photography in the Operating Room to same day digital color printing, our goal is to provide fast top quality service. The philosophy of the department is to serve the faculty, staff and students with the best service available in the field of medicine.
To facilitate research involving small molecules, the Department maintains a Bruker Avance III 500 MHz NMR spectrometer equipped with an autosampler. The automation is configured for a convenient queue up of common 1D (1H, 13C, 31P, DEPT, 1H with solvent suppression) and 2D (COSY, TOCSY, HSQC, HMBC, and NOESY) experiments.
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nanoACQUITY UPLC system from Waters - Non-iLab Service (see description below for details)
The MS Facility comprises a Triple Quadrupole Mass Spectrometer, TSQ Vantage from Thermo Scientific and a nanoACQUITY UPLC system from Waters. The TSQ bears a HESI-II electrospray ionization source and this UPLC/MS system is well-suited for quantification and identification of small molecules as well as biomolecules.
These services are open to members of the JHU community. For training and further assistance, please contact the NMR/MS Facility Manager.
Shridhar Bhat, Ph.D. NMR/MS Facility Manager Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine 725 North Wolfe Street / WBSB-322 shri@jhu.edu
Inquire
Triple Quadrupole Mass Spectrometer - Non-iLab Service (see description below for details)
The MS Facility comprises a Triple Quadrupole Mass Spectrometer, TSQ Vantage from Thermo Scientific and a nanoACQUITY UPLC system from Waters. The TSQ bears a HESI-II electrospray ionization source and this UPLC/MS system is well-suited for quantification and identification of small molecules as well as biomolecules.
These services are open to members of the JHU community. For training and further assistance, please contact the NMR/MS Facility Manager.
Shridhar Bhat, Ph.D. NMR/MS Facility Manager Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine 725 North Wolfe Street / WBSB-322 shri@jhu.edu 410-502-4803
Inquire
TSQ Vantage from Thermo Scientific - Non-iLab Service (see description below for details)
The MS Facility comprises a Triple Quadrupole Mass Spectrometer, TSQ Vantage from Thermo Scientific and a nanoACQUITY UPLC system from Waters. The TSQ bears a HESI-II electrospray ionization source and this UPLC/MS system is well-suited for quantification and identification of small molecules as well as biomolecules.
These services are open to members of the JHU community. For training and further assistance, please contact the NMR/MS Facility Manager.
Shridhar Bhat, Ph.D. NMR/MS Facility Manager Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine 725 North Wolfe Street / WBSB-322 shri@jhu.edu
The research radiology lab has 3 spacious rooms to perform a variety of research projects involving animals. The lab has two fluoroscopy suites (Toshiba Infinix-I and Philips Allura Xper FD) with fixed table c-arms and a 1-slice CT. An additional room is available to perform procedures that do not require fluoroscopy, such as endoscopy or surgery. All rooms are equipped with physiological monitoring equipment (end tidal CO2, invasive blood pressure, ECG), gas anesthesia machines, and defibrillators. There is also a portable x-ray machine available for radiographs. The lab has technicians available to help prepare the animals, monitor anesthesia and assist with the fluoroscopy equipment. The lab also has a veterinarian available to help with developing animal models, writing protocols, and other animal issues.
Research Animal Resources (RAR) is Johns Hopkins’ centralized provider of veterinary medical care and research animal support. Visit these pages for information regarding all aspects of animal care and veterinary assistance for your animal research.
This is not the animal care and use committee (ACUC) website. For regulatory (ACUC) issues please visit the IACUC Website or call (443) 287 3738; acuc@jhmi.edu
Clinical calls: Unexpected mortality? Colony problems? Could it be related to an infectious or environmental cause? Call a vet for help on 410-955-3273
Small Animal Imaging - Non-iLab Service (see description below for details)
This core is not active in iLab. To access this core click here: Small Animal Imaging
Small animal imaging is increasingly recognized as an important facet of preclinical and translational cancer research. Perhaps most significant among the clear advantages of imaging experimental animals is that physiology, pathology and novel phenotypes can be understood in the most relevant milieu — in an intact, living system. Less obvious is the fact that often the most significant leap forward an already important biological study takes is when its results can be extended to the in vivo case — a necessary and often sufficient precondition for success in the clinic.
The Johns Hopkins Small Animal Imaging Resource Program (SAIRP) labors to provide that translational step, generating the confidence necessary to move new cancer therapies to patients. Our ultimate goal is to move small animal imaging science forward to the point that the incorporation of these imaging techniques is second nature to the daily practice of cancer researchers.
The Synthesis and Sequencing Facility uses five 394 DNA synthesizers. We offer synthesis in four scales at the following rates:
Scale
Price per Base
Approximate Purified Yield
40 nmol
$0.50
NOT AVAILABLE
0.2 umol
$1.00
200-500 ug
1.0 umol
$5.00
1-2 mg
10 umol
$24.00
10 mg
Turnaround time is usually the next day for crude oligos. Oligos that need HPLC purification will take 2 days normally. Longer oligos that require trityl-on purifications may take longer so please inquire when dropping these orders off.
Oligo orders delivered with a template will be cycle sequenced and subsequently loaded on our automated DNA sequencer as soon as the oligo is ready.
Next Generation Sequencing is now being offered at our facility using Illumina's MiSeq platform.
The MiSeq uses a "Sequencing by Synthesis" concept whereby prepared libraries are loaded onto the MiSeq flow cell, cluster generation is performed and sequencing by synthesis (SBS) occurs.
There are four different reagent kits available: 50 cycles, 150 cycles, 300 cycles, and 600 cycles.
Dual index sequencing is available with the capacity to multiplex up to 96 samples in one run. The coverage you require will determine how many samples can be multiplexed and run at one time.
Cost: Costs vary depending on the number of cycles you need and the type of library prep needed. Please inquire about pricing for individual projects with Jodie.
We will break down the individual cost of each project for you rather than just giving you a generic library prep cost.
As an example, we ran 24 bacterial genomes using a 2 x 300 sequencing kit and Illumina's Nextera Library prep kit at the cost of approximately $188/library.
We partner with the Genomic Analysis and Sequencing Core Facility located in the SOPH. Please visit their website to see a list of their services.
Applications include:
Targeted Resequencing
Amplicon Sequencing
Hybrid Capture
Clone Checking
Small Genome Sequencing
De novo
Resequencing - includes alignment to your reference genome
Plasmids
RNA Sequencing
16S Metagenomics
Small RNA Sequencing
Quality Control
Library QC
Regulation
ChIP-Seq usually for QC before scaling up to a HiSeq run
The steps to generating sequence include the following:
Consultation. We need to sit down and discuss your particular project.
Building a Library. Illumina has sample prep kits for each of their applications. A lot of labs like to save money by doing their own library prep and we are happy to run these samples but please consult with the sequencing staff as to the requirements. Low diversity libraries will require a 5 to 10% PhiX control spike-in to normalize the library and enable better sequencing results.
Each Illumina sample prep kit requires a different amount of starting material and we will advise you as to how much we need depending on your project and library generation needs.
Sequencing run times vary depending on the application but are usually done within 2-3 days.
Data is typically stored in Illumina's BaseSpace Cloud and subsequently be shared with you via email invite. However, we do have a dedicated server where data can be stored as well.
Data analysis - The analysis strategy should be discussed during consultation. You will receive the following files depending on the application.
Raw data in the form of compressed fastq data files.
Aligned reads will provide bam formatted files (.bam) which can be viewed using a Genome Browser such as the Broad's Integrated Genome Viewer (IGV).
Variant calling identifies SNPs and short indels and are generated in a Variant Call Format (.vcf) file.
Further analysis can be performed by a bioinformatician. We do not have a bioinformatics person on staff but rather have someone we can refer you to who is an independent contractor. His contact information is James White, PhD at james.dna.white@gmail.com or http://jameswhitephd.com. James has extensive experience and references can be supplied.
Instrumentation consists of an Aapptec Focus Synthesizer. The synthesis is run utilizing Fmoc chemistry. Purification is performed by Reverse-phase HPLC. Molecular weights are checked by Maldi TOF. All peptides made in the facility are for research purposes only.
The Aapptec Focus Synthesizer allows me to synthesize multiple peptides at once.
Also for those of you that only need a few mgs of peptide, we are offering some "ready-made and purified" peptides. The cost per mg is much lower than what you will find outside. Please click on the following link for a list of peptides that are available.
If you need a lot of peptide, it is cheaper to get a custom synthesis done. Also, if you have suggestions for peptides that we should stock, please send Jodie an email at jfrankl1@jhmi.edu. Thanks.
Large Scale Synthesis:
Expected yields are 300-450 mg of crude peptide and approximately 20-50 mg of purified peptide per each HPLC run consisting of a 150 mg injection. You can have the entire synthesis purified or half of it and receive the remaining crude for any future experiments. Crude peptides can be brought back to us at a later date for purification.
Cost:
$30.00 for each amino acid $150.00 for each preparative HPLC run
Small Scale Synthesis:
Expected yields are 150-200 mg of crude peptide and approximately 5 to 20 mg of purified peptide.
Cost:
$20.00 for each amino acid $150.00 for each preparative HPLC run
We will routinely accept peptides of 30 amino acids or less. Anything greater than 30 will be accepted only after consultation. For longer peptides, please consult with Jodie to see if there are any anticipated problems with your chosen sequence.
Purification of peptides NOT synthesized by the SSF:
Cost: $200 for each preparative HPLC Run
Peptide Modifications:
There are many modifications available including, phosphorylated amino acids, N-terminal acetylation, N-terminal biotinylation, N-terminal myristolation, and N-terminal flourescent dyes. Please inquire about pricing. For any other unusual modifications, please see Jodie.
Peptides for Antibody Production:
The range of purity for peptides used for antibody production is 70% or greater. If your peptide is less than 70% pure, you can expect approximately 20-50 mg after purification
Instrumentation consists of a state-of-the-art Perkin-Elmer/Applied Biosystems Procise Protein Sequencing System. This is a highly sensitive system that can detect quantities as low as 1 picomole. It is also compatible with samples that have been electroblotted onto PVDF.
Cost:
$200.00 set-up and first three cycles (3 amino acids) $20.00 each additional amino acid
$5.00 Prosorb sample clean up (optional)
Chemistry:
The Edman chemistry cycle consists of three stages:
1. Coupling
The N-terminus of the protein couples with PITC under basic conditions to form a phenylthiocarbamyl (PTC)-polypeptide.
2. Cleavage
The peptide bond of the N-terminal PTC-residue undergoes acid cleavage from the polypeptide chain. This results in the release of an unstable anilinothiazolinone (ATZ) derivative of the amino acid.
3. Conversion
The unstable ATZ-amino acid is converted into the corresponding phenylthiohydantoin (PTH) derivative. The PTH-amino acid is stable.
At the end of each cycle of Edman degradation, the PTH-amino acid is separated from reaction by-products and identified, by HPLC chromatography and UV absorbance. Although not part of the Edman degradation cycle per se, PTH-amino acid analysis, like Edman degradation, is an essential step in the protein sequencing process.
Sample Purity -- What to Avoid:
Sample purity is one of the most critical factors for successful protein sequencing. Samples should:
Contain one protein component only.
Be free of reagents which interfere with Edman degradation and the sequencing process (e.g., Tris, glycine, guanidine, glycerol, sucrose, ethanolamine, SDS, Triton X-100, Tween,, ammonium sulfate and other ammonium salts)
The two basic approaches that can be used to purify samples for protein sequencing are:
SDS-PAGE and electroblotting
ProSorb sample preparation cartridges (available in our lab)
SDS-PAGE and electroblotting should be used if the protein of interest is in a complex mixture of proteins. For proteins isolated in solution which are free of contaminating proteins but contain salts, buffers and/or detergents, use ProSorb cartridges.
Sample Preparation: Proteins/Peptides in solution:
For best results an optimal amount of to load on the sequencer is 200 pmole of peptide or protein.
Samples should be as homogeneous as possible and free of salts, detergents, lipids and other non-volatile ingredients (SDS, TRIS, etc.). Solutions used in dissolving samples should, therefore, contain only volatile components such as water, acetonitrile, etc. and be concentrated in a volume of no more than 60 ul. If your sample is supplied dried, it will be brought up in a 1:1:1 mixture of acetonitrile, water and acetic acid unless otherwise specified.
If your sample contains these non-volatile ingredients, we can pass it through a Prosorb column which will clean up your sample while at the same time deposit it onto a piece of PVDF. The fee for this service will be $5.00.
For proteins/peptides adsorbed onto PVDF, again the optimal amount protein/peptide to load on the sequencer is 200 pmole. The piece of PVDF should be no larger than 3 x 7 mm and the number of pieces no more than five. Keep in mind that transfer is not 100% efficient so load an adequate amount of protein or peptide onto the gel prior to electrophoresis. Remember that the intensity of the stain is not indicative of sample amount and that the presence of a single band does not always indicate that there is only one species present.
Please note that nitrocellulose cannot be used in our automated sequencer.
If you would like to have a more detailed description of sample preparation, please look at the Perkin-Elmer/Applied Biosystems Guide to Sample Preparation.
Instrumentation consists of an Applied Biosystems 3730xl DNA Analyzer.
NEWS:
DNA Sequencing $6.00/reaction
PeakTrace is now being used to give you longer reads of around 1020 good bases.
We are offering Ampure PCR clean-up using our robot for $1.00 a sample.
If you drop your sample off by 1:00 p.m., you can expect your data to be ready the next day. Please look at the white board when you drop off your samples for the date your data will be ready. The date listed is the worse case scenario, it is always a good idea to check the server the next day in the afternoon anyway no matter what time you drop your samples off.
We also offer Saturday delivery of your data to the server.
Sequencing Cost: $6.00 per reaction (includes universal primer -- see universal primer link below for a complete list of our free primers. We can add to the list if there is a primer that you think we should stock.)
Note: For samples with an RNAi insert, we charge 50 cents more per sample so $6.50. Large templates such as BACS are $20.00 per sample.
Campus Sample Drop-Off Locations:
We have three drop-off locations located on campus.
WBSB: Outside of Room 418 for after hours.
BRB: Outside of room 372
SOPH: Inside the Monument street entrance where the FedEx box is located. Look for the black "mailbox" on the wall. Instructions are on the box.
Requested Concentrations:
Custom Primers Supplied by You:4.0 uM in water with a total of 7 ul per reaction
Plasmid Templates:0.1 to 0.2 ug/ul for (ds) plasmids with 7 ul per reaction in water.
ShRNAi Templates: 0.2 ug/ul with 10 ul per reaction in water. DO NOT MIX WITH PRIMER, please provide template and primer separately if using custom primers.
PCR Products: 10 to 15 ng/ul (with an average length of 500 bp) adjust amount accordingly for longer PCR products. If your PCR products are large, i.e., 4 Kb or something like that, then use the amounts requested under Plasmid Template.
BACs and COSMIDs: 0.5 ug/ul with 12 ul per reaction in water. Must be very clean. The charge for this is $20.00 per reaction. DO NOT MIX WITH PRIMER.
---------------------------------------------------------------------- The benefits of using YOUR JHMI Sequencing Facility:
First and foremost, we are here for YOU. This is the sole reason the facility exists. So please make use of your Hopkins facility.
Template and Primer can be mixed by you or we can do it here in the lab. There is no extra charge if we mix it. If mixing, use equal amounts.
We also offer other discounted pricing for samples that are already cycle sequenced by you. Ask the staff for more details.
All samples will be stored for a month. We will store your samples longer if you request this. We also will hold on to primers that you use frequently as well.
Every chromatogram is analyzed by hand after printing. We will repeat samples, at our discretion, should we see that something failed when everything else worked.
We are available to talk with you from 7:30 a.m. to 5:00 p.m. Monday through Friday regarding your sequencing. Email is checked over the weekend as well; and if possible, we will try to resolve any problems you may have.
The Welch Library’s Informationists provide consultation, collaboration, and training on information tools and questions that arise throughout the research lifecycle. This includes consulting or engaging with teams on systematic reviews and other expert searching; data management planning and sharing; bibliographic citation management; grants and funding; publication of findings; research impact; clinical evidence; and bioinformatics resources.
Welch Informationists services range from simple consultation on best practices and training to full collaboration as members of a research team.
Service Areas
Systematic reviews; expert literature searching; bibliographic citation management; grants and scholarly output; clinical evidence; bioinformatics tools.
Location
Multiple locations: 2024 East Monument St., Welch Medical Library building, staffed locations in Zayed, BSPH, SON, or your office/lab
Nikon TU2000 Inverted Microscope This PC has a CD burner, a shared directory on the network, and a USB port for either external hard drives or flash (memory) keys.
Zeiss LSM 510 Meta Confocal The LSM has both CD and DVD burners available. The USB port may be used with an external hard drive or flash key. This PC is not networked to protect it from viruses, spyware, and mis-use.
FINZ is the Institute of Genetic Medicine Center for Functional INvestigation in Zebrafish
"FINZ center construction was funded by a generous gift from Joel J. and Lillian Cohen"
FINZ is your entry point for all things zebrafish. Whether you want to rapidly determine the function of a candidate gene identified in the human population or other systems or assay the regulatory potential of selected sequences – we are here to help.
Location:
FINZ is located in the Edward D. Miller Research Building (452) on the East Baltimore Campus. Services: We provide specialized services that include, microinjection of zebrafish embryos, establishment of transgenic lines, morpholino-based gene knockdown strategies, whole mount in situ hybridizations, and in vitro fertilization. Other services comprise adult fish and embryo sales, and transgenic line screenings. Training courses are also available at times to be advertised during the year.
