Dr. Jennifer W Weller @ UNC Charlotte

I will post descriptions of procedures, images, videos amd manuals here. This page will be updated frequently.

Aug 22 ^nd

Comments

Aug 29 ^th

Combined Spectrophotometry and Electrophoresis Labs

Comments

I expect it will take us two periods to get through both spectrophotometers and both types of gels, but we will have some of the group work on each each time in order to reduce pressure on the instruments.

Sept 12 ^th

Combined Plant harvesting and DNA extraction protocol

Comments

Sept 19th ^th

DNA purification protocol Second revision
DNA ladders we use on gels in this class. Guide

Sample loading description for 4 gels Sample Directory
Gel A jpg version
Gel A tif version
Gel B jpg version
Gel B tif version
Gel C jpg version
Gel C tif version
Gel D jpg version

Comments

Sept 26 ^th

PCR test of Soy DNA with Actin and Tubulin primers

Key to lanes in the gels for each team Gel Key
Team 1 gel image tif version
Team 2 gel image tif version
Team 3 gel image tif version
Team 4 gel image tif version
Team 5 gel image tif version
Team 1 gel image jpg version
Team 2 gel image jpg version
Team 3 gel image jpg version
Team 4 gel image jpg version
Team 5 gel image jpg version

Comments

Oct 3 ^rd

Comments

Oct 17 ^th

Revised PCR test of Soy DNA with Actin and Tubulin primers

Comments

Oct 24^th

Key to lanes in the gels for each team Description of gels and lanes.
Team 1 8% gel image Group1_GlycinePCRtest
Team 2 8% gel image Group2_GlycinePCRtest
Team 3 8% gel image Group3_GlycinePCRtest
Team 4 8% gel image Group4_GlycinePCRtest
Team 5 8% gel image Group5_GlycinePCRtest
Loraine Agarose gel Loraine gel
WilliamsYen-BaxterBrown gel WYBB gel
SmithTurner-SuttlemeyrSong gel STSS gel
Phaseolus PCR test using tubulin primers (all but group 1) 8-bit jpeg inverted gel image
Key to lanes in the gels for each team Key to Phaseolus PCR test gel.

Comments

Oct 31 ^st

Excel sheet with primer sequences and Tms List
The protocol for this days activities is posted here PCR product precipitation, test of library degenerate primers
Here is a document that shows thumbnails of the results and the key for 4 agarose gels that were run on Monday. Note that two groups do seem to have amplifued the tubulin in Phaseolus (the samples that you re-precipitated in order to concentrate the product). However the F3H-2 aND f3h-4 primers do not seem to have worked. See the Readings page, Qiagen newletter for a likely explanation as to why (note the levels of degeneracy, the average Tm and the need for stable 3' ends). Description of 4 gels and their lanes.

Comments

Nov 7 ^th

The protocol for the days activities is posted here Fragment modification, size selection

Comments

Nov 14^th

The protocol for the days activities is posted here qPCR test and Fragmentase test

Comments

Nov 21^st

emPCR with ISPs

Comments

http://www.iontorrent.com/videos-introduction-to-semiconductor-sequencing/
The Qubit Excel worksheet for calculating the ISP loading is provided here Qubit Calculator V2.0

Nov 28^th

Enrichment and sequencing protocols
The Qubit spreadsheet for the measurements we made in class. Note that the calibration factor is instrument-specific and the converison factor is kit-specific.Class values in spreadsheet
ION Torrent Data! Good data! You guys rock - Library 1 did better than Library 5, as we expected. The summary report on Phaseolus Library 1
The zipped-fastq file of the Phaseolus Library 1 sequences. Other file types available upon request. The compressed fastq data for Library 1 Phaseolus
We ran the second half of Phaseolus Library 1 sequences and got even more data (~250,000 reads) so for those with an interest in analysis I post them here. Summary Report Library 1 part 2
The zipped fastq files are provided here - ask if you need a different format. Zipped Library 1 part 2 fastq files
We ran half of the Phaseolus-5 library, but in this case there were very few reads (~30,000) - however we post them here in case you want to take a look. Library 5 Phaseolus Report
The zipped fastq files for Library 5 are provided here (very small file). Library 5 Phaseolus fastq zipped file

Comments

frequently

Fragment Preparation Module
Template attachment Module
ISP enrichment Module
PGM sequencing Version 2 Module
Kapa Biosciences Ion Library test protocol

Dec 5^th

Work on your projects! Comments

I want to express my thanks to all of the students who participated this year, for hard work, extra hours and lots of feedback on protocols and lectures. You earned yoursuccess.
Dedicated to the BINF 8350 students of Fall 2011:Dr. Ann Loraine, Kyle Suttlemyre, Xiao Song, Matthew Brown, Adam Baxter, Tiffany Willliams, Chi-Yu (Jack) Yen, Jason Smith and Dan Turner.

My thanks also go to Deepthi Chaturvedi who saw us through the first part of the semester, and Timm Hamp who provided expert assistance in the second part.