LIS 532G: Scientific Research Data Management Midterm Project Presentation: Zebrafish and Data Management Research project at The Ohio State University; data interview with research graduate student; data management plan and evaluation; about data management at Ohio State.

1. Zebrafishand
Data Management
Julie Goldman
LIS 532G Fall 2013

2. Ohio State

3. Buckeyes

4. Scientific Research

5. Researcher
third year graduate student
areas of focus: neurotrauma,
neurological disorders, gene therapy

6. Initial
Interview
Instrument
40 minute conversation

7. Follow up Email

8. Second Interview
30 minute conversation

9. Beattie Lab

10. Zebrafish Facility
facility supports three
research labs
1200 sq ft
1234 tanks & 40,000 fish
tank labels : research’s name,
fish name, DOB, stock number

11. Research
investigating the biological basis of
motoneuron diseases
genetic and molecular cues that guide
motor axons to their target muscle
research since 1996

12. Research Questions
What 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?

13. SMA
spinal 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

14. 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

15. ALS
amyotrophic 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

16. ALS
genetic mutation:
SOD1 gene to generate
SOD G93A and G85R
transgenic zebrafish
drug screens with
zebra fish larva
rescue motor neurons
early in development

17. Motor Axons

18. Zebrafish Model DNA & RNA injections
Zebrafish

19. 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

21. NIH Grant
research 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

22. Other Funding
private funding
SMA & ALA families
and foundations
concerned with clinical
implications and
research outcomes

23. Who’s Who
1 PI (principal investigator)
1 lab technician
1 postdoctoral scholar
1 graduate student

24. 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

25. Bio-Rad RT-qPCR : excel files
Thermo Scientific nano-drop : excel files
Western Blots : film developed in a dark room
agarose gels : read on a gel box and printed/
scanned for densitometry quantification
microscopes : .TIFF and .JPEG files
data analysis : excel or SPSS
Equipment and Products

26. SPSS : statistics software
ImageJ : public domain, Java-
based image processing
program developed by NIH
Adobe photoshop : photo editing
Microsoft Office Suite : word,
excel, powerpoint
Programs

27. data produced on old computers attached
to equipment
transferred 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

28. naming conventions are personal and
involve initials/name
become more professional when sent to
the PI and goes to publication
File Naming

29. paper lab notebooks for non-digital data
personal data keeping techniques
my researcher keeps a more detailed lab
notebook compared to the post doc
records detailed descriptions of experiments
and pastes hard copy images (gels, microscope)
into notebook
notebooks stay in the lab
Lab Notebooks

30. use personal computers in the lab
therefore responsible for keeping
personal external hard drives
security : passwords
key access to building and lab
Backup and Security

31. sharing via Dropbox and Google Drive on
the university server
data passed down through CDs with
images and data analysis
PI : responsible for data
Sharing

32. once published : public access to data
anyone can ask for reagents and
animals used in published study
fish genetic lines are submitted to the
international database for zebrafish
Access

33. 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

34. Zebrafish Resources

35. Preservation
archive : duration of the grant
NIH : 3 years to have access to it

36. so what are the data
management issues?

37. Lab Notebooks
paper lab notebooks
graduate students
better than postdoc
must link between
description of the
experiment and the
experimental results
Jen Ferguson, Lurking in the Lab

38. ELNs

39. Naming Conventions
personal and individual naming of files
disorganization can occur
by creating conventions for the whole
lab to adhere to, data will be more
organized and already have proper
formatting for sharing, publications
and preservation

40. CDs
data 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 use
if you must : regular copying, data
migration, upgrade to current formats

41. Cloud Storage
sharing via
Dropbox and
Google Drive
what happens
to data stored
in the cloud
when a vendor
ceases to exist?
Jen Ferguson, Lurking in the Lab

42. No Repository
publications and zebrafish lines are
shared with the science community
BUT how will the raw data be preserved
more on this is a minute...

43. 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.”

44. you’ve never heard of
it you say?
well guess what!...

45. DSpace: manage a wide variety of digital content
bit preservation: ensure files remain exactly the
same over time
functional preservation: files do change over time
so that the material continues to be immediately
usable in the same way it was originally
Knowledge Bank

46. that’s it!?

47. 2011

48. NEW
POSITION

49. Data Management Plan

51. References
Ferguson (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/

52. Questions?
Thanks!