Finding Post-translational Modifications:

PhosphoSitePlus 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 comprehensive.

Phosidia 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. 

or

SnapGene, which can be downloaded here.  Check with Rita for a registration code.


RNA structure:

NUPACK can be downloaded here.


Online protocols:

BenchFly.com 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:

Emage

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 expression

eMap Edinburgh mouse atlas


Guidelines 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.com

http://www.novusbio.com

Ordering Posters:

Posterpresentations.com.  Should be ordered 4 days in advance.