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Sample GSM1142030 Query DataSets for GSM1142030
Status Public on Aug 01, 2013
Title Arabidopsis root_no gold_rep3
Sample type RNA
 
Source name Arabidopsis roots untreated 24 h
Organism Arabidopsis thaliana
Characteristics ecotype: Col 0
tissue: roots
treatment: untreated
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 not 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
 
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

Data table header descriptions
ID_REF
VALUE genespring normalized

Data table
ID_REF VALUE
AFFX-BioB-5_at -0.18209314
AFFX-BioB-M_at -0.10736132
AFFX-BioB-3_at -0.189569
AFFX-BioC-5_at -0.08604336
AFFX-BioC-3_at -0.09167957
AFFX-BioDn-5_at -0.018011093
AFFX-BioDn-3_at 0.14820099
AFFX-CreX-5_at 0.027013779
AFFX-CreX-3_at -0.194664
AFFX-DapX-5_at 0.4194007
AFFX-DapX-M_at 0.05736208
AFFX-DapX-3_at -0.07566261
AFFX-LysX-5_at -0.001697063
AFFX-LysX-M_at -0.08078718
AFFX-LysX-3_at -0.276711
AFFX-PheX-5_at 0.12967205
AFFX-PheX-M_at 0.06162834
AFFX-PheX-3_at -0.19973183
AFFX-ThrX-5_at 0.12825465
AFFX-ThrX-M_at 0.2499528

Total number of rows: 22810

Table truncated, full table size 480 Kbytes.




Supplementary file Size Download File type/resource
GSM1142030_No_gold_rep3.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM1142030_No_gold_rep3.CHP.gz 189.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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