|
| Status |
Public on Mar 24, 2015 |
| Title |
4 day old sco3phyb seedling, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
4 day old sco3phyb seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 4 days old
tissue: seedlings
genotype/variation: sco3phyb
|
| Growth protocol |
Seedlings grown on sterile Murashige Skoog media with 0.8% Agar under longday growth conditions (16 hr light/8hr dark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated and DNAse treated using the Spectrum Total RNA Kit (Sigma, St Louis, MO, USA) according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Samples were labelled by the Ramaciotti Centre (Sydney, NSW, Australia) according to Affymetrix protocols
|
| |
|
| Hybridization protocol |
Samples were hybridized by the Ramaciotti Centre (Sydney, NSW, Australia) according to Affymetrix protocols
|
| Scan protocol |
Samples were washed and scanned by the Ramaciotti Centre (Sydney, NSW, Australia) according to Affymetrix protocols
|
| Description |
Sample name: Arabidopsis_sco3phyb_2
Gene expression data from 4 day old sco3phyb seedlings
|
| Data processing |
Raw CEL files were processed using Partek Genomic Suite (i.e., RMA background correction followed by quantile normalization) using recommended settings. In brief, raw fluorescence values were log2 transformed and subsequently analyzed to detect differentially expressed genes between each line utilizing a 1-way ANOVA based on the Method of Moments (Eisenhart, 1947) and Fisher's Least Significance Difference Contrast methods for differential regulation in all pairwise comparisons using the work-flow of Partej Genomic Suite (http://www.partek.com/pgs)
|
| |
|
| Submission date |
Mar 23, 2015 |
| Last update date |
Mar 24, 2015 |
| Contact name |
Diep R Ganguly |
| E-mail(s) |
dganguly@sas.upenn.edu
|
| Phone |
+1 215-898-0808
|
| Organization name |
University of Pennsylvania
|
| Department |
Department of Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 S University Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19103 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE67168 |
Genetic Suppression of Plant Development and Chloroplast Biogenesis by SCO3 and PhyB Pathways |
|
