Lab protocols

These are the laboratory protocols used in Dustin Edwards's lab at Tarleton State University: the phage methods taught in the SEA-PHAGES course, and PCR primers with their reaction and cycling conditions. Each protocol has its own page with the full method, a printable bench sheet and a markdown copy. They are written for students in the lab and for anyone running the same methods elsewhere.

Search the library below, or narrow it by method, organism, target or course. Every filtered view has its own address, so a link to it shows the same list.

How these facts are made#

Each fact on these pages is stored once, in a record the lab can read, and the pages draw what they show from those records. The protocols are records, and so are the primers, the host strains, the reagents and the equipment in the lab registry. A protocol names a primer, a strain, a reagent or an item of equipment by its id and keeps only what is its own: its steps, its amounts, its stock and final concentrations, and its settings.

• Primers. The sequence is stored as the lab uses it. Its length, GC content and reverse complement are computed from it, and so is a melting temperature estimate, with the method and conditions stated on the page. The estimate is for comparing primers and is not an annealing temperature: for that, use the polymerase maker's calculator, such as the NEB Tm Calculator.
• Positions and product sizes. Where a primer binds is computed by placing it on a named GenBank reference, which is genomic unless the protocol amplifies cDNA, and a pair's product size is computed from where its two primers bind. A mismatch is shown, not absorbed.
• What the literature says. The paper that first printed a primer, its name for it, the sequence it prints and the product size it states are recorded as read, and the printed sequence is compared with the stored one. A difference is shown and reported, never corrected quietly.
• Host strains. The phages isolated on a strain are counted from the phage table by host.
• Reagents and equipment. Each is a row of one table. A bought reagent has a supplier and a catalog number, and a reagent the lab prepares links its recipe. Each protocol's own tables carry its amounts and settings beside where each item comes from.

Anything no record states is shown as not found, with the reason, and is listed for Dustin to fill in. Nothing is filled from memory.

Related pages#

• Research
• Bacteriophages
• Phage table
• Publications
• Phage discovery guide