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 Involved in Plant Programmed Cell Death (PCD)
Description:Purpose: To identify genes involved in the induction and execution of plant PCD. Rationale: PCD is a genetically-controlled form of cellular suicide that is essential in many aspects of animal and plant development. In plants the mechanisms of PCD are poorly understood and much work to date has focused on the specialised case of the hypersensitive response. To investigate the regulation of PCD in a more general manner we have established an Arabidopsis cell suspension system in which PCD may be induced by a variety of treatments. We have characterised this system extensively using molecular and biochemical approaches including the use of a custom microarray of 80-plus genes which may play a role in plant PCD (Swidzinski et al.2002 The Plant Journal; in press). We have demonstrated the feasibility of extracting sufficient quantities of RNA and performing microarray analysis during PCD - a transition during which the majority of cellular transcripts are downregulated. Using a number of different treatments to induce PCD we have been able to distinguish between genes that are apparently specific to cell death from those that are a consequence of the treatment itself. We have established that 14 day-old cell cultures undergoing PCD and 6 day-old cultures one hour post-heat treatment (55C for 10 min) provide ideal timepoints for a representative examination of PCD-related gene expression. Additionally we have characterised these systems at the level of the total cellular proteome identifying and sequencing several proteins that are commonly upregulated in both systems. Our current custom microarray data while providing valuable information on the regulation of many genes during plant PCD is limited by the small number of transcripts studied. In order to gain a fuller understanding of the molecular mechanisms of plant PCD it is necessary to examine a much larger proportion of total Arabidopsis gene sequences. Such a widely inclusive study will aid in the identification of factors which may be involved in plant PCD but would not have been identifed based on the current molecular models about this cellular event. We propose to use the large number of genes available on the Affymetrix RNAs to examine gene expression in cells induced to undergo PCD by either heat treatment or senescence. Finally by comparing this data to our existing proteome analysis it should be possible to assess whether the genes of interest are being regulated at the transcriptional or post-transcriptional level during plant PCD.
ftp Link:ftp Link

Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Swidzinski_1-10_Control_Rep1_AG300Cell suspension N20Swidzinski_1-5_Heat_Rep2_AG.cel
Swidzinski_1-11_Control_Rep2_AG301Cell suspension N20Swidzinski_1-1_Control_Rep1_AG.cel
Swidzinski_1-12_Heat_Rep1_AG302Cell suspension N20Swidzinski_1-2_Control_Rep2_AG.cel
Swidzinski_1-13_Heat_Rep2_AG328Cell suspension N20Swidzinski_1-9_Senescence_Rep3_AG.cel
Swidzinski_1-14_Senescence_Rep1_AG329Cell suspension N20Swidzinski_1-6_Heat_Rep3_AG.cel
Swidzinski_1-15_Senescence_Rep2_AG330Cell suspension N20Swidzinski_1-3_Control_Rep3_AG.cel
Swidzinski_1-1_Control_Rep1_ATH1214Cell suspension N20Swidzinski_1-11_Control_Rep2_ATH1.cel
Swidzinski_1-2_Control_Rep2_ATH1215Cell suspension N20Swidzinski_1-14_Senescence_Rep1_ATH1.cel
Swidzinski_1-3_Control_Rep3_ATH1216Cell suspension N20Swidzinski_1-13_Heat_Rep2_ATH1.cel
Swidzinski_1-4_Heat_Rep1_ATH1217Cell suspension N20Swidzinski_1-12_Heat_Rep1_ATH1.cel
Swidzinski_1-5_Heat_Rep2_ATH1218Cell suspension N20Swidzinski_1-10_Control_Rep1_ATH1.cel
Swidzinski_1-6_Heat_Rep3_ATH1219Cell suspension N20Swidzinski_1-15_Senescence_Rep2_ATH1.cel
Swidzinski_1-7_Senescence_Rep1_AG297Cell suspension N20Swidzinski_1-7_Senescence_Rep1_AG.cel
Swidzinski_1-8_Senescence_Rep2_AG298Cell suspension N20Swidzinski_1-8_Senescence_Rep2_AG.cel
Swidzinski_1-9_Senescence_Rep3_AG299Cell suspension N20Swidzinski_1-4_Heat_Rep1_AG.cel