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Sample GSM5970423 Query DataSets for GSM5970423
Status Public on Sep 20, 2022
Title wt30m2
Sample type RNA
 
Source name wt30m Cd 100uM 0.5h
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: leaves
expt condition: wt30m Cd 100uM 0.5h
Treatment protocol Seedlings were incubated with 100uM cadmium for 30 minutes or 24 hours. Controls were incubated in a cadmium-free solution.
Growth protocol Seedlings were grown for two weeks on solid MS medium, three independent biological replicates, each composed of at least five different seedlings, were used per experimental condition
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from seedlings by the acid guanidine thiocyanate–phenol–chloroform method using the Trizol reagent kit according to the manufacturer's instructions.
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description Cd 100uM 0.5h
Data processing Differential expression analysis has been performed with LIMMA (Linear Models Microarray Analysis; G. K. Smyth, 2005) R package and custom functions. Data preprocessing:background correction: normexp, quantile normalization, internal replicate summarization: median. Statistical analysis:linear models approach for the assessment of differential expression, P values were adjusted for multiplicity with BH method (Benjamini and Hochberg, 1995).
 
Submission date Mar 24, 2022
Last update date Sep 20, 2022
Contact name Laura Carmen Terron Camero
E-mail(s) lauteca@ipb.csic.es
Phone 658638526
Organization name IPBLN
Department Bioinformática
Street address Avda. del Conocimiento 17. P. T. Ciencias de la Salud
City Granada
State/province Granada
ZIP/Postal code 18016
Country Spain
 
Platform ID GPL13970
Series (1)
GSE199325 Gene network downstream plant stress response modulated by peroxisomal H2O2

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AT1G01010_1 3370.2178
AT1G01020_1 87.6091
AT1G01020_2 64.1222
AT1G01030_1 1033.5152
AT1G01040_1 3387.2842
AT1G01046_1 429.3155
AT1G01050_1 13202.3874
AT1G01060_1 8343.5244
AT1G01060_3 95.3729
AT1G01070_1 2122.9747
AT1G01070_2 28.1273
AT1G01073_1 17.3219
AT1G01080_1 11015.0612
AT1G01080_2 9680.0283
AT1G01090_1 29510.0733
AT1G01100_1 15353.9830
AT1G01100_2 17728.1164
AT1G01100_3 20496.4179
AT1G01110_1 2532.0501
AT1G01110_2 2705.9695

Total number of rows: 37118

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM5970423_545373A02_560_100_532.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM5970423_545373A02_560_100_532_RMA.calls.gz 412.7 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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