The status quo of wet lab experiments

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• The status quo of wet lab experiments
• Dept. Plant Systems Biology
• VIB/Univ. Ghent
• Marseille, 14-16 June 2006

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Cell cycle transcript profiling

• thaliana cell culture, aphidicolin block, 10 time
  points
• Synchronization quality checked by qPCR (30
  genes)
• 2 biological repeats, 4 technical repeats,
  interwoven loop design
• CATMA arrays
• Unsatisfactory hybridization quality

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DNA damage checkpoint

• Substituted with DNA replication checkpoint
• thaliana root tips, wild type and 2 Wee1 mutants
• Hydroxyurea treatment, 3 time-points
• 4 biological repeats, pooled pair wise
• Affimetrix arrays
• Samples are ready for hybridization

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Cell cycle exit/entry in response to nutrients
availability
Phosphate starvation experiments have been
performed elsewhere No experiments planned
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Cell cycle exit/entry in response to
extracellular signaling
Transcriptional response to auxin in Arabidopsis
roots has been earlier investigated in the
Department (outside DIAMONDS) No experiments
planned
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Proteome analysis
TAP Technology fully established, 3
baits/week Goal 125 baits 14 baits fully
processed, 2 baits no interactions, 12 baits 2-50
interactions 65 baits in the pipeline, 50 more
will be chosen among the preys Dynamics will be
studied for a few baits (CDKA1, CDKB11,
CKS1?) Y2H
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Functional validation and characterization
131 genes expressed specifically in proliferating
cells (identified outside DIAMONDS) Analysis
focused on genes of unknown function 20 genes
selected 3 small families 10 unique genes
(all possessing mammalian homologues) T-DNA
insertions found in 12 genes, some have growth
phenotypes, analysis in progress Complementary
approach amiRNA, constructs are ready, no
results yet
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