NASCArrays Information at The BAR

Welcome to NASCArrays information at the BAR. This page hosts meta-information from the NASCArrays service (2002-2013). This information was parsed from text files available on the NASCArrays site. NASCArrays data is on iPlant server. To download experiment data from iPlant, please click on the experiment number. To download the CEL files, please click on the ftp link.

Title:Genes affected by hog1 alleviation of CHS silencing
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.
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Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Jordan_A-1.1-Jorda-ECG_SLD655Lertotal tissue N1695Jordan_A-1.1_ECG_Rep1_ATH1.cel
Jordan_A-1.2-Jorda-ECG_SLD656Lertotal tissue N1695Jordan_A-1.2_ECG_Rep2_ATH1.cel
Jordan_A-1.3-Jorda-ECG_SLD657Lertotal tissue N1695Jordan_A-1.3_ECG_Rep3_ATH1.cel
Jordan_A-1.4-Jorda-ECG_SLD658Lertotal tissue N1695Jordan_A-1.4_ECG_Rep4_ATH1.cel
Jordan_A-2.1-Jorda-15B_SLD659Lertotal tissue Jordan_A-2.1_15B_Rep1_ATH1.cel
Jordan_A-2.2-Jorda-15B_SLD660Lertotal tissue Jordan_A-2.2_15B_Rep2_ATH1.cel
Jordan_A-2.3-Jorda-15B_SLD661Lertotal tissue Jordan_A-2.3_15B_Rep3_ATH1.cel
Jordan_A-2.4-Jorda-15B_SLD662Lertotal tissue Jordan_A-2.4_15B_Rep4_ATH1.cel