|
| Status |
Public on Feb 07, 2013 |
| Title |
7096 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
pad4-Field-2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
organism: Arabidopsis thaliana
tissue: pool of rosette material of three individual plants
age: five-week-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA), according to manufacturer's instructions. Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).
|
| Label |
Cy5
|
| Label protocol |
1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
WT-Field-2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
organism: Arabidopsis thaliana
tissue: pool of rosette material of three individual plants
age: five-week-old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA), according to manufacturer's instructions. Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).
|
| Label |
Cy3
|
| Label protocol |
1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
For Cy3 14pmol, and for Cy5 10pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.
|
| Scan protocol |
After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 10.1.1.1 (Agilent Technologies).
|
| Description |
-
|
| Data processing |
Prior to normalization, data from control spots was removed. We used the processed signals obtained with the Agilent Feature extraction software (version 10.1.1.1). The presented values are log2-(Cy5/Cy3)-ratios.
|
| |
|
| Submission date |
Oct 18, 2010 |
| Last update date |
Feb 08, 2013 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL9020 |
| Series (1) |
| GSE24766 |
LSD1, EDS1 and PAD4 Conditionally Regulate Cellular Signaling Homeostasis, Photosynthesis, Water Use Efficiency and Seed Yield in Arabidopsis |
|
