Transcriptomics During One-Step Growth Curves for Cellulophaga Phages
Do a plaque assay to determine the PFU/ml of the lysate you plan to use Inoculate a new culture; i.e., pick a colony into a 125 ml flask containing MLB media. 
The next day, transfer 10 ml of this culture to 500 ml of new media in a Fernbach flask (short and fat 2800 ml). 
Inoculate enough 500 ml cultures for your experiment. 
Immediately after the transfer, take a 'time 0' growth reading. 
Continue taking readings in this way periodically.  
Graph the results as you go!
Determine the concentration of your culture at the time you want to start the infection. 
Calculate the total number of cells in each of your 500 ml cultures. 
Calculate how many phages you should add for MOI 3.  
Add phages to the experimental flask and an equal volume of MSM to the control flask and start your timer. 
Immediately, dilute the infection 1:1 in MLB media; i.e., add 500 ml fresh media to each flask and swirl to mix.  
Take a sample immediately after dilution Steps for centrifuged plaque assay:  
Steps for non-centrifuged plaque assay:  
Steps for RNA samples: 
The next day, count the plaques on all plates that have a countable number of them  The next day, count any new plaques that have appeared; add these to your original count.  
Count again on the third day. 
Continue sampling in this way for 8 hours. 
Calculate PFU/ml at each time point for both the centrifuged (free phage only) and not centrifuged (total phage) samples.  
Graph the results. 
Calculate burst size.
