Matthew Escobar

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Genomics at California State University San Marcos

Course Overview

BIOL 503 (Modern Molecular Biology and Genomics) is a four unit graduate-level course which meets 3 hr/wk lecture and 3 hr/wk lab. Typical enrollment is 10-20 students, with ~75% upper division undergraduates and ~25% Master's students. GEP sequence annotation components are implemented in the lab.


In lab, students are first introduced to "automated" tools to identify potential genes in raw genomic DNA (e.g. BLASTX, GenScan, FGENESH, cDNA sequence alignment, RepeatMasker) via a tutorial (Lab 1). This provides background on the tracks in the UCSC genome browser, explaining where this information comes from. Students are then introduced to the UCSC Browser and we perform manual annotation of a single two-exon gene. We annotate the first exon together (instructor-led) and the students annotate the second exon independently to complete the gene model (Lab 2). In week 3, the students are assigned a contig and they will independently annotate their contig during weeks 3-8. More complex concepts in annotation such as exon phase and synteny are introduced during these weeks. During weeks 9-10, students deliver brief (10 minute) oral presentations summarizing their research results and hand in a final written report. The report contains an electronic appendix which contains all files to be submitted to GEP (GFF, peptide, transcript, GEP annotation reports).   

Lessons Learned and Future Plans

Syllabus for

BIOL 503L: Modern Molecular Biology and Genomics Laboratory
Thursdays, 12:00-2:45 pm, Science Hall II, Rm. 157

Instructor: Dr. Matt Escobar
Office: Science Hall II, Rm. 123
Phone: (760) 750-8083
Office hours: Tuesdays 1:00-4:00 PM (or by appointment)

Materials Required
• USB memory stick (at least 250 Mb)
• Laptop computer (optional- you may also use the Biology departmental laptops)

Student Learning Outcomes
1. Students will participate in an independent research project through the annotation of previously uncharacterized genomic DNA sequence from Drosophila biarmipes
2. Students will learn to use computational tools such as BLAST, RepeatMasker, Genscan, UCSC Genome Browser, GEP Gene Record Finder, etc. to perform structural and functional annotation of eukaryotic genomic DNA.
3. Students will learn to computationally analyze global gene expression data generated by RNA-sequencing using RobiNA, MapMan, and other bioinformatics software.
4. Students will gain experience in presenting their research results in both oral and written formats (oral presentations, research reports)

Lab Grading
Genome Annotation project (written and oral reports): 120 pts.
RNAseq data analysis tutorial: 20 pts.
Microarray data analysis tutorial: 20 pts.
Preparation and participation: 40 pts.
200 pts. total

• Specific instructions for the Genome Annotation Report and the Transcriptomics Report will be provided in separate Assignment Guidelines.
• Preparation and Participation will be based upon:
o Attendance (Unexcused absence from a lab will result in the loss of at least 15 points)
o Performance on in-lab assignments
o Active engagement and positive contributions to in-lab activities (e.g. active engagement in computer exercises, asking/answering questions during article discussions, asking questions during research presentations, helping fellow students with bioinformatic challenges)
• Late submission of any assignment results in the loss of at least 20 points per late day

Tentative Lab Schedule

Date Topics Readings
1/24 Course Overview; Pre-course survey and Pre-course quiz -
1/31 Genome Annotation: Ab initio, homology-based, and gene expression-based Dynamic Gene Structure Tutorial; Stein et al., 2001
2/7 Annotating a Drosophila biarmipes gene: Tutorial -
2/14 Contig Annotation- Week 1
Overview of GEP; Contig introduction; CDS Workbooks Annotation Instruction Sheet
2/21 Contig Annotation- Week 2
Intron phase concept Annotation Strategy Guide
2/28 Contig Annotation- Week 3
Discuss Annotation Reports assignment guideline Annotation Reports assignment guideline (posted on course website)
3/7 Contig Annotation- Week 4
Discuss synteny analysis -
3/14 Contig Annotation- Week 5
Discussion of Leung et al., 2010 Leung et al., 2010 (posted on course website)
3/21 Contig Annotation- Week 6
Free Annotation -
3/28 Oral presentations of research findings -
4/11 Oral presentations of research findings (ctd.); Annotation report due; Post-course survey + post-course quiz; Conceptual overview of transcriptome data analysis -
4/18 Microarray data analysis- Week 1
Magic Tool User Guide
4/25 Microarray data analysis- Week 2; Discussion of Lohse et al. (2012); RNA-seq data analysis- Week 1; Lohse et al., 2012 (posted on course website)
5/2 Analysis of RNA-seq data- Week 2 Microarray data analysis questions due RobiNA User Guide
5/9 Open lab; RNA-seq data analysis questions due; course evaluations -