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Sample GSM5970415 Query DataSets for GSM5970415
Status Public on Sep 20, 2022
Title wt24h3
Sample type RNA
 
Source name wt Cd 100uM 24h
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: leaves
expt condition: wt Cd 100uM 24h
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 24h
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 5781.1258
AT1G01020_1 121.7517
AT1G01020_2 69.4670
AT1G01030_1 1090.0609
AT1G01040_1 3320.2395
AT1G01046_1 500.3163
AT1G01050_1 11858.3845
AT1G01060_1 10932.5747
AT1G01060_3 72.6465
AT1G01070_1 2257.0703
AT1G01070_2 35.7542
AT1G01073_1 19.0661
AT1G01080_1 9589.8931
AT1G01080_2 8009.6636
AT1G01090_1 29046.9998
AT1G01100_1 14088.3321
AT1G01100_2 15362.0261
AT1G01100_3 19055.2295
AT1G01110_1 2667.8856
AT1G01110_2 2817.6581

Total number of rows: 37118

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM5970415_545357A06_570_532.pair.gz 2.2 Mb (ftp)(http) PAIR
GSM5970415_545357A06_570_532_RMA.calls.gz 398.7 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

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