 GEP Digital Laboratory Notebook Nick Reeves, Mt. San Jacinto Community College

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Transcript of  GEP Digital Laboratory Notebook Nick Reeves, Mt. San Jacinto Community College

GEP Implementation First Year

GEP Digital Laboratory NotebookNick Reeves, Mt. San Jacinto Community College

Claiming and Delivering Files and ProjectsI claimed lower difficulty contigs (level 4 or 5) with 2 genes identified by the BLASTX evidence trackAll 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

2DLN Page 1 - SyntenyBasic 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 divisionIntroduces students to the GEP genome browser and Flybase gbrowse

https://www.dropbox.com/s/9z1p2zqzbhcgpu0/DLN%20Page%201%20Synteny%20Instructions.docx?dl=0DLN Page 2 Gene StructurePick one of the two genes in the contig and compare the gene structure of the query BLASTX track and the reference D. melanogaster annotationEmphasizeNumber of isoforms Number of exonsAlternative splicingOpen reading frameNot considering the sequence yet

https://www.dropbox.com/s/giwiam66e9k3fa6/DLN%20Page%202%20Gene%20Structure%20Instructions.docx?dl=0DLN Page 3 Coding DNA Sequence The actual CDS annotation!Important coordinates in yellow box. Several pages long Start at the start codon Its painted green!Watch what strand is being analyzed! Reveals student misconceptions - UTRsSynthesis of evidenceBLAST track finds homologsGene predictions indicate boundariesRNA-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=0Gene Record Finder

DLN Page 3 Coding DNA Sequence Intron boundaries defined by splice site consensus sequence AG/GT and synthesis of evidence tracksFrame 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 tracksFrame vs. phase critical thinking! A practice activity would be helpful.

DLN Page 3 Coding DNA Sequence Stop at the stop codon Its painted redCheck whether amino acids match D. melanogasterDont get confused by BLASTX track (ends before stop codon does not an amino acid) and RNA-seq track (ends after stop codon 3UTR)Final CDS Coordinates are now collected in the yellow boxes

DLN Page 4 Project ReportDLN Page 3 coordinates in yellow boxes can be used to run the gene model checkerAll 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/CollaborationLab 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 extentDigital Laboratory NotebookOnline doc? Google docs/Office 365Example 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 responseLess data entry? Remove repeat track; less gene record finder analysisPre-selected projects and pre-formatted notebook pages?

CURE (course-based undergraduate research experience) AchievedQuestions?Contact Information Nick Reeves Mt. San Jacinto College nreeves@msjc.edu 951-639-5735