Brant Faircloth
Protocol descriptions have been given where possible. New protocols will be posted as they become available. All protocols are presented in .pdf format.
Sample Collection and Extraction
Collecting feathers for DNA Extraction
Feather collection protocol used in John Carroll’s lab.
DNA extraction from plucked feathers
Extraction protocol (modified by addition of DTT and reduction in elution volume) from John Carroll’s lab.
Avian DNA Storage and Extraction
DNA storage and extraction protocols from the lab of Gillian Baker. Some additions made by Brant Faircloth.
PCR
Regular PCR
General PCR protocol from John Carroll’s lab. 10ul final volume.
Nested PCR
Nested PCR protocol. Originally from Travis Glenn’s lab, but modified for use with bobwhite primers in John Carroll’s lab. See
Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF (2001)M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele sizing methods. Biotechniques, 31, 24–28
for description of the method and
Schable NA, Faircloth BC, Palmer WE, Carroll JP, Burger LW Jr., Brennan LA, Hagen C, and Glenn TC (2004) Tetranucleotide and dinucleotide microsatellite loci from the northern bobwhite (Colinus virginianus). Molecular Ecology Notes, 4, 415-419.
for sequence and citation of 5’ CAG tag.
Sequencer
Prepping 12 in. gel for use with ABI 377
Instructions on preparing a 12 inch well-to-read gel for use with the ABI 377. Protocol from the lab of John Carroll.
Preparing Samples for Sizing Run
Details sample prep prior to run on 377.
Setting up ABI 377 for gel run
Details sequencer prep for fragment sizing run. From John Carroll’s lab.
h1. Scoring
Scoring Alleles
Incomplete! Brant Faircloth’s preliminary guide to scoring alleles.
Other
Lab Solutions
A cheat sheet of common lab solutions.
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Databases
NCBI Taxonomy DatabaseNCBI Taxonomy database search for Order Galliformes holdings (listed by genus and genus-specific epithet)
Specialist Groups
Cracid GroupGrouse Group
Megapode Group
Pheasant Group
PQF Group
Other Labs and Protocols
Bruce Roe's Lab ProtocolsVery thorough site from the lab of Bruce Roe
Sheffield Molecular Genetics Facility
The University of Sheffield’s molecular genetics website.
SREL DNA Lab
Travis Glenn’s lab at Savannah River Ecology Lab.
SREL DNA Lab Protocols
Protocols from the Glenn Lab
Tavi's PCR Protocols
Discusses PCR and associated protocols/problems
Suppliers
Applied BiosystemsEquipment, reagents, and primers
Bio-Rad
Equipment, reagents, and consumables
Brinkman-Eppendorf
Equipment, reagents, and consumables
Fisher Scientific
Equipment, reagents, and consumables
IDT DNA
Primers
Marsh Bio-Products
Reagents, consumables
Molecular Probes
Picogreen quantitation reagents
MWG Biotech
Primers, small-scale syntheses
Rainin, Inc.
Pipets and tips
Sigma-Aldrich
Reagents and other chemicals