Assignments

2011 Flow chart for lab activities
Lab Syllabus for Winter 2011 (Microsoft Word 26kB Jan9 11)

Week 1 lab handout (Microsoft Word 54kB Jan10 11) to begin explore a biological strategy

LD/SD data sheet for week 1 lab (Excel 78kB Jan9 11)

McKnight flowering data for week 1 lab (Excel 29kB Jan9 11)

Weaver Dunes flowering data for week 1 lab (Excel 63kB Jan9 11)

Weeks 2 and 3 lab handout (Microsoft Word 51kB Jan9 11) to accompany transcriptome analysis work on the Chamaecrista Explorer

Primer design tips for weeks 3 - 4 (Microsoft Word 2007 (.docx) 35kB Jan17 11)

Primers designed by Tuesday lab (Excel 2007 (.xlsx) 33kB Feb3 11)

Primers designed by Thursday lab (Excel 2007 (.xlsx) 40kB Feb3 11)

Week 5 RNA isolation handout (Microsoft Word 35kB Feb3 11)

Week 6 lab handout (Microsoft Word 2007 (.docx) 119kB Jan30 10) on determining RNA concentration

Spreadsheet to help calculate RNA concetration (Excel 25kB Jan30 10)

RNA quality and concentrations for Tuesday and Thursday labs (Excel 2007 (.xlsx) 57kB Feb4 10)

Week 6 RT PCR protocol (Microsoft Word 79kB Feb8 11)

Week 6 TA tips (Microsoft Word 2007 (.docx) 126kB Feb7 11)

Week 7 Gel electrophoresis handout (Microsoft Word 2007 (.docx) 56kB Jan30 10)

Week 7 Quantifying cDNA on a gel (Microsoft Word 48kB Jan30 10)

Week 7 Preparing your PCR products for sequencing (Microsoft Word 2007 (.docx) 112kB Feb5 10)

Week 8 Analyzing your PCR sequences (Microsoft Word 2007 (.docx) 129kB Feb5 10)

PCR sequences (Stuffit Archive 398kB Feb18 10)

Due at beginning of week 2 lab:
  • One to two pages (double spaced) describing your findings, your proposed flowering model, and one experiment to test an aspect of your model
  • Figures from your data analyses.
  • A model (visual representation). If you need some more tips on developing a model, go to What is a Model?

Due at the end of week 2:
  • Conclusions based on your work with the Soybean Genome Browser and JMP Genomics should be entered in Moodle and your electronic notebook.
  • Question about flowering in Chamaecrista and a strategy(ies) that you will use to address using bioinformatics tools and resources in lab next week. Your question should be entered in Moodle and your journal.
  • Each group will describe their question and approach to the class.

Due at the end of week 3:

  • Data and conclusions from your bioinformatics analysis should be recorded for your final presentation and paper.
  • Flow chart showing the strategies you have used on your research to date (entered in Moodle and recorded in your journal).
  • Thoughtfully framed question and strategy that flows from your bioinformatics analysis and can be answered in the next three weeks in the lab. This question and strategy should be recorded in your electronic notebook, submitted via Moodle, and shared orally with the class at the end of lab.

Due at the end of week 4:

  • Two primer sets you would like ordered for next week.
Due at the end of week 5:

  • RNA stored in freezer for next week

Due at the end of week 6:

  • RNA spec readings and concentrations recorded on lab spreadsheet.
  • PCR reaction running
  • Good notes on your experiment in your electronic notebook

Due at the end of week 7:

  • Annotated gels submitted via Moodle
  • PCR product and primers that you would like to have sequenced should be turned in before leaving lab.

Due at the end of week 8:

  • Electronic notebook submitted via Moodle

Due at the end of week 9:

  • Powerpoint submitted via Moodle
  • Feedback forms

Due last day of class:

  • Final paper and individual model