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:	89
Title:	Seedling transcriptome affected by a far-red light preconditioning treatment to block chloroplast de
Date:	2004-06-09
Description:	This application is the second part of a BBSRC-funded grant to compare and contrast the plastid-signalling pathways disrupted by Norflurazon and far-red light treatment of Arabidopsis seedlings. The first application of this laboratory to GARNet's Affymetrix service (2002-08-25-17.41.49_McCormac) addressed the Norflurazon pathway; this application addresses the far-red pathway. The assembly of photosynthetic complexes in developing chloroplasts is critical to the establishment of the autotrophic plant. This requires light-mediated upregulation of both nuclear- and chloroplast-encoded genes. The expression of such photosynthetically-associated nuclear genes is also often dependant on a retrograde plastid signal which emanates from chloroplasts to modulate nuclear transcription. Extensive studies using the herbicide Norflurazon to knock-out the plastid signal (including this lab's previous Affymetrix application to GARNet) are identifying the affected gene sets. However, genetic studies have indicated the existence of more than one plastid signalling pathway. We have recently investigated a phytochrome A-mediated, far-red (FR) input pathway which blocks subsequent chloroplast development under white light (WL). This has also been found to inhibit the transcription of a small group of known nuclear-encoded plastidic proteins. Here we wish to establish how wide-reaching this FR-effect is on nuclear transcription, and will directly compare the affected gene groups with those identified from our earlier (and other's) studies with a Norflurazon treatment. In this array experiment we will compare RNA from seedlings grown in complete darkness (D) before transfer to WL, with that of seedlings preconditioned under a restricted wavelength FR source before exposure to WL. This comparison of FR- and Norflurazon-affected gene groupings will indicate whether the plastid signalling pathways are likely to be the same, overlapping or highly divergent. As well as wild-type seedlings, the gun1,gun5 mutant line is to be used as both these alleles are well established as alleviating the Norflurazon-inhibited pathway, but their affect on the FR-pathway is less clear. A single replicate of a phyA-null mutant line will also be included in order to differentiate between specific phytochromeA-mediated responses and other FR effects. It is envisaged that, in general, D- and FR-treated samples of the phyA mutant line will respond in the same way as each other and as the wild-type D-treated samples and, thus, the lack of a biological repeat in this case is not a major short-fall. The proposed experiment will consist of:wild-type: D-pretreated (x2 biological replicates) wild-type: FR-preconditioned (x2)gun1,gun5: D-pretreated (x2)gun1,gun5: FR-preconditioned (x2)phyA: D-pretreated (x1)phyA: FR-preconditioned (x1)
ftp Link:	ftp Link

Slide Information:

Slide ID	Slide Name	Tissue	Stock Code	Cel File
McCormac_2-10_phyAmutant-Dpretreated_Rep1_ATH1	778	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).	N6219	AM002_ATH1_A10-MCCOR-ADA.CEL
McCormac_2-10_phyAmutant-Dpretreated_Rep1_ATH1	Treatment: phyA mutant seedlings which did not receive far-red light before transfer to white light.
McCormac_2-1_wildtype-Frprecon_Rep1_ATH1	770	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).	N1092	AM002_ATH1_A1-MCCOR-WFA.CEL
McCormac_2-1_wildtype-Frprecon_Rep1_ATH1	Treatment: wild type seedlings pre-conditioned under far-red light before transfer to white light.
McCormac_2-2_wildtype-Dpretreated_Rep1_ATH1	771	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).	N1092	AM002_ATH1_A2-MCCOR-WDA.CEL
McCormac_2-2_wildtype-Dpretreated_Rep1_ATH1	Treatment: control wild type seedlings i.e. did not receive far-red before transfer to white light.
McCormac_2-3_gun-mutant-Frprecon_Rep1_ATH1	772	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).		AM002_ATH1_A3-MCCOR-GFA.CEL
McCormac_2-3_gun-mutant-Frprecon_Rep1_ATH1	Treatment: gun1,gun5 double mutant seedlings which were pre-conditioned under far-red light before transfer to white light.
McCormac_2-4_gun-mutant-Dpretreated_Rep1_ATH1	773	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).		AM002_ATH1_A4-MCCOR-GDA.CEL
McCormac_2-4_gun-mutant-Dpretreated_Rep1_ATH1	Treatment: gun1,gun5 double mutant seedlings which did not receive far-red light before transfer to white light.
McCormac_2-5_wildtype-Frprecon_Rep2_ATH1	774	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).	N1092	AM002_ATH1_A5-MCCOR-WFB.CEL
McCormac_2-5_wildtype-Frprecon_Rep2_ATH1	Treatment: wild type seedlings pre-conditioned under far-red light before transfer to white light.
McCormac_2-6_wildtype-Dpretreated_Rep2_ATH1	775	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).	N1092	AM002_ATH1_A6-MCCOR-WDB.CEL
McCormac_2-6_wildtype-Dpretreated_Rep2_ATH1	Treatment: control wild type seedlings i.e. did not receive far-red before transfer to white light.
McCormac_2-7_gun-mutant-Frprecon_Rep2_ATH1	776	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).		AM002_ATH1_A7-MCCOR-GFB.CEL
McCormac_2-7_gun-mutant-Frprecon_Rep2_ATH1	Treatment: gun1,gun5 double mutant seedlings which were pre-conditioned under far-red light before transfer to white light.
McCormac_2-8_gun-mutant-Dpretreated_Rep2_ATH1	777	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).		AM002_ATH1_A8-MCCOR-GDB.CEL
McCormac_2-8_gun-mutant-Dpretreated_Rep2_ATH1	Treatment: gun1,gun5 double mutant seedlings which did not receive far-red light before transfer to white light.
McCormac_2-9_phyAmutant-FRprecon_Rep1_ATH1	779	young seedlings in entirety with cotyledons, hypocotyl and primary roots - (no emerged true leaves).	N6219	AM002_ATH1_A9-MCCOR-AFA.CEL
McCormac_2-9_phyAmutant-FRprecon_Rep1_ATH1	Treatment: phyA mutant seedlings which were pre-conditioned under far-red light before transfer to white light.