TX-TL Workshop, Aug 2013: Detailed Schedule

The detailed schedule below describes that is happening in each track of the TX-TL workshop and roughly when different groups should be doing different things. Zach and Clare are responsible for keeping track of what is going on. The master copy of this schedule is on the wiki (not publicly accessible). A summary of the workshop schedule is available on the main workshop page.

Monday

Goals:

• TX-TL basics: Get everyone up to speed on the basics of TX-TL and the tools we will need for the rest of the week
• TX-TL extract: Create colonies from stocks

Time	TX-TL basics	TX-TL implement	TX-TL design	TX-TL extract
9:30	Optional tutorials Geneious (Emzo)
12:00	Lunch at Chandler: meet outside of Keck Lab at noon
1:30	Welcome and Introductions, 114 Steele Lab
2:00	Overview (Richard, Vincent) Biomolecular breadboards, Richard TX-TL toolbox, Vincent Schedule for the week, Richard
3:30	Lab safety session (Clare)
4:00	Set up reactions for inducible promoter reactions (Zach, Clare) Use the TX-TL spreadsheet to set up reactions at 4 different inducer levels Pipette reactions into 384 well plate (two columns per team, run in duplicate) Run overnight on plate reader at 29 degC
5:30				Streak out colonies
6:00	Done for the day
7:30	Optional tutorials MATLAB/Simbiology (Zoltan) Lab techniques (Enoch)

Tuesday

Goals:

• TX-TL basics: plot experimental data and learn about TX-TL modeling and simulation
• TX-TL implement: create and run linear DNA, create "3X" plasmid DNA plates
• TX-TL design: meet with TAs to discuss projects
• TX-TL extract: pick colonies and grow up cells
• TX-TL extras: prepare phospholipids for use on Wed

Time	TX-TL basics	TX-TL implement	TX-TL design	TX-TL extract
9:00	Analyze TX-TL results from previous day Take data off of plate reader, plot in Excel (or MATLAB) Golden Gate cloning overview (1 hr, Zach)
10:00				Pick colonies, start cultures
10:30	TX-TL modeling toolbox (Vipul, Zoltan) Toolbox overview (45 m) Hands-on demo (30 m) Run models of results from previous evening (script)
12:00	Lunch
1:00		DNA assembly (Zach, Clare, Shaobin) Assemble feedforward loop onto individual plasmids ("3X"): AraC, TetR, deGFP Start PCR reactions to amplify linear Transform plasmids (3X) and streak out on plates
3:00	G4, G5: Vesicles prep. Reaction and feeding solutions [Vincent] G6: ALL intro session [Enoch]	PCR runs (2 hr)	G1-G3: Breakout discussions (w/ TAs) Each group will choose a circuit to prototype using linear DNA on Wed, Thu Choices: RNA circuit, negative auto-regulation, genetic switch, IFFL2 TAs: Emzo de los Santos (vesicles), Victoria Hsiao (ALL), Dan Siegal-Gaskins (logic), Vipul Singhal (RNA), Zoltan Tuza (genetic switch), Yong Wu (vesicles)
5:00		Set up linear DNA runs Run gels to confirm PCR results PCR cleanup linear DNA segments Each group will set up 2 columns of runs (duplicates). Vary aTc and arabinose (2 each + controls) Biotek 1: Run linear FFL overnight at 29 degC [Pre-prepared linear DNA available for all circuits in case your PCR didn't work]		Passage cells
7:00	Done for the day
Homework: Simulate feedfoward loops + individual circuits

Wednesday

Goals

• TX-TL implement: analyze linear DNA, set up and run 3X plasmids in TX-TL, create 1X plasmids for use on Thursday
• TX-TL design: create circuits and set up overnight runs
• TX-TL extract: bead beating and dialysis
• TX-TL extras: set up and run vesicles, set up and run droplets

Time	TX-TL extras	TX-TL implement	TX-TL design	TX-TL extract
10:00	G4, G5: Vesicles prep: phospholipids [Vincent] G6: ALL protocol development [Enoch]		G1-G3: Plan out circuits designs to build and test (with TAs) Decide on what experiments you want to run Check availability of parts; plan out assemblies for the day, if needed	Pellet and wash cells (Jongmin, Anu) Demonstrate how to pellet and wash cells
12:00		Go over data from previous night
12:30	Lunch
2:00	G4-G6: demonstration sessions (optional) Vesicles demo (Vincent): review preparation of feeding, reaction, phospholipids + live vesicles prep [Vincent] + view pre-prepared vesicles on microscope Droplets (Enoch): ALL overview + set up reactions for evening run			G1-G3: bead beating, centrifugation, dialysis (Jongmin, Anu, Clare) Each student to set up at least one bead beating tube Run bead beating and centrifuge results Load dialysis cassettes
4:00	Start ALL runs (Enoch)	Set up overnight runs Biotek1: FFL 3X plasmids Victor: student-designed circuits (linear DNA)
5:00	Done for the day

Thursday

Goals

• TX-TL implement: analyze 3X plasmid DNA circuits, set up and run 1X plasmids in TX-TL + cells with 1X plasmid
• TX-TL design: modify circuits and/or set up plasmid versions; set up overnight runs
• TX-TL extract: bead beating and dialysis (second set of groups)
• TX-TL extras: set up and run vesicles, set up and run droplets (first set of groups)

Time	TX-TL extras	TX-TL implement	TX-TL design	TX-TL extract
9:00		Analyze TX-TL results from previous day Grab and analyze 3X plasmid FFL results Pick colonies and start cultures for plasmid FFL circuits Pick colonies for 1X plasmid FFL circuit Set up colony PCR + start cell cultures [Pre-prepared plates of all circuits available as backups]	Analyze TX-TL results from previous day Grab and analyze linear DNA results
10:00	G1-G3: demonstration sessions (optional) Vesicles demo (Vincent): review prep of reaction, feeding, phospholipid, vesicles + view vesicles from previous day on microscope Droplets (Enoch): ALL overview + set up reactions for afternoon run		Circuit design and preparation (if needed) Decide on new runs to be done with circuit variants	G4-G6: bead beating, centrifugation, dialysis (Anu, Jongmin, Clare) Each student to set up at least one bead beating tube Run bead beating and centrifuge results Load dialysis cassettes
1:00	Lunch
2:00	Start ALL runs (Enoch)			Extract prep overview (Clare) Use slides to go through whole process and calibration procedure Discuss variability between extract batches (with data)
4:00		1X plasmid runs Mini-prep plasmids; run gel to verify In vivo runs Dilute cells and set up in 96 well plate [Pre-prepared 1X plasmids available as backup]
5:00		Set up overnight runs Biotek1: FFL 1X plasmids Biotek2: FFL in vivo Victor: student-designed circuits
6:00	Done for the day

Friday

Goals:

• TX-TL implement: compare simulations, linear, 3X plasmid, 1X plasmid and in vivo results
• TX-TL design: analyze results and make short presentation
• TX-TL extras: present data from previous days

Time	TX-TL extras	TX-TL implement	TX-TL design	TX-TL extract
9:00		Analyze and compare data Simulations (Tue night), linear TX-TL (Tue night), plasmid TX-TL (Wed/Thu nights), cells (Thu night)	Analyze data Collect data from plate reader Create 10 minute presentation of results (with TAs)
10:30	Group presentations 10 minute presentation of circuit results to the group Enoch: ALL data
12:00	Group lunch (optional)