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: | 161 |
| Title: | Environmental Genomics of calcicole-calcifuge physiology |
| Date: | 2011-10-20 |
| Description: | Calcareous grasslands are among the most species-rich plant communities in Europe. Huge losses among these grasslands and their continuing vulnerability to either agricultural improvement or neglect have focused attention on the need for conservation of their biodiversity. In addition, the potential impact of climatic stresses on the structure, composition and function of calcicolous grassland ecosystems is a topic of concern. A clear understanding of the molecular mechanisms that enable calcicole species to thrive on calcareous soils is therefore essential to enable us to predict how these plant communities and their constituent species will be affected by environmental change and how the biodiversity of these ecosystems can be sustained. We are testing the hypothesis that adaptation to a calcareous environment reflects altered patterns of gene expression in Arabidopsis thaliana and related Arabis species. We have employed transcriptome analysis using the NASC Affymetrix service to identify a cohort of genes that are differentially expressed (>2-fold increase/decrease in expression) between non-calcicolous (Col-4) and the calcicolous (Cal-0) ecotypes of A. thaliana at low (1mM)and high (12.5mM)concentrations of rhizospheric calcium. We would now like to compare expression profiles of further 2 ecotypes of Arabidopsis, collected from 2 different locations in Britain, firstly from area (W1), an of low soil pH, Penicuik near Edinburgh and secondly from area (W2), an area of high soil pH, Elland near Leeds. We have collected seed from these plants and have grown them under the same laboratory conditions of low and high rhizospheric calcium described above.Plants were grown in controlled environment growth cabinets on sterile sand and were watered daily with 0.5 X Long Ashton Nutrient solution containing either 1 mM or 12.5 mM CaCl2. Plants were grown at 10 hours of light (160 PAR) and 55% humidity to growth stage 3.90 (full rossette), which occurred after approximately 30 days after the begining of treatment. RNA was extracted from 10 pooled plants for each sample using Qiagen RNEasy kits. |
| ftp Link: | ftp Link |
| Slide ID | Slide Name | Genetic Background | Tissue | Stock Code | Cel File |
|---|---|---|---|---|---|
| Shirras_2-1_low-soil-pH-1mM-CaCl2_Rep1_ATH1 | 2634 | whole plant | Shirras_2-1_low-soil-pH-1mM-CaCl2_Rep1_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 1 mM CaCl2 during the course of the expt | |||||
| Shirras_2-2_low-soil-pH-1mM-CaCl2_Rep2_ATH1 | 2635 | whole plant | Shirras_2-2_low-soil-pH-1mM-CaCl2_Rep2_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 1 mM CaCl2 during the course of the expt | |||||
| Shirras_2-3_high-soil-pH-1mM-CaCl2_Rep1_ATH1 | 2636 | whole plant | Shirras_2-3_high-soil-pH-1mM-CaCl2_Rep1_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 12.5 mM CaCl2 during the course of the expt | |||||
| Shirras_2-4_high-soil-pH-1mM-CaCl2_Rep2_ATH1 | 2637 | whole plant | Shirras_2-4_high-soil-pH-1mM-CaCl2_Rep2_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 1 mM CaCl2 during the course of the expt | |||||
| Shirras_2-5_low-soil-pH-12.5mM-CaCl2_Rep1_ATH1 | 2638 | whole plant | Shirras_2-5_low-soil-pH-12.5mM-CaCl2_Rep1_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 12.5 mM CaCl2 during the course of the expt | |||||
| Shirras_2-6_low-soil-pH-12.5mM-CaCl2_Rep2_ATH1 | 2639 | whole plant | Shirras_2-6_low-soil-pH-12.5mM-CaCl2_Rep2_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 12.5 mM CaCl2 during the course of the expt | |||||
| Shirras_2-7_high-soil-pH-12.5mM-CaCl2_Rep1_ATH1 | 2640 | whole plant | Shirras_2-7_high-soil-pH-12.5mM-CaCl2_Rep1_ATH1.CEL | ||
| Treatment: Plants grown from Arabidopsis seed collected from plants growing wild at Penicuik nr Edinburgh (an area of low soil pH). Plants were watered with nutrient solution containing 12.5 mM CaCl2 during the course of the expt | |||||
| Shirras_2-8_high-soil-pH-12.5mM-CaCl2_Rep2_ATH1 | 2641 | whole plant | Shirras_2-8_high-soil-pH-12.5mM-CaCl2_Rep2_ATH1.CEL | ||
| Treatment: 12.5 mM CaCl2 | |||||