VIB-PSB/Inze:

Synchronised cells (aphidicolin): sampled at 0,2,4,6,8,10,12,14,16,18 hrs

Experiment design: interwoven-loop, number of samples: 22, number of arrays: 44.

http://exgen.ma.umist.ac.uk/

 

Additonal follow-up:

Block cells with hydroxyurea or propyzamide, nocodazole, colcemid
Analysis of mutants, double mutants
Col-0
DEL1 / overexpresser (2)
DEL1 / Knock-out
KRP2 / overexpresser (2 strong, 2 weak)
CDKB1;1.N161 (2)
CCS52A2KO
ATM mutant, UV

 

BRIC-Helin:

DNA damage experiments.
treat wild type and p53 mutated diploid fibroblasts with UV or ionizing radiation
Affy gene expression profiling after different length of time.
What is the required number of replicates?

In Bilbao we came up with the following::

There was discussion on the preferred number of replicates for such an experiment. This in fact is difficult to answer. Following broadly accepted guidelines the number of replicates for Affymetrix should be 3. However, in time-course experiments adjacent points can confirm each other. In some situations it may even be better to have single observations, but every few minutes rather than triplicate measurements every few hours. It would be best to first have a detailed dissection of the dynamics of gene expression in single observations, followed by replicates or triplicates in those areas where increased dynamics is observed. For this, dense time series samples should be harvested multiple times.