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Matt Hudson Lab - Bioinformatics & Plant Genomics

CPSC 265: Genetic Engineering Laboratory

CPSC 265: Genetic Engineering Laboratory: Fall 2015 (Grade requirements, Syllabus)

Week 1 Aug 27 Overview, Safety, Notebooks. Micropipettes and Buffers Lecture : ppt, pdf

Protocol: doc

Week 2 Sep 3 Genomic DNA extraction

Lecture : ppt, pdf

Protocol: doc, pdf

Week 3 Sep 10 A. Exam 1 on DNA extraction
B. Extraction of RNA

Lecture : ppt, pdf

Protocol: doc, pdf

Week 4 Sep 18 A. Exam 2 on RNA extraction
B. RNA electrophoresis, photograph and blot
C. Discuss DNA gel blots

Lecture : ppt, pdf

Protocol: doc, pdf

Week 5 Sep 24 A. Quantifying mRNA
B. Discuss probes and qPCR

Lecture : ppt, pdf

Protocol: doc, pdf

Week 6 Oct 1 A. Exam 3 on measuring mRNA
B. PCR amplification of a DNA fragment from genomic soybean DNA
C. Separation of PCR products by gel electrophoresis

Lecture : ppt, pdf

Protocol: doc, pdf

Week 7 Oct 8 A. Exam 4 on PCR
Lecture 6 1/2 on restriction enzymes (short class due to career fair).

Lecture : ppt, pdf

Week 8 Oct 15 A. Ligate PCR product into a plasmid vector
B. Transform ligation products into E. coli

Lecture : ppt, pdf

Protocol: doc, pdf

Week 9 Oct 22 A. Exam 5 on PCR, ligation and transformation
B. PCR amplify the plasmid insert from bacterial colonies
C. Use agarose gel electrophoresis to determine DNA size

Lecture : ppt, pdf

Protocol: doc, pdf

Week 10 Oct 29 DNA Sequencing and High Throughput Technology

Lecture : ppt, pdf

Home Assignment: doc, pdf

Movie Files:
Colony picker robot
Biomek robot
Roche movies
Illumina movie
Pac Biosci movie

Sequencing Output Data Files:
1(f)
2(f)
1(r)
2(r)
Failed sequence
Control sequence

Week 11 Nov 5 A. Discuss DNA sequencing
B. Computer analysis of DNA sequences
C. Homework Project handed out to take home
Lecture : ppt, pdf

Week 12 Nov 12 A. Exam 6 on sequencing and analysis
B. Expression of a recombinant soybean protein in E. coli
C. Analyze proteins using SDS - PAGE
D. Visit to functional genomics and proteomics while gel is running

Lecture : ppt, pdf

Protocol: doc, pdf

Week 13 Nov 19 A. Exam 7 on protein expression
B. Hand in homework on Bioinformatics
C. Discuss the results of protein expression in E. coli
D. Purify the protein using affinity chromatography
E. Run a new protein gel

Lecture : ppt, pdf

Protocol: doc, pdf

  Nov 26 Thanksgiving break  
Week 14 Dec 3 A. Exam 8 on protein purification
B. Electroblot proteins onto nitrocellulose (Demonstration)
C. Immunodetection of proteins (Western blot)

Lecture : ppt, pdf

Protocol: doc, pdf