sample and data quality

last update; Mar, 12, 2003
YYoung leaf2 weeks oldMS plate containing 1% sucrose
LLeaf2 months oldsoil
TStem3 months oldsoil
BBud2 months oldsoil
FFlower2 months oldsoil
SSilique2 months oldsoil
RRoot2 weeks oldMS plate containing 1% sucrose
For the preparation of rosette leaf, stem, bud, flower and silique, Arabidopsis thaliana (accession Colombia) was grown on soil at 22C under continuous light for 2 months. To perform a set of macroarray experiments for one tissue, 40-80 plants were sampled. To obtain young leaf and root, plants were grown on MS medium plate containing 1% sucrose and 0.8% agarose under continuous light.
The samples of the young leaf (about 6 leaves per plant except for cotyledons) and root were obtained from 17 day-old plants. For the young leaf and root, 300-600 plants were used for one array expriment.

Evaluation of Data Quality

Example of data distribution with high SN (A) and low SN (B) values. mBG, membrane background. vBG, virtual background. SN, signal to noise. Dmed, median of signal intensity for cDNA spots. Nmed, median of signal intensity for negative controls.

We used a value of signal to noise (SN) ratio to express data quality in cDNA macroarray. The formula is;
SN = (Dmed - vBG) / (Nmed - vBG)
where Nmed is the median of all negative controls, and Dmed is the median of all EST spots on the membrane. Typical examples of SN are pictured above. And the SN values in our experiments were shown bellow.
SN values of macroarray data in ATTED. Since 13516 ESTs were spotted on 3 membranes, each tissue has 3 SN values. Experiments were repeated in 3 to 5 times for each tissue.