Genomic Biotchnology Lab
BINF 8350/BINF 6350
UNCC
Fall 2011
Bioinformatics 347, Monday 9:30-10:45
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Class Schedule:
(Subject to change)
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Week
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Dates/Lecturer
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Topics
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Resource Title
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Note
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| 1
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Aug 22 nd Weller
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Lecture: Lab Safety, Measurement, Record keeping
Lab Skills: Lab tour, pipetting, making and maintaining stock solutions and dilutions, using a mass balance
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Lecture 1
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Practice dilution calculations Worksheet
Practice making solutions from stocks
Worksheet
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| 2
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Aug 29 th Weller
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Lecture:Spectrophotometry and Gel Electrophoresis.
Lab Skills: Spectrophotometry - using the NanoDrop. Gel Electrophoresis: Pouring Agarose and Polyacrylamide Gels.
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Lecture 2
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Extinction coefficients for fluorescent dyes are given here
IDT link
Recipes for common lab solutions
Promega Notes - I
Base number for calculations involving nucleic acids
Promega Notes -II
Marker dye migration in various gels
Promega Notes III
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3
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Sept 5 th
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Labor Day - HOLIDAY
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No Class
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| 4
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Sept 12 th Weller
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Lecture: Experimental Design. Biological properties of the samples (Dr. Jess Schlueter)
Lab Skills: Load, run and document an agarose and acrylamide gels. Sample harvesting and storage.
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Lecture 3
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Sample harvesting and extraction protocol is on the Protocols page
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| 5
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Sept 19 th Weller
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Lecture:Experimental design - technical. Principles of sample disruption and fractionation.
Lab Skills: Harvest and disrupt plant tissue, Stage I fractionation. Use VisionWorks software to analyze gels.
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Lecture 4
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| 6
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Sept 26 th Weller
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Lecture: The polymerase chain reaction , primer design methods, principles of PCR optimization
Lab Skills:Precipitation methods for DNA and RNA, chemical and enzymatic clean-up, sample concentration methods.
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Lecture 5
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| 7
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Oct 3 rd Weller
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Cancelled
Lab: Cancelled.
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Cancelled
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8
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Oct 10 th
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Fall Recess
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No Class
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| 9
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Oct 17 th Weller
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Lecture:Principles of qRT-PCR. Review primer design concepts.
Lab Skills:Set up PCR reactions, pour acrylamide gels and run samples to check for products.
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Lecture 6
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Dr. Van Dyke's REPSA presentation
REPSA slides
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| 10
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Oct 24 th Weller
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Lecture:Continue discussion of qRT-PCR principles
Lab Skills:Test phaseolus DNA with tubulin primers. Set up amplicon reaction.
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Lecture 7
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See Readings for papers on uMelt for qPCR analysis, and other tips for producing good data
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| 11
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Oct 31 st Weller
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Lecture:Principles of fragment production, DNA shearing, .
Lab Skills:Use Ampure beads to clean up amplicons;ligate adaptors.
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Lecture 8
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| 12
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Nov 7 th Weller
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Lecture:Principles of Polishing, and modes of adding adaptors
Lab Skills:Set up emulsion PCR, perform sphere enrichment on OneTouch system.
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Lecture 9
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| 13
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Nov 14 th Weller
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Lecture: The Ion Torrent PGM and One Touch Platforms.
Lab Skills:Determine the number of fragments per bead by qPCR using the Kapa Biosciences kit, emulsion PCR reactors.
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Lecture 10
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| 14
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Nov 21 th Weller
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Lecture: Ion Torrent bead attachment and purificaton
Lab Skills:using the IKA Turrax and the OneTouch-ES (we'll compare outcomes)
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Lecture 11
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| 15
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Nov 28 th Weller
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Lecture:The PGM chip and software
Lab Skills:Perform ISP enrichment, test the fragment loading with the Qubit, initialize and run a 314 chip on the PGM.
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Notebook Inspection!!
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I will grade notebooks again on this day (in class, so be prepared)
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| 16
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Dec 5 th Weller
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No lecture - project work day
Please make use of the time well!
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Project Work Day
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Final Experiment Report work day
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17
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Dec 12 th
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Finals Week
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Project Report AND Experiment Report DUE by 5pm
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Everything is due!!
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Course Home
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Course Syllabus
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Course Readings
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Course Schedule
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Course Protocols
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Dr. Jennifer W Weller 