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 nreeves@msjc.edu 951-639-

5735