|
| Status |
Public on Dec 31, 2011 |
| Title |
RNAi-Root-+Zn-2 |
| Sample type |
RNA |
| |
|
| Source name |
RNAi_Root_+10 µM Zn2+ medium
|
| Organism |
Arabidopsis halleri |
| Characteristics |
genotype: AhNAS2-RNAi-1-2
age: 5 weeks old
tissue: Root
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from homogenized A. halleri root tissue with Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
250 ng of total RNA, purified with RNeasy Mini columns (Qiagen, Hilden, Germany) according to the manufacturer's directions, were used to generate double-stranded cDNA and subsequently biotin-labeled cRNA. The length of the cRNA products was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA)
|
| |
|
| Hybridization protocol |
cRNA products were hybridized to the array for 16 h at 45C in a rotating chamber.
|
| Scan protocol |
Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000.
|
| Description |
Hydroponically grown 5-weeks old plants
|
| Data processing |
CEL files from the Affymetrix microarray hybridization were processed by use of the R program and Bioconductor packages (Gentleman et al., 2004). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function (Irizarry et al., 2003). To estimate the amount of expressed mRNAs, the present call information of the non-parametric Wilcoxon signed rank test (PMA values) was computed with the 'affy' package (Gautier et al., 2004). Hybridization data from three biological replicates were generated for each Langelsheim wild-type and RNAi line 1-2.
|
| |
|
| Submission date |
Aug 31, 2011 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Stephan Clemens |
| E-mail(s) |
stephan.clemens@uni-bayreuth.de
|
| Organization name |
University of Bayreuth
|
| Department |
Plant Physiology
|
| Street address |
Universitaetsstrasse 30
|
| City |
Bayreuth |
| ZIP/Postal code |
95440 |
| Country |
Germany |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE31778 |
AhNAS2 suppression in Arabidopsis halleri roots |
|
| Relations |
| Reanalyzed by |
GSE118579 |
