Zebrafish and Data Management Midterm Project
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Transcript of Zebrafish and Data Management Midterm Project
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Zebrafishand
Data ManagementJulie Goldman
LIS 532G Fall 2013
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Ohio State
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Buckeyes
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Scientific Research
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Researcherthird year graduate studentareas of focus: neurotrauma, neurological disorders, gene therapy
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InitialInterview
Instrument40 minute conversation
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Follow up Email
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Second Interview
30 minute conversation
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Beattie Lab
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Zebrafish Facilityfacility supports three research labs
1200 sq ft
1234 tanks & 40,000 fish
tank labels : research’s name, fish name, DOB, stock number
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Research
investigating the biological basis of motoneuron diseasesgenetic and molecular cues that guide motor axons to their target muscleresearch since 1996
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Research QuestionsWhat is the biological basis of the motoneuron disease SMA?How can modeling ALS in zebrafish be useful as a tool for drug and genetic screening?What genes define motor axon outgrowth?
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SMAspinal muscular atrophy
caused by mutations in the survival motoneuron gene (SMN)
SMN protein is critical to the health and survival of nerve cells in the spinal cord responsible for muscle contraction
occurs early in life and is the leading genetic cause of death in infants and toddlers
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genetic model of SMA in zebrafish
what function of SMN leads to motoneuron dysfunction
cell death in SMA caused by motor neuron defects during early development
protein knockdown technology in zebrafish development
use scoring system on florescent microscope images to determine conditions
drug screens to treat disease
SMA
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ALSamyotrophic lateral sclerosis or Lou Gehrig’s disease
muscle weakness and atrophy throughout the body due to degeneration of the upper and lower motor neurons
defect on chromosome 21 which codes for superoxide dismutase (SOD1) enzyme
20% of familial cases
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ALSgenetic mutation: SOD1 gene to generate SOD G93A and G85R transgenic zebrafish
drug screens with zebra fish larva
rescue motor neurons early in development
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Motor Axons
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Zebrafish Model DNA & RNA injections
Zebrafish
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genome fully sequenced
well-understood, easily observable and testable developmental behaviors
rapid embryonic development
large, robust, transparent embryos
develop outside mother
similar to mammalian models and humans
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NIH Grantresearch project grant (r01)award made to support a discrete, specified, circumscribed project
government is strict about data keeping and can ask to see data and notebooks any time
NIH has the legal right to audit and examine record relevant to any research grant award
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Other Funding
private funding
SMA & ALA families and foundations
concerned with clinical implications and research outcomes
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Who’s Who
1 PI (principal investigator)1 lab technician1 postdoctoral scholar1 graduate student
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PCR: polymerase chain reaction amplifies copies of a particular DNA sequence
agarose gel electrophoresis: separate DNA
Western Blot: detect protein levels in tissue
microscopy: scoring system (axon morphology)
General Lab Work
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Bio-Rad RT-qPCR : excel filesThermo Scientific nano-drop : excel filesWestern Blots : film developed in a dark roomagarose gels : read on a gel box and printed/scanned for densitometry quantificationmicroscopes : .TIFF and .JPEG filesdata analysis : excel or SPSS
Equipment and Products
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SPSS : statistics softwareImageJ : public domain, Java-based image processing program developed by NIHAdobe photoshop : photo editingMicrosoft Office Suite : word, excel, powerpoint
Programs
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data produced on old computers attached to equipmenttransferred to the (old) big lab computer for processing and data analysis
example: florescent microscopy images are saved on the computer attached to the microscope which are then printed out and sent to other computers
Data Flow
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naming conventions are personal and involve initials/namebecome more professional when sent to the PI and goes to publication
File Naming
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paper lab notebooks for non-digital datapersonal data keeping techniquesmy researcher keeps a more detailed lab notebook compared to the post docrecords detailed descriptions of experiments and pastes hard copy images (gels, microscope) into notebooknotebooks stay in the lab
Lab Notebooks
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use personal computers in the labtherefore responsible for keeping personal external hard drivessecurity : passwordskey access to building and lab
Backup and Security
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sharing via Dropbox and Google Drive on the university serverdata passed down through CDs with images and data analysisPI : responsible for data
Sharing
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once published : public access to dataanyone can ask for reagents and animals used in published studyfish genetic lines are submitted to the international database for zebrafish
Access
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Nature
Science
PubMed
any one can ask for reagents, antibodies, enzymes, and/or fish that were used in any published study
OSU: get anything pre-publication
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Zebrafish Resources
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Preservation
archive : duration of the grantNIH : 3 years to have access to it
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so what are the data management issues?
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Lab Notebookspaper lab notebooksgraduate students better than postdocmust link between description of the experiment and the experimental results
Jen Ferguson, Lurking in the Lab
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ELNs
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Naming Conventionspersonal and individual naming of filesdisorganization can occurby creating conventions for the whole lab to adhere to, data will be more organized and already have proper formatting for sharing, publications and preservation
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CDsdata from previous graduate students passed down through the use of CDs CDs are not regarded as long-term technological obsolescence is a major factor that threatens long-term useif you must : regular copying, data migration, upgrade to current formats
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Cloud Storagesharing via Dropbox and Google Drivewhat happens to data stored in the cloud when a vendor ceases to exist?
Jen Ferguson, Lurking in the Lab
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No Repository
publications and zebrafish lines are shared with the science communityBUT how will the raw data be preserved
more on this is a minute...
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Researcher Onboard“A lot of the things you have
asked me, like I’ve never heard of them. I mean they sound like a good idea and we should have
something like that.”
“It’s a matter of educating us about the resources we don’t have.”
“We are so low tech. We use Dropbox.”
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you’ve never heard of it you say?
well guess what!...
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DSpace: manage a wide variety of digital contentbit preservation: ensure files remain exactly the same over timefunctional preservation: files do change over time so that the material continues to be immediately usable in the same way it was originally
Knowledge Bank
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that’s it!?
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2011
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NEW POSITION
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Data Management Plan
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ReferencesFerguson (2012) Lurking in the Lab: Analysis of Data from Molecular Biology Laboratory Instruments http://escholarship.umassmed.edu/jeslib/vol1/iss3/5/
http://www.neurobiotech.ohio-state.edu/ChristineBeattieLab/home.html
http://medicine.osu.edu/neuroscience/Pages/index.aspx
http://kb.osu.edu/dspace/
http://library.osu.edu/staff/admin-plus/AdminPlusNotes_20110427.pdf
http://www.nature.com/news/going-paperless-the-digital-lab-1.9881
http://dmp.data.jhu.edu/sites/default/files/Questionnaire.doc
http://www.niehs.nih.gov/news/newsletter/2013/9/science-ntptalk/
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Questions?Thanks!