Phenotyping Practical

Glasshouse practical day 2

Instructions for the last day of the bioinformatics practical

The questions you should be asking yourself

• You planted 6 pots, these were 3 replicates of two conditions
  Did the condition (stratification) make any difference ?

  Please collect the data from each other and make a graph over time comparing the variability between replicates and between the experimentals.
  Did you sow the same amount of seeds in each pot ? Should you have done ?
  If not, can you make a calculation of the proportion of each stage present at each chronological sampling ? Does this solve the sowing size problem ?
  Are there clear differences in the stratification effect between groups ? Can you express this in the data presentation ?
  

• You analysed 7 lines by planting them as replicates in your groups
  Are there differences between the phenotypes ? Are the phenotypes consistent within a pot and between pots ?
  Distinguish between phenotype descriptions that record development and those that record traits.
  Can you see biological variability and distinguish the 'noise' of the background.
• The developmental profile of each mutant has been measured by you over several days
  You have analysed your planted seeds, the ones of your peers, and the ones that we planted earlier (which were all non-cold treated)
  Can you put the observations together to make a continuous profile like that in:
• Boyles et al ?
• Compare your results and your error bars to theirs for the mutants you grew.

You had 7 sequences given to you - Please briefly describe each one.

1. What is the gene called ?
2. Where is it in the genome of arabidopsis ?
3. What is the gene structure and proposed / annotated function ?
4. What clues did you get from the transcript profiles that you did in the second practical.
5. Anything else interesting ?

• You had seven seed stocks given to you as a group

  Using the N code that was on the practical sheet (and on the pots) please look up the stock on the web catalogue for the stock centre
  What is the phenotype description ? Does it overlap with yours (if not, do you have any idea why ?).
  What is the gene locus (if known) - can you find out more in AtEnsembl ?
  

  Can you correlate the seed stocks and the sequences that we gave you (clue: yes, but not for all) ?