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:Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Controls)
Description:We were awarded a BBSRC grant about a year ago to undertake some affymetrix gene chip profiling of light and CO2 systemic signalling in Arabidopsis. The design of the proposed experiment is given below and the appropriate funding has been provided by the BBSRC.The aim of the project is to identify the temporal profile of those genes that respond to light and CO2 systemic signals in developing leaves. Moreover, as thes two signals have opposing effects on leaf development to ascertain whether they involve similar or parallel signalling pathways.The experiment is to examine the effect of exposing mature leaves to high CO2 or low light or both on the gene expression profile of developing leaves. We already have data for maize that changes in gene expression profile occur within 4h and that there are a variety of temporal responses that differ between individual gene transcripts. We have also demonstrated that Arabidopsis leaf development is altered by these systemmic signals and that lesions in the jasmonate and ethylene signalling pathways block these responses. Our experimental design is shown below:We have 4 treatments and 7 timepoints. (0, 2, 4, 12, 24, 48, 96 h)We would sample from 5 individual plants that would be pooled for each RNA preparation.This would require 28 chips and this would include extra replication of the 0 time-point control (deemed by many as nessary). Experimental details:All plants were germinated for 7 days under the following conditions:Humax multi-purpose compost, ambient carbon dioxide (370 ppm) and ambient light (250 µmol/m/s), constant temperature of 20°C and a 10 h photoperiod (8 am until 6 pm). After a week the the seedlings were potted up into 104-cell plug trays for a further 2 weeks and then potted up into 10 cm pots and the bottom part of the signalling cuvette system attached (see Lake et al., Nature 10th May 2001 Vol. 411, pp 154). Twenty four, 4 week old plants, then had the top part of the signalling system attached, trapping leaf insertions 5-13. Humidified, ambient air was passed through them at 500 mls/min via an oil-free air compressor. The three target leaves (19-21) were then marked with non-toxic, acrylic paint. After a 24 h period (the plants were sealed into the cuvettes from 10 am until 10am) of adjustment, the experiment was started by harvesting the target leaves from 4 plants and immediately freezing the tissue in liquid nitrogen to give the 0 h sample before RNA extraction. The remaining 20 plants were divided into 4 groups of five and given one of the following treatments:Ambient carbon dioxide/ambient light (Control) (A)Elevated carbon dioxide (750 ppm)/ambient light (E)Ambient carbon dioxide/low light (50 µmol/m/s) (AS)Elevated carbon dioxide/low light (ES)- For the Elevated CO2, elevated CO2 was pumped in using a CT room next door set to same temperature but with a CO2 cylinder inside and the same pump as used in the ambient room to supply the elevated CO2 laden, humidified air into the signalling room using rubber tubing.- Shade treatment consisted of neutral density filter (Cat. 210 0.6ND, Lee Filters) that had a hole cut in the middle to allow the middle developing leaves to grow through.A timecourse of 2, 4, 12, 24, 48 and 96 h were carried out each using a batch of 24 plants. This whole process was repeated with another batch of 24 plants at the same developmental stage to give a 2, 4, 12, 24, 48 and 96 hour sample from each of the four treatments. The whole timecourse was then repeated 4 times.For the mature leaves:We had 8 chips left over so we devised this little experiment to assess the gene changes that were occurring in the enclosed, treated, mature leaves that were signalling the environment to the young developing leaves.
ftp Link:ftp Link

Slide Information:
Slide IDSlide NameGenetic BackgroundTissueStock CodeCel File
Quick_A104_5-0hr_Rep4_ATH12625developing leaf insertions 19-21 N1092Quick_A104_5-0hr_Rep4_ATH1.cel
Treatment: This sample is rep 4, steady state elevated 0h control.
Quick_A1_1-0hr_Rep1_ATH12522developing leaf insertions 19-21 N1092Quick_A1_1-0hr_Rep1_ATH1.cel
Treatment: This sample is rep 1, 0h A.
Quick_A26_5-0hr_Rep1_ATH12547developing leaf insertions 19-21 N1092Quick_A26_5-0hr_Rep1_ATH1.cel
Treatment: This sample is from the steady state elevated control where plants were grown as above but in an elevated carbon dioxide atmosphere at 750 ppm. The plants were at the same stage when placed into the cuvette system and the same three leaves were harvested at time 0 h after the same 24 h adjustment period. These are therefore acting as elevated carbon dioxide steady state controls.
Quick_A27_0-0hr_Rep2_ATH12548developing leaf insertions 19-21 N1092Quick_A27_0-0hr_Rep2_ATH1.cel
Treatment: This sample is rep 2, 0h control.
Quick_A52_5-0hr_Rep2_ATH12573developing leaf insertions 19-21 N1092Quick_A52_5-0hr_Rep2_ATH1.cel
Treatment: This sample is rep 2, steady-state grown in elevated CO2, 0h control.
Quick_A53_0-0hr_Rep3_ATH12574developing leaf insertions 19-21 N1092Quick_A53_0-0hr_Rep3_ATH1.cel
Treatment: This sample is rep 3, 0h control.
Quick_A78_5-0hr_Rep3_ATH12599developing leaf insertions 19-21 N1092Quick_A78_5-0hr_Rep3_ATH1.cel
Treatment: This sample is rep 3, steady-state, elevated CO2 0hr control.
Quick_A79_0-0hr_Rep4_ATH12600developing leaf insertions 19-21 N1092Quick_A79_0-0hr_Rep4_ATH1.cel
Treatment: This sample is rep 4, 0h control.