Finding Post-translational Modifications
is very comprehensive and has a good search function to allow you to
find sites of phosphorylation, ubiquitination, acetylation, and other
modifications in proteins of interest. It seems to be very
seem redundant with PhosphositePlus, and only tabulates
phosphorylation, ubiquitination, and glycosylation, but it is worth
looking at just in case.DNA cloning and plasmid organization software
We use the following packages (Mac and PC versions are available):
ApE (A plasmid Editor), which can be dowloaded here
SnapGene, which can be downloaded here
. Check with Rita for a registration code.RNA structure
NUPACK can be downloaded here
mFOLD can be accessed here
KineFold (for animating RNA folding) can be accessed here
: an online interaction repository.
Molecular INTeraction Database (MINT
): Website has an interactive viewer for visualizing interaction networks.
Database of Interacting Proteins (DIP)
Biomolecular Interaction Network Database (BIND): Database of molecular interactions, complexes, and pathways from data submissions and scientific literature.
Agile Protein Interaction DataAnalyzer (APID): Integrated platform for exploring PPIs from experimentally validated data. Incorporates data from BIND, BioGRID, DIP, HPRD, IntAct, and MINT.
Useful numbers for biologists
: hereOnline protocols
has a lot of useful protocols and techniques. Many movies are shown to demonstrate procedures.
The Journal of Visualized Experiments
has movies for many detailed protocols for advanced techniques,
including several useful culturing protocols. It is worth searching
their movie library to see how they recommend performing various
protocols.Repositories of embryo/animal-wide gene expression patterns
The Gene expression database
from Jackson Labs allows you to search for gene expression by gene,
tissue, Affymetrix gene identifier, and several other parameters. Click
"Expression" from this page.Mouse atlas of gene expressioneMap Edinburgh mouse atlasGuidelines for performing specific techniques
For qRT-PCR experiments, we follow the MIQE (Minimum Information for Publication of Quantitative
Real-Time PCR Experiments) guidelines
. These guidelines affect how to peform qRT-PCR, and how to describe them in the Methods sections of papers.
Antibody companies with "small size" aliquots:http://www.genetex.comhttp://www.novusbio.com Ordering Posters:Posterpresentations.com
. Should be ordered 4 days in advance.