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 and 6 plates, 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 ?
  

• Your graphs should show error/variance bars based on the replicate results.
• Your reports should use appropriate statistics to report significance of your results (e.g. anova, t-tests).
• 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.
• The line N933 is the wild-type, make sure that all phenotype descriptions refer to this line as a comparison. A description of NORMAL development would be useful.
• In the 2010 cohort, line N6259 showed no phenotype. This was due to plants being grown from seed collected from last year's practical. The original line is homozygous lethal - explain what is likely to have happened and why you see no phenotype.
• For N6259 - what is the reported background for the line? What are the backgrounds for all of the other lines? Can you compare lines if they have different backgrounds? Can you group the backgrounds and observations? What issues do backgrounds hold for researchers?

You had 7 sequences given to you - Please briefly describe each one in a separate APPENDIX to your report.

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) ?

  Structure suggestions:

  1. You should have an introduction, a materials & methods section, a results section and a discussion section.
  2. Write the report as if the reader knows nothing about the experiment, do not assume any knowledge.
  3. You should have one appendix for EACH gene sequence.
  4. Data sheets and other raw data should be in a separate appendix.
  5. Materials given to you can be reproduced in your report, and can be referenced/acknowledged as 'course materials provided'.
  6. Images of the plants will help your descriptions and can be taken by you, and/or acquired from websites and papers (you must acknowledge/reference appropriately). Images MUST be clear and bold.
  7. If YOU know that your grammar/spelling is poor then get someone to proof-read it. You have time, so last minute writing without proof-reading by you or others is not acceptable as a reason for poor writing.
  8. Write professionally: mistakes, errors and problems should be reported but not excused or dismissed. Suggest possible corrections and alternative approaches. Write positively even if your results are negative or inconclusive but do not speculate without evidence.