Transcript GEP Implementation * First Year

GEP Digital Laboratory Notebook
Nick Reeves, Mt. San Jacinto Community College

Claiming and Delivering Files and Projects
 I claimed lower difficulty
contigs (level 4 or 5) with 2
genes identified by the
BLASTX evidence track
 All files were delivered to
student computers through
the course Blackboard
website and the Dropbox file
sharing program which
worked but was a little
clunky… Google docs may be
a better delivery method
DLN Page 1 - Synteny
https://www.dropbox.com/s/9z1p2zqzbhcgpu0/DLN%20Page%201%20Synteny%20Instructions.docx?dl=0
 Basic synteny analysis that
compares the query genome
to the reference D.
melanogaster genome
 Aligns well with basic
chromosome concepts
covered in class –
loci/linkage/cell division
 Introduces students to the
GEP genome browser and
Flybase gbrowse
DLN Page 2 – Gene Structure
https://www.dropbox.com/s/giwiam66e9k3fa6/DLN%20Page%202%20Gene%20Structure%20Instructions.docx?dl=0

Pick one of the two genes in
the contig and compare the
gene structure of the query
BLASTX track and the reference
D. melanogaster annotation

Emphasize
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Number of isoforms
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Number of exons
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Alternative splicing
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Open reading frame
Not considering the sequence
yet
DLN Page 3 – Coding DNA Sequence
https://www.dropbox.com/s/l54ago79qlcys47/DLN%20Page%203%20Coding%20DNA%20Sequence%20Instructions%20Part%201.docx?dl=0

The actual CDS annotation!
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Important coordinates in yellow box.
Several pages long…
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Start at the start codon – It’s painted
green!
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Watch what strand is being analyzed!
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Reveals student misconceptions - UTRs
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Synthesis of evidence
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BLAST track finds homologs
Gene predictions indicate
boundaries
RNA-seq shows expression and
verifies boundaries
Gene Record Finder for amino
acid sequence – students identify
the matching amino acids
Gene Record Finder
DLN Page 3 – Coding DNA Sequence
 Intron boundaries defined
by splice site consensus
sequence AG/GT and
synthesis of evidence tracks
 Frame vs. phase – critical
thinking! A practice activity
would be helpful.
DLN Page 3 – Coding DNA Sequence
 Intron boundaries defined
by splice site consensus
sequence AG/GT and
synthesis of evidence tracks
 Frame vs. phase – critical
thinking! A practice activity
would be helpful.
DLN Page 3 – Coding DNA Sequence

Stop at the stop codon – It’s
painted red

Check whether amino acids
match D. melanogaster

Don’t get confused by BLASTX
track (ends before stop codon –
does not an amino acid) and
RNA-seq track (ends after stop
codon – 3’UTR)

Final CDS Coordinates are now
collected in the yellow boxes
DLN Page 4 – Project Report
 DLN Page 3 coordinates in
yellow boxes can be used to
run the gene model checker
 All groups finished a single
isoform of one gene on their
own in ~15 hours of class
time
 Honors students completely
finished a project during the
summer
Constraints/Comments/Collaboration

Lab time to work on new projects is precious. Students can
(should?!) complete the example RpS3A annotation on their
own by following the instructions and watching the videos.

Shared projects = peer instruction = work through student
misconceptions on own to some extent
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Digital Laboratory Notebook
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Online doc? Google docs/Office 365
Example gene – simple two exon gene (RpS3A or challenging
tra (goes with gene intro)
Make the pages like an online form? – pull down menus with
limited options instead of free response
Less data entry? Remove repeat track; less gene record
finder analysis
Pre-selected projects and pre-formatted notebook pages?
CURE (course-based undergraduate
research experience) Achieved
 Questions?
 Contact Information
Nick Reeves
Mt. San Jacinto College
[email protected]
951-6395735