|
| Status |
Public on Aug 01, 2013 |
| Title |
Arabidopsis root_Dosed with gold_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis roots 0.125 mM gold 24 h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col 0
tissue: roots
treatment: 0.125 mM gold 24 h
|
| Treatment protocol |
0.125 mM KAuCl4 was prepared in water and pH adjusted to pH 5.7 using NaOH. 1/2 Murashige and Skoog (1962) liquid growth medium was replaced with 0.125 mM KAuCl4 solution for six hours, and plants grown at 80 μmol.m-2.s-1 21 oC for 6 hours. then roots harvested, snap frozen in liquid nitrogen and total RNA extracted.
|
| Growth protocol |
For the microarray experiment, Arabidopsis was grown according to the method described by Kumari et al. (Kumari et al. 2008). Rafts were made from circular lightweight plastic, 75 mm diameter and 6 mm thick. Approximately 100 holes (3-4 mm diameter) were drilled into each disk. These rafts were sterilised by autoclaving and the holes were plugged with ½MS(A). Sterile Arabidopsis seeds, which had been stratified for two nights in the dark at 4 ºC, were pipetted onto each plugged hole. Rafts were transferred to liquid Richard’s medium (pH 5.7). Plants were grown in sealed sterile jars for 14 days at 22 ºC / 19 ºC day / night temperatures on a 16 hour light (80 μmol.m-2.s-1) / 8 hour dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted usign Qiagen RNAeasy kit for plants. RNA quality was tested using a Bioanalyser (Agilent Technologies)
|
| Label |
biotin
|
| Label protocol |
The cDNA was labelled using a MessageAmp™ II-Biotin Enhanced Kit (Ambion)
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 array.
|
| Scan protocol |
GeneChips were scanned using an Affyimetrix GCS3000 scanner with Command Console Software (AGCC)
|
| Description |
Root gene expression data from hydroponically-grown Arabidopsis treated with gold
|
| Data processing |
Data was processed using GeneSpring GX10 Expression software (Agilent Technologies) and global scaling as normalisation method. Differentially expressed genes were identified using a two-class t-test (p< 0.05 significance level). Genes that were up or down-regulated more than 2-fold were selected
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| |
|
| Submission date |
May 15, 2013 |
| Last update date |
Aug 01, 2013 |
| Contact name |
Elizabeth L Rylott |
| E-mail(s) |
liz.rylott@york.ac.uk
|
| Phone |
1904328754
|
| Organization name |
University of York
|
| Department |
Department of Biology
|
| Lab |
Prof. Neil Bruce
|
| Street address |
Wentworth Way
|
| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE46958 |
Gene expression profiles in roots of hydroponically grown Arabidopsis treated with 0.125 mM gold |
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