E-NASC-36 - Transcription profiling of Arabidopsis mutants CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B)

Status
Released on 11 January 2005, last updated on 2 May 2014
Organism
Arabidopsis thaliana
Samples (8)
Array (1)
Protocols (13)
Description
As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Results showed that there were over 100 genes with at least a 10-fold increase or decrease in expression. However, the variation between 2 reps of each genetic variant was high. We would now like to carry out a modified version of this experiment using the 25K Affymetrix chip. It is intended to increase the number of reps to 4, and take samples at an earlier stage than previously in order to decrease the effect of developmental spread. To reduce the effects of interplant variability, samples will be generated from total plant tissue from a pool of 10 plants at GS 1.04. RNA will be purified using RNeasy kits from Qiagen.
Experiment types
transcription profiling by array, strain or line
Contacts
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-NASC-36.idf.txt
Sample and data relationshipE-NASC-36.sdrf.txt
Raw data (1)E-NASC-36.raw.1.zip
Processed data (1)E-NASC-36.processed.1.zip
Array designA-AFFY-2.adf.txt
R ExpressionSetE-NASC-36.eSet.r
Links