|
| Status |
Public on Jul 28, 2020 |
| Title |
CSN8 + DTT, batch 1 |
| Sample type |
RNA |
| |
|
| Source name |
light grown DTT treated CSN8 seedlings batch 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
genotype: CSN8 mutant
age: 12-d-old
|
| Treatment protocol |
After 12 days the seedlings were collected for RNA extraction with no additional treatment
|
| Growth protocol |
Seedlings were grown for 12 days on agar plates containing MS salts, pH 5.7, under a light-and-dark cycle with 16 h of white light at 75 lmol m-2 s-1 and 8 h of darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-Reagent (Molecular Research Center, Inc., USA) extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS 3000 Scanner
|
| Description |
Gene expression data from young seedlings
|
| Data processing |
data analysis was performed by MATLAB: (i) Expression values were computed from raw CEL files by applying the background adjustment using Robust Multi-array Average (RMA) background correction algorithm, then applying quantile normalization over the multiple arrays, and finally performed the RMA procedure to get final gene expression values. (ii) In the next step, in each of the samples (Col/Csn5a-1 and Ws/Csn8), we computed significantly over/under-expressed genes based on: For Col/csn5a-1 we used t-test based on data of six6 chips. For Ws/csn8 we used ANOVA(Rutherford, 2001), considering batch effects such as the scan date of each chip, etc.
|
| |
|
| Submission date |
Dec 20, 2017 |
| Last update date |
Jul 28, 2020 |
| Contact name |
Tamir Tuller |
| Organization name |
Tel Aviv University
|
| Department |
Biomedical Engineering
|
| Lab |
Laboratory of Computational Systems and Synthetic Biology
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE108376 |
Expression data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes |
| GSE119363 |
Expression and methylation data from seedlings of two light grown Arabidopsis thaliana CSN mutants and two wild type ecotypes. |
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