|
| Status |
Public on Aug 08, 2019 |
| Title |
5-CCR |
| Sample type |
RNA |
| |
|
| Source name |
Inflorescence stem
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
genotype: loss of function ccr-1 mutant
tissue: Inflorescence stem
|
| Treatment protocol |
Stems were harvested, frozen at -80C and ground
|
| Growth protocol |
Seeds were exposed to 4˚C for 2 days and then sown in a seedling mix substrate (Metro-Mix 360, SUN GRO) with controlled fertilizer (20-10-20; 20%N, 10%P2O5 and 20%K2O at the dose 200 ppm per gallon at 21˚C under a 16h-light/8h-dark photoperiod. Light intensity was 110 µmol m-2 s-1, supplied by both incandescent and fluorescent lights.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.RNA was cleaned using the RNA cleanup kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Arabidopsis Genome Array (Affymetrix, http://www.affymetrix.com/) . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
total RNA from lignin modified 1.5 months old plants
|
| Data processing |
Data normalization was conducted using robust multichip average (RMA) (Irizarry et al., 2003). The presence/absence call for each probe set was obtained from dCHIP (Li and Wong, 2001). Genes with significantly different expression levels between the wild-type control and mutants were selected using associative analysis, as described by Dozmorov and Centola (Dozmorov and Centola, 2003). The type-I family-wise error rate was reduced by using a Bonferroni corrected P-value threshold of 0.05/N, where N represents the number of genes present on the chip. The false discovery rate was monitored and controlled by Q value (false discovery rate), calculated using Extraction of Differential Gene Expression (EDGE, http://www.biostat.washington.edu/software/
value normalized using robust multichip average (RMA) from MAS5.0 signal intensity
|
| |
|
| Submission date |
Jan 28, 2019 |
| Last update date |
Aug 09, 2019 |
| Contact name |
Lina Gallego-Giraldo |
| E-mail(s) |
[email protected]
|
| Organization name |
University of north Texas, Biodiscovery Institute
|
| Department |
Biology
|
| Lab |
Dixon's lab
|
| Street address |
1155 Union Circle #311428
|
| City |
Denton |
| State/province |
Texas |
| ZIP/Postal code |
76201 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE125721 |
Transcriptomic analysis of lignin mutants in Arabidopsis |
|
