Growth Conditions: Columbia (Col-0) Arabidopsis thaliana plants were grown at a density of 4 plants per 5" square pot in a growth chamber set to 25*C by day, 20*C by night. Days were set to a 16hr photoperiod with 125 micro mol m-2s-1 fluorescent irradiation. Expanding upper 2" of the stem with siliques and pedicels removed were harvested 29 days post germination in the middle of the photoperiod. RNA and Microarray Methods: Total RNA was extracted from the plants using the Trizol method (Invitrogen, Ramonell et al. (2002) Mol. Plant Pathol. 3: 301) and purified with a silica membrane column (Qiagen, RNeasy). Twenty micrograms biotinylated complementary RNA (cRNA) was prepared as described (Hernan et al. (2003) Cancer Res. 63, 140) from the purified total RNA. The resulting cRNA was used to hybridize ATH1 Arabidopsis GeneChips (Affymetrix) using the manufacturer’s protocols. The array images were analyzed with the Affymetrix Microarray Suite 5.0 software with the target intensity set to 500. Normalized signal intensities were generated by multiplying signal intensities by 1.072704 the ratio which will set GapC (ID_REF = 258588_s_at) to 8500. Keywords = Tissue Type, stem Lot batch = 2003262
Arabidopsis thaliana leaf, stem and flower tissues.
Data table header descriptions
ID_REF
As defined by Affymetrix, there are the probe set identifiers, each of which is unique to a specific probe set defining a specific reagion of a singal gene or set.
VALUE
This is the final calculated measurement for each probe set idendifier that has been made comparable across all samples and rows.
DETECTION
A qualitative measurement indicating if the probe set is detected (Present; P), not detected (Absent; A), or marginally detected (Marginal;M)
Detection p-value
A p-value indicating the significance of the Detection call. A Detection p-value measures the probability that the discrimination scores of all probe pairs in the probe set are above a certain level, and that the target is likely to be Present.
Normalized Value
An adjusted signal value which sets the baseline transcript, GapC (ID_REF = 258588_s_at) to a target value of 8500. This normalized signal is more accurately comparable across different tissue type experiments our group has submitted.
