## Growth chambers and scheduling
## How to grow your plants
* __Read [this article](http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=102&f=FP12028)__
* __Always__ measure and record actual temperature, day length, and light spectrum, as well as chamber settings at the beginning of your experiment. If you are in the greenhouse or field use a data logger to continuously measure this inf.
* Use appropriate experimental design, including randomization, blocking, and replication. Whenever possible use a complete randomized block design. If you are new to this talk over your design with Julin or Kazu __before you plant.__ The R package [agricolae](https://cran.r-project.org/web/packages/agricolae/index.html) has tools for design and randomization.
* Label your plants or flats with your name.
* Check your plants at least every other day for water, pests, health, etc.
* Be considerate of other users:
* Do not change chamber settings without checking with other users.
* Clean up after yourself.
* Dispose of plants promptly at the end of the experiment
* Transgenic plants and soil need to be autoclaved.
## Data Loggers (Cody to complete)
## Growth Facilities
### CEF
We grow plants in the [Controlled Environment Facility](http://greenhouse.ucdavis.edu/cef/index.html). Please register as a CEF user before using this facility.
Space in the CEF is coordinated by Kazu
### growth chambers
[CEF501]()(a big walk in chamber equipped with simulated sun (right side) or shade (left side) condition; calendar is under construction)
[CEF64](https://calendar.google.com/calendar/embed?src=qou4hqf9g0nliq4ddoeoj7entc%40group.calendar.google.com&ctz=America/Los_Angeles) (a small growth chamber)
* ICAL feed `https://calendar.google.com/calendar/ical/qou4hqf9g0nliq4ddoeoj7entc%40group.calendar.google.com/public/basic.ics`
[CEF65](https://calendar.google.com/calendar/embed?src=5vo1b9o7fduediirus0n5qdua4%40group.calendar.google.com&ctz=America/Los_Angeles
) (a small growth chamber)
* ICAL feed `https://calendar.google.com/calendar/ical/5vo1b9o7fduediirus0n5qdua4%40group.calendar.google.com/public/basic.ics
`
[CEF503](https://calendar.google.com/calendar/embed?src=3j17q3lqm0igne2b1se6966g9s%40group.calendar.google.com&ctz=America/Los_Angeles) (Small right hand walk in chamber in CEFB)
* ICAL feed `https://calendar.google.com/calendar/ical/3j17q3lqm0igne2b1se6966g9s%40group.calendar.google.com/public/basic.ics
`
[CEF504](
https://calendar.google.com/calendar/embed?src=q68ig8dcsagsneu31tbrrits1k%40group.calendar.google.com&ctz=America/Los_Angeles) (Small walk-in chamber on Left hand side in CEF B. Please specify which Shelf # you will be using.)
* ICAL feed `https://calendar.google.com/calendar/ical/q68ig8dcsagsneu31tbrrits1k%40group.calendar.google.com/public/basic.ics`
Greenhouse 215
* ICAL feed
`https://calendar.google.com/calendar/ical/6kl8p940bl9sppmm55jigmjmko%40group.calendar.google.com/public/basic.ics
`
### LED Chambers
For seedling experiments we have two "custom" LED chambers with Quantum Devices SnapLites. These are in the basement of Briggs and are called [Maloof Left LEDs](https://calendar.google.com/calendar/embed?src=4c4mabdtrgs928scnapjj176qc%40group.calendar.google.com&ctz=America/Los_Angeles) and [Maloof Right LEDs](https://calendar.google.com/calendar/embed?src=t5qqna0ot4ijet026hq53rnjl0%40group.calendar.google.com&ctz=America/Los_Angeles) on Google Calendar used for sign up.
We also have an Andor CCD camera for luciferase imaging. This is in a Percival chamber with red, far-red, and blue LEDs. This is known as [Kirkwood](https://calendar.google.com/calendar/embed?src=159vcp21bsd0kna985v4ekgh70%40group.calendar.google.com&ctz=America/Los_Angeles) on the Google Calendar sign up.
For permission to sign up for these chambers please contact Kazu
Maloof Left ICAL feed:
`https://calendar.google.com/calendar/ical/4c4mabdtrgs928scnapjj176qc%40group.calendar.google.com/public/basic.ics`
Maloof Right ICAL feed: `https://calendar.google.com/calendar/ical/t5qqna0ot4ijet026hq53rnjl0%40group.calendar.google.com/public/basic.ics`
Kirkwood ICAL feed: `https://calendar.google.com/calendar/ical/159vcp21bsd0kna985v4ekgh70%40group.calendar.google.com/public/basic.ics`
### Maloof lab standard growth condition for shade avoidance responses
#### hypocotyl (Nozue (2015) PLoS Genetics, which used modified protocol in Filiault(2012) PLoS Genetics)
light condition (LED chambers): R (34 µE) + B (7 µE) and FR adjusted (R/FR = 1.3 for simulated sun and 0.5 for simulated shade).
Notes:
- Switch right and left chambers due to possible temperature differences. Eg. Replicate 1 (left chamber (R/FR=1.3) and right chamber (R/FR=0.5), Replicate 2 (left chamber (R/FR=0.5) and right chamber (R/fR=1.3).
- Use squire plates without grids for scanning plates and place plates at vertical position in growth chambers (use 1ml blue tips and tip boxes as custom plate holders).
- After four days stratification in a tin box, let seeds germinate under simulated sun chamber for three days and score non-germinated seeds on the third day (eliminate slow germinators from data analysis).
- Split plates into simulated sun and shade and grow plants for four days and scan plates.
- Sprinkle ethanol sterilized seeds on plates 5 mm apart (in two or three rows). You can use marked grid square plate as position template underneath of your plates.
- Randomize genotypes position within plate to avoid position effects.
### Greenhouses
We rent greenhouse space in the [Orchard Park Greenhouse Facility](http://greenhouse.ucdavis.edu/research/index.html). Before using greenhouse, take greenhouse training (contact Ron Lane, relane@ucdavis.edu). And then contact Plant Biology greenhouse manager (Ian Baker <idbaker@ucdavis.edu>).
*_TMV prevention_
*_Safety Training_
Before you begin to grow you plants in the greenhouse, please first finish _greenhouse_ Safety Trainning