|
| Status |
Public on Oct 15, 2015 |
| Title |
CCA1-ox, 6pm, total RNA, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
CCA1-ox_6pm
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Columbia
genotype/variation: CCA1-ox
age: 10 days
tissue: aerial part
harvested at: 6pm
|
| Growth protocol |
Plants were grown on agar plates with full strength Murashige and Skoog salts, pH 5.7, 1% sucrose, in a 16-hour light/8-hour dark cycle (lights on at 6am) for 10 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, polysome fractionation, and microarray hybridization were performed as described previously (Genome Biol. 2007;8(4):R60)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from total and polysome-fractionated RNA (Expression Analysis Technical Manual, 2001, Affymetrix) after priming cDNA synthesis with oligo(dT).
|
| |
|
| Hybridization protocol |
cRNA was hybridized for 16 hr at 45C on the GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained with streptavidin-phycoerythrin (Invitrogen-Molecular Probes, Carlsbad, CA, USA), followed by a wash with biotinylated antibody goat IgG and another staining with streptavidin-phycoerythrin.
|
| Scan protocol |
GeneChips were scanned using the GeneChip 7G high-resolution scanner.
|
| Description |
6pm_T_3
|
| Data processing |
The data were analyzed using R version 3.1. Normalization was performed using the gcrma function from the gcrma package from Bioconductor (version 2.36), and absolute calls (columns labeled ABS_CALL) were generated using the mas5calls function from the affy package (version 1.42.3), all with default settings. AGI annotations (column labeled AGI) were matched with Affymetrix probe IDs using the ath1121501.db package from Bioconductor (version 2.14). Translation state (TL) was calculated as (2*small polysomal + 7*large polysomal)/(non-polysomal + small polysomal + large polysomal) after back-transforming the log2 values.
|
| |
|
| Submission date |
Sep 30, 2014 |
| Last update date |
Oct 15, 2015 |
| Contact name |
Albrecht G von Arnim |
| E-mail(s) |
[email protected]
|
| Phone |
1-865-974-6206
|
| Organization name |
The University of Tennessee
|
| Department |
Biochemistry, Cellular and Molecular Biology
|
| Lab |
von Arnim Lab
|
| Street address |
M407 Walters Life Science Building
|
| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE61896 |
Transcript levels in CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle |
| GSE61899 |
Polysome profiling in wild type and CIRCADIAN CLOCK ASSOCIATED 1-overexpressing (CCA1-ox) Arabidopsis thaliana over a 24-hour diurnal cycle |
|
