NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5970433 Query DataSets for GSM5970433
Status Public on Sep 20, 2022
Title atgox2
Sample type RNA
 
Source name atgox Control condition
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: leaves
expt condition: atgox Control condition
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 Control condition
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 5217.4106
AT1G01020_1 105.2280
AT1G01020_2 92.3067
AT1G01030_1 1090.2883
AT1G01040_1 3057.2387
AT1G01046_1 491.4189
AT1G01050_1 12142.2754
AT1G01060_1 11103.5868
AT1G01060_3 82.7664
AT1G01070_1 1677.9351
AT1G01070_2 42.5564
AT1G01073_1 16.7053
AT1G01080_1 10076.0535
AT1G01080_2 8910.7916
AT1G01090_1 31425.0574
AT1G01100_1 15524.6466
AT1G01100_2 18051.8458
AT1G01100_3 21981.8457
AT1G01110_1 1240.3321
AT1G01110_2 1713.0353

Total number of rows: 37118

Table truncated, full table size 773 Kbytes.




Supplementary file Size Download File type/resource
GSM5970433_545437A07_590_532.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM5970433_545437A07_590_532_RMA.calls.gz 404.4 Kb (ftp)(http) CALLS
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap