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Sample GSM2384930 Query DataSets for GSM2384930
Status Public on Jan 09, 2017
Title WT_for_met1-3_rep1
Sample type RNA
 
Source name wild type
Organism Arabidopsis thaliana
Characteristics genotype/variation: WT
ecotype: Col-0
tissue: seedling
age: 2 weeks
Growth protocol Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Trizol (Invitrogen) method according to the manufacturer’s instructions.
Label biotin
Label protocol Libraries were prepared with the GeneChip Whole Transcript Amplified Double-Stranded Target Assay (Affymetrix), according to the manufacturer’s protocol.
 
Hybridization protocol Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm.
Scan protocol The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.
Description wt Arabidopsis RNA chip 4
Data processing Data was processed in R as described in Naouar et al. Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. Plant J (2009) vol. 57 (1) pp. 184-94. Briefly, RMA was used for normalization, and the 'limma' and 'QValue' packages from Bioconductor were used for statistical analysis.
met1-1_processed.csv; met1-3_processed.csv
The resulting csv files were generated in Bioconductor (R software environment) and report normalized log2 genes expression differences for met1-1 and met1-3 compared to wild type, with p-values and corrections for multiple comparison (FDR).
 
Submission date Nov 07, 2016
Last update date Jan 09, 2017
Contact name Marco Catoni
Organization name University of Birmingham
Department School of Biosciences
Street address Edgbaston
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL10977
Series (2)
GSE89586 DNA sequence properties that determine susceptibility to epiallelic switching [Affymetrix]
GSE89592 DNA sequence properties that determine susceptibility to epiallelic switching

Supplementary file Size Download File type/resource
GSM2384930_WT_met13_1.CEL.gz 24.8 Mb (ftp)(http) CEL
Processed data are available on Series record

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