NASCArrays Information at The BAR
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.
| Experiment: | 51 |
| Title: | Seedling transcriptome affected by Norflurazon-induced photobleaching of chloroplasts |
| Date: | 2004-06-09 |
| Description: | Regulation of expression of genes encoding chloroplast components is critical to the autotrophic plant and never more so than in the cotyledons of the de-etiolating seedling. Many chloroplast proteins are nuclear-encoded and a retrograde signal from the chloroplasts (the Plastid Signal) modulates nuclear transcription. However, not all chloroplast-targeted genes are subject to this control and not all plastid-dependent nuclear genes are chloroplast-targeted. We therefore aim to provide the most comprehensive screen yet of which genes are affected by plastid-signalling. To specifically knock-out positive plastid signalling in light-grown cotyledons, the herbicide Norflurazon (NF) is supplied in the growth medium, causing a carotenoid deficiency that leaves the chloroplasts vulnerable to photobleaching. This blocks the expression of a subset of nuclear genes, such as Lhcb and HEMA1. Two pairs of RNAs will directly compare the transcription in seedlings grown under continuous white light with and without NF. A third RNA will also be compared from a mutant that shows a degree of constitutive positive plastid signalling. These two mutants act synergistically to counteract the effect of NF on nuclear transcription. The gun1,gun5 double mutant maintains a significantly higher level of Lhcb and HEMA1 expression in the presence of photobeached chloroplasts than the NF-treated wild-type. This transcriptome set will therefore complement RNA1 (wild-type+NF) and indicate which of the genes identified from the RNA1/RNA2 comparison are subject to the particular gun1/gun5 plastid signalling pathway(s). The growth of conditions of the seedlings (namely on MS medium supplemented with 1.5% sucrose, for 3 days under continuous WL following 2 days germination in darkness) has been chosen from the results of our own recent studies using Northern blotting techniques that show these conditions to maximise the respective NF and gun mutant effects on Lhcb and HEMA1 gene expression. This experiment is part one of a two-part study to compare the transcriptional output of this NF-affected pathway with that of a newly discovered FR-mediated pathway. A subsequent array experiment will assess the nuclear response as affected by this FR/ phyA-input pathway and the two sets of array data will be compared and contrasted.Note: Col-0 wild-type (NASC code N1092). gun1,gun5 double mutant(obtained from Enriquez Lopez-Juez, Royal Holloway, University of London.(Mochizuki et al. 2001 PNAS 98: 2053-2058). This line cannot be donated by us as it is the IP of Joanne Chory (SALK Institute, USA). Treatment = a herbicide (Norflurazon) application which leads to chloroplast photobleaching and hence down regulation of nuclear genes dependent on plastid signalling from intact chloroplasts. |
| ftp Link: | ftp Link |
| Slide ID | Slide Name | Genetic Background | Tissue | Stock Code | Cel File |
|---|---|---|---|---|---|
| McCormac_1-1_wildtype-NFtreated_Rep1_ATH1 | 403 | whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). | N1092 | McCormac_1-1_wildtype-NFtreated_Rep1_ATH1.cel | |
| Treatment: WT seedlings treated with the herbicide Norflurazon. | |||||
| McCormac_1-2_wildtype-Contrl_Rep1_ATH1 | 404 | whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). | N1092 | McCormac_1-2_wildtype-Contrl_Rep1_ATH1.cel | |
| Treatment: WT seedlings which had not been treated with Norflurazon and therefore are the control sample. | |||||
| McCormac_1-3_mutant-NFtreated_Rep1_ATH1 | 405 | whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). | McCormac_1-3_mutant-NFtreated_Rep1_ATH1.cel | ||
| Treatment: Seedlings of a double mutant line gun1,gun5 which had been treated with Norflurazon. | |||||
| McCormac_1-4_wildtype-NFtreated_Rep2_ATH1 | 406 | whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). | N1092 | McCormac_1-4_wildtype-NFtreated_Rep2_ATH1.cel | |
| Treatment: Seedlings of WT which had been treated with Norflurazon. | |||||
| McCormac_1-5_wildtype-Contrl_Rep2_ATH1 | 407 | whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). | N1092 | McCormac_1-5_wildtype-Contrl_Rep2_ATH1.cel | |
| Treatment: Seedlings of WT which had not been treated with Norflurazon. | |||||
| McCormac_1-6_mutant-NFtreated_Rep2_ATH1 | 408 | whole young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves). | McCormac_1-6_mutant-NFtreated_Rep2_ATH1.cel | ||
| Treatment: Seedlings of a double mutant line gun1,gun5 treated with Norflurazon. | |||||