[Arabidopsis] Using Affymetrix arrays to analyze chloroplast transcript levels?

Sue Gibson via arab-gen%40net.bio.net (by gibso043 from umn.edu)
Fri Sep 30 17:19:13 EST 2011

Our lab used Affymetrix Arabidopsis GeneChips to compare transcript levels
in wild-type versus mutant tissue samples.  We noticed that transcript
levels for approximately half of the chloroplast-encoded genes for which
probesets are included on the arrays are significantly altered in the mutant
samples and are trying to interpret this result.  As we used oligo dT to
prime synthesis of the 1st strand cDNAs used to make our probes, the signals
we detected may be coming from the fractions of the chloroplast-encoded
transcripts that are polyadenylated.  However, our understanding is that
only a small percentage of the transcripts made from each chloroplast gene
are typically polyadenylated and the signal intensities for many of the
chloroplast-encoded transcripts seem quite high for all of the signal to be
arising from polyadenylated transcripts.  In fact, average signal
intensities for chloroplast-encoded transcripts are higher than for
nuclear-encoded transcripts.

Is anyone aware of any research looking at the extent to which probes made
using oligo dT will detect polyadenylated and non-polyadenylated chloroplast
transcripts on Affymetrix arrays?

Thanks for any help.

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