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Status |
Public on Jan 09, 2017 |
Title |
met1-1_rep1 |
Sample type |
RNA |
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|
Source name |
met1-1
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype/variation: met1-1 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.
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|
|
Hybridization protocol |
Approximately 7.5 μg of fragmented cDNA was hybridized for 16 hours at 60 rpm.
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Scan protocol |
The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.
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Description |
met1-1 Arabidopsis RNA chip 1
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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).
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|
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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 |
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