kindly provided by Dr. P. Boukamp, DKFZ, Heidelberg, Germany through Dr. T.C., Lee, SINICA, Taipei, Taiwan
Treatment protocol
Cells were harvested at time point 8.5h without any UVB irradiation
Growth protocol
Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100μg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone).
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracte by lying directly in the 100mm petri dish with 2 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).
kindly provided by Dr. P. Boukamp, DKFZ, Heidelberg, Germany through Dr. T.C., Lee, SINICA, Taipei, Taiwan
Treatment protocol
Cells were irradiated by 10 J/m2 UVB at time points 0h and 8hr ,and then harvested at time point 8.5h
Growth protocol
Cells were maintained at 37 oC and 5 % CO2 /95% air in DMEM (Gibico) supplemented with 2mM L-glutamine, 100 U/ml penicillin/ 100μg/ml streptomycin(Gibico), and 10% fetal bovine serum(Hyclone).
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracte by lying directly in the 100mm petri dish with 2 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).
We applied loop design for our microarray experiments in order to reduce the systemic error.
Data processing
Data filtering method:
The following three criteria were used to validate spots: 1) SNR ((signal-background)/ S.D. of background) of Cy3 and Cy5 both greater than 5. 2) Diameter of spot greater than 75 ìm. 3) C.V. (coefficient of variation) of pixels within a spot in the Cy3 and Cy5 channels both less than 100%. After this filtering process, on average about 45% of the spots were identified as valid.
