|
| Status |
Public on Jan 09, 2017 |
| Title |
met1-1_rep1 |
| Sample type |
RNA |
| |
|
| 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.
|
| |
|
| 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 |
met1-1 Arabidopsis RNA chip 1
|
| 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 |
|
