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 (Treatment 1:Ambient CO2 and
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_A100_1-96hr_Rep4_ATH12621developing leaf insertions 19-21 N1092PQ001_ATH1_A100-Quick-174.CEL
Treatment: This sample is rep 4, 96h A.
Quick_A105_1-24hr_Rep1m_ATH12626mature leaves N1092PQ001_ATH1_A105-Quick-151.CEL
Treatment: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 1 24 h Am.
Quick_A109_1-24hr_Rep2m_ATH12630mature leaves N1092PQ001_ATH1_A109-Quick-152.CEL
Treatment: This sample is taken from the mature leaves of plants that have had the above treatments for 24h. This sample is Rep 2 24 h Am.
Quick_A10_1-12hr_Rep1_ATH12531developing leaf insertions 19-21 N1092PG001_ATH1_A10-Quick-141.CEL
Treatment: This sample is from the 12h A treatment, rep 1.
Quick_A14_1-24hr_Rep1_ATH12535developing leaf insertions 19-21 N1092PQ001_ATH1_A14-Quick-151.CEL
Treatment: This sample is from the 24h A treatment, rep 1.
Quick_A18_1-48hr_Rep1_ATH12539developing leaf insertions 19-21 N1092PQ001_ATH1_A18-Quick_161_repeat.CEL
Treatment: This sample is from the 48h A treatment, rep 1.
Quick_A22_1-96hr_Rep1_ATH12543developing leaf insertions 19-21 N1092PQ001_ATH1_A22-Quick-171.CEL
Treatment: This sample is from the 96h A treatment, rep 1.
Quick_A28_1-2hr_Rep2_ATH12549developing leaf insertions 19-21 N1092PQ001_ATH1_A28-Quick-122.CEL
Treatment: This sample is rep 2, 2h A.
Quick_A2_1-2hr_Rep1_ATH12523developing leaf insertions 19-21 N1092PG001_ATH1_A2-Quick-121.CEL
Treatment: This sample is from the 2h A treatment, rep 1.
Quick_A32_1-4hr-Rep2_ATH12553developing leaf insertions 19-21 N1092PQ001_ATH1_A32-Quick-132.CEL
Treatment: This sample is rep 2, 4h A.
Quick_A36_1-12hr_Rep2_ATH12557developing leaf insertions 19-21 N1092PQ001_ATH1_A36-Quick-142.CEL
Treatment: This sample is rep 2, 12h A.
Quick_A40_1-24hr_Rep2_ATH12561developing leaf insertions 19-21 N1092PQ001_ATH1_A40-Quick-152.CEL
Treatment: This sample is rep 2, 24h A.
Quick_A44_1-48hr_Rep2_ATH12565developing leaf insertions 19-21 N1092PQ001_ATH1_A44-Quick-162.CEL
Treatment: This sample is rep 2, 48h A.
Quick_A48_1-96hr_Rep2_ATH12569developing leaf insertions 19-21 N1092PQ001_ATH1_A48-Quick-172.CEL
Treatment: This sample is rep 2, 96h A.
Quick_A54_1-2hr_Rep3_ATH12575developing leaf insertions 19-21 N1092PQ001_ATH1_A54-Quick-123.CEL
Treatment: This sample is rep 3, 2h A.
Quick_A58_1-4hr-Rep3_ATH12579developing leaf insertions 19-21 N1092PQ001_ATH1_A58-Quick-133.CEL
Treatment: This sample is rep 3, 4h A.
Quick_A62_1-12hr_Rep3_ATH12583developing leaf insertions 19-21 N1092PQ001_ATH1_A62-Quick-143.CEL
Treatment: This sample is rep 3, 12h A.
Quick_A66_1-24hr_Rep3_ATH12587developing leaf insertions 19-21 N1092PQ001_ATH1_A66-Quick-153.CEL
Treatment: This sample is rep 3, 24h A.
Quick_A6_1-4hr-Rep1_ATH12527developing leaf insertions 19-21 N1092PG001_ATH1_A6-Quick-131.CEL
Treatment: This sample is from the 4h A treatment, rep 1.
Quick_A70_1-48hr_Rep3_ATH12591developing leaf insertions 19-21 N1092PQ001_ATH1_A70-Quick-163.CEL
Treatment: This sample is rep 3, 48h A.
Quick_A74_1-96hr_Rep3_ATH12595developing leaf insertions 19-21 N1092PQ001_ATH1_A74-Quick-173.CEL
Treatment: This sample is rep 3, 96h A.
Quick_A80_1-2hr_Rep4_ATH12601developing leaf insertions 19-21 N1092PQ001_ATH1_80-Quick-124.CEL
Treatment: This sample is rep 4, 2h A.
Quick_A84_1-4hr-Rep4_ATH12605developing leaf insertions 19-21 N1092PQ001_ATH1_84-Quick-134.CEL
Treatment: This sample is rep 4, 4h A.
Quick_A88_1-12hr_Rep4_ATH12609developing leaf insertions 19-21 N1092PQ001_ATH1_88-Quick-144.CEL
Treatment: This sample is rep 4, 12h A.
Quick_A92_1-24hr_Rep4_ATH12613developing leaf insertions 19-21 N1092PQ001_ATH1_A92-Quick-154.CEL
Treatment: This sample is rep 4, 24h A.
Quick_A96_1-48hr_Rep4_ATH12617developing leaf insertions 19-21 N1092PQ001_ATH1_A96-Quick-164.CEL
Treatment: This sample is rep 4, 48h A.