Zebrafishand

Data ManagementJulie Goldman

LIS 532G Fall 2013

Ohio State

Buckeyes

Scientific Research

Researcherthird year graduate studentareas of focus: neurotrauma, neurological disorders, gene therapy

InitialInterview

Instrument40 minute conversation

Follow up Email

Second Interview

30 minute conversation

Beattie Lab

Zebrafish Facilityfacility supports three research labs

1200 sq ft

1234 tanks & 40,000 fish

tank labels : research’s name, fish name, DOB, stock number

Research

investigating the biological basis of motoneuron diseasesgenetic and molecular cues that guide motor axons to their target muscleresearch since 1996

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?

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

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

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

ALSgenetic mutation: SOD1 gene to generate SOD G93A and G85R transgenic zebrafish

drug screens with zebra fish larva

rescue motor neurons early in development

Motor Axons

Zebrafish Model DNA & RNA injections

Zebrafish

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

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

Other Funding

private funding

SMA & ALA families and foundations

concerned with clinical implications and research outcomes

Who’s Who

1 PI (principal investigator)1 lab technician1 postdoctoral scholar1 graduate student

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

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

SPSS : statistics softwareImageJ : public domain, Java-based image processing program developed by NIHAdobe photoshop : photo editingMicrosoft Office Suite : word, excel, powerpoint

Programs

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

naming conventions are personal and involve initials/namebecome more professional when sent to the PI and goes to publication

File Naming

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

use personal computers in the labtherefore responsible for keeping personal external hard drivessecurity : passwordskey access to building and lab

Backup and Security

sharing via Dropbox and Google Drive on the university serverdata passed down through CDs with images and data analysisPI : responsible for data

Sharing

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

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

Zebrafish Resources

Preservation

archive : duration of the grantNIH : 3 years to have access to it

so what are the data management issues?

Lab Notebookspaper lab notebooksgraduate students better than postdocmust link between description of the experiment and the experimental results

Jen Ferguson, Lurking in the Lab

ELNs

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

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

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

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...

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.”

you’ve never heard of it you say?

well guess what!...

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

that’s it!?

2011

NEW POSITION

Data Management Plan

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/

Questions?Thanks!