|
| Status |
Public on Sep 11, 2014 |
| Title |
ti_wt_03_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
flax inner stem tissues
|
| Organism |
Linum usitatissimum |
| Characteristics |
developmental stage: vegetative
cultivar: Diane
genotype/variation: wild-type
|
| Growth protocol |
plants were grown under field conditions at the University of Lille, France
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from peeled inner tissues using the TriReagent (Molecular Research Center) method
|
| Label |
Cy3
|
| Label protocol |
Following manufacture's instruction for One-Color Microarray base gene Expression Analysis (Agilent Technologies)
|
| |
|
| Hybridization protocol |
Following manufacture's instruction for One-Color Microarray base gene Expression Analysis (Agilent Technologies)
|
| Scan protocol |
Using an Axon GenePix 4000B scanner (Molecular Devices) piloted by GenePix Pro 6.0 software (Axon)
|
| Description |
b25 and b26 data come from the same sample
|
| Data processing |
After background noise elimination, medians values of overall hybridization were normalized by robust local regression (Yang et al., 2002). Artefact spots were manually eliminated. Differential analysis was performed with the method varmixt (Delmar et al., 2005) , available in the package anapuce of the software R. A double-sided, unpaired t-test was computed for each gene between the two conditions. Variance of the difference in gene expression was split between subgroups of genes with homogeneous variance (Delmar et al., 2005). The raw P values were adjusted by the Bonferroni method, which controls the Family Wise Error Rate (FWER) (Ge et al., 2003). A gene is declared differentially expressed if the Bonferroni-corrected P-Value is less than 0.05
|
| |
|
| Submission date |
Sep 10, 2014 |
| Last update date |
Sep 11, 2014 |
| Contact name |
Chantreau Maxime |
| E-mail(s) |
maxime.chantreau@ed.univ-lille1.fr
|
| Organization name |
Université de Lille 1
|
| Department |
SN2
|
| Lab |
Stress Abiotique et Différenciation des Végétaux cultivés
|
| Street address |
Université de lille 1
|
| City |
Villeneuve d'Ascq |
| State/province |
Nord |
| ZIP/Postal code |
59260 |
| Country |
France |
| |
|
| Platform ID |
GPL19181 |
| Series (2) |
| GSE61309 |
Transcriptomics modifications in inner stem tissues of the flax lignified bast fiber mutant1 (lbf1) |
| GSE61311 |
Transcriptomics modifications in inner/outer stem tissues of the flax lignified bast fiber mutant1 (lbf1) |
|
