20 August 2013


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Tuesday notes



Finished knockdown assays!

Date Colony completed
13 Aug AA05
13 Aug AA11
14 Aug AA10
14 Aug AA02
15 Aug AA04
16 Aug AA06
16 Aug AA03
19 Aug AA08
19 Aug AA09
20 Aug AA01
20 Aug AA07

Total of 339 ants.

Climate Cascade group meeting

  1. Aphaenogaster samples
  • Map of locations
  1. Phytotron update
  • One colony from each site at 20C and 26C
  • Colonies seem to be okay with reduced ramp to +-1.5C daily
  • Transferred to Phytotron from July 9th to 25th, with replacement colonies added July 29th

SCH: I should go down and help with protocol for first round of sample collection for gene expression Samples to collect:

  • 8 ants heat-shocked at 37C for one hour, flash frozen for gene expression
  • 8 ants control temp for one hour, flash frozen for gene expression
  • 10 ants (2 sets of 5) for protein stability (Andrew)
  • 3 ants for cuticular hydrocarbons (Mike) frozen
  • Lacy will be doing CTmax on 10 ants per sample
  • Total: 39 ants. This will substantially reduce small colonies.
  1. Transcriptome update
  • JSG: preliminary pipeline including in silico spike-in nearly done
  1. Genome plans
  • 1 lane Illumina 200bp fragment library (160 million 100bp paired-end reads) ~ $3k
  • ~90x coverage assuming 350Mbp genome size
  • 1 lane Illumina 3kbp jump library
  • ALLPATHS-LG assembly
  • BioNano physical mapping ~$5k
  1. Adaptive Potential experiment

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