GEP Digital Laboratory Notebook Nick Reeves, Mt. San Jacinto Community College
GEP Digital Laboratory NotebookNick 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
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
https://www.dropbox.com/s/9z1p2zqzbhcgpu0/DLN%20Page%201%20Synteny%20Instructions.docx?dl=0
DLN Page 2 – Gene Structure
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 Number of isoforms Number of exons Alternative splicing Open reading frame
Not considering the sequence yet
https://www.dropbox.com/s/giwiam66e9k3fa6/DLN%20Page%202%20Gene%20Structure%20Instructions.docx?dl=0
DLN Page 3 – Coding DNA Sequence
The actual CDS annotation!
Important coordinates in yellow box. Several pages long…
Start at the start codon – It’s painted green!
Watch what strand is being analyzed!
Reveals student misconceptions - UTRs
Synthesis of evidence 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
https://www.dropbox.com/s/l54ago79qlcys47/DLN%20Page%203%20Coding%20DNA%20Sequence%20Instructions%20Part%201.docx?dl=0
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
Digital Laboratory Notebook 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] 951-639-
5735