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Protocols
and Tutorials
[Under
construction] This page
is used by the Scott group as a reservoir of detailed information about
tools and techniques used in our research. Group members create individual
tutorials on common methods, software, etc., and these are itemized in
the Tutorials section. Detailed guidance about
laboratory practices are available within a set of protocols.
Some of these are created as "primers" to aid students just
getting started in the laboratory.
Protocols
- Methods
for the Discovery of Prospective Transcription Factors
- This is a set of custom
protocols used in the Scott group regulatory transcription factor discovery
project. Included are protocols for DNA pull-down, MS-based protein
identification, biophysical characterization of transcription factor
binding sites, and in vitro regulated transcription assays.
- Primer
on cloning, expression, purification
- This is a detailed protocol
for cloning a selected gene into a pET-style vector for N-terminal His•Tag
fusion expression from a T7 promoter, followed by metal ion affinity
purification. It is designed to be appropriate for a beginning molecular
biology student.
- DNA
Manipulation and Gel Electrophoresis
- Detailed protocols for isolation
and manipulation of DNA including extraction, precipitation, gel purification,
staining.
- Protein
Gel Electrophoresis
- Detailed protocols for protein
gels including preparing, running, staining, and blotting gels.
Tutorials
(Methods)
- Data Analysis /
Error Propagation
- Determination of [metal]/[protein]
ratio is used to discuss uncertainties in measured quantities, distributions
of replicate measurements, and propagation of errors during data analysis.
Methods for proper estimation and handling of errors in measurements
are provided [pdf
revised 2004.08.20 by R.A.Scott]
- Protein Determination
- An introduction to protein
quantification assays [.ppt
revised 2005.05.10 by X.Li]
- DNA Quantification
- A description of the use
of the DynaQuant fluorimeter for DNA quantification [.doc
revised 2005.04.15 by J.J.Shonka]
- PCR Optimization
/ Primer Design
- description
- Cloning
- An introduction to cloning
and its applications in molecular biology [.ppt
revised 2004.12.13 by G.Yuan]
- Protein Expression
- description
- Protein Purification
- An introduction to various
types of protein chromatography [.ppt
revised 2005.07.12 by M.Murugesan]
- Mass Spectrometry
/ Proteomics Analysis
- description
- Site-Directed Mutagenesis
- description
Tutorials
(Software)
- EndNote™
[ zip
archive revised 2005.07.14 by R.A.Scott]
- The UGA library has purchased
a site license to EndNote v8 for any UGA student/faculty. This tutorial
introduces this reference manager and describes how to use it to search
web databases, how to export hits from web databases to EndNote, and
how to use it to create bibliographies and citations within manuscripts.
- Igor™
[ .doc
revised 2006.01.23 by J.E.Shokes]
- Igor is a powerful and vesatile
graphing program for (x,y) data. It allows creation of publication quality
figures and incorporates sophisticated numerical analysis tools. It
can import data in many formats and can export graphs to many formats.
This tutorial will get you started.
- PowerPoint™
- description
- Molecular Graphics
/ Visualization
- description
- Bioinformatics /
Sequence Analysis
- description
Tutorials
(XAS)
This is a suite of tutorials
and manuals for working with XAS data in the Scott group. It is strongly
recommended that the user first have basic knowledge about the EXAFS technique
[general references can be found in our XAS
Tutorial (this is a pdf of slides/notes from a PowerPoint presentation)].
We describe collection, handling, processing, reduction, and analysis
of XAS data collected at SSRL.
Step-by-step examples use Fe K edge EXAFS data of two samples from T.
Iwasaki: SdhB-NTD, reduced (filename FSBRA) and FdxB (filename FX12B).
To get started, make sure you
have performed at least the first two software installation procedures
below (we try to maintain a Windows-based "beam line laptop"
in the group that has all the necessary software installed and updated),
then select a set of raw data to use for practice. Look at the Data Handling
tutorial on Data Organization, Storage, Archiving to learn about our data
index, our directory hierarchy, and where to find the raw data files.
Then you can go through Data Pre-processing, Data Reduction, and Data
Analysis, in that order. Become comfortable with standard single-scattering
data analysis before trying your hand at advanced concepts of multiple
scattering, force constants, etc.
- Software Installation
Data Handling
- Beam line Data Collection
(pdf download)
- Data Organization, Storage,
Archiving (pdf
download)
Data Pre-processing
Data Reduction
Data Analysis
Data Exchange
Data Presentation
- Igor™ [
.doc revised
2006.01.23 by J.E.Shokes]
scott@chem.uga.edu
Department of Chemistry
University of Georgia
Athens, GA 30602-2556
706 542-2240 | FAX: 706
542-2295 |
