Useful tips

These are only suggestions, but they can make the procedures easier.

1. Have at least 30 |g total RNA for each sample before you start; even if labeling of one sample causes problems, you can still repeat the labeling using the remaining RNA.

Table 9.1. Public tools for analyzing Arabidopsis microarray data






GO-classification index.jsp


TAIR Aracyc

Display of expression data on a metabolic map html


TAIR promoter analysis

Identification of enriched promoter motifs motiffinder/index.jsp


TAIR Chromosome Map Tool

Mapping genes on chromosomes Map/tool.jsp



Analysis of expression patterns during development and stress



Data visualization


2. For difficult tissue like seeds use a borate buffer method (13).

3. Use a double-labeling kit (e.g. from Affymetrix or Ambion) if you have limited amounts of RNA to start with (works with as little as 50 ng total RNA).

4. For better recovery, pass RNA-containing solutions twice over RNeasy columns and elute twice (first with 30 ^l, then with 20 ^l water).

5. Store wash buffers at 4°C, but leave at room temperature over night before use to avoid air bubbles in the fluidics station.

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