|
| Status |
Public on May 24, 2008 |
| Title |
Col-0 grown at 30ºC (Cy3) vs. Col-0 grown at 22ºC (cy5) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Arabidopsis thaliana Col-0 grown at 30ºC, biological replicate 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
4-week-old whole plants
|
| Treatment protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3ºC-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.
|
| |
|
| Channel 2 |
| Source name |
Arabidopsis thaliana Col-0 grown at 22ºC, biological replicate 2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
4-week-old whole plants
|
| Treatment protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3ºC-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was extracted using Trizol (Invitrogen). The assay started from 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed overnight on a µParafloTM microfluidic chip.
|
| Scan protocol |
Array images were obtained using an Axon GenePix 4000B laser scanner and digitized using the Array-Pro image software (Media Cybernetics).
|
| Description |
The small RNAs (< 300 nt) were purified, labeled and hybridized by LC Sciences (Houston, TX, USA).
|
| Data processing |
Total Data on all six chips were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).
|
| |
|
| Submission date |
May 22, 2008 |
| Last update date |
May 23, 2008 |
| Contact name |
Li Qun |
| E-mail(s) |
qli@sibs.ac.cn
|
| Phone |
+86 21 54924122
|
| Organization name |
Institute of plant physiology & ecology, SIBS, CAS
|
| Department |
National Key Laboratory of Plant Molecular Genetics
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL6820 |
| Series (1) |
| GSE11535 |
Expression profiles of MicroRNA and SiRNA of Arabidopsis thaliana Col-0 and transgenic plants |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Normalized Log2 of Cy3 Density mean / Cy5 Density mean |
| Cy3 Density (mean){A} |
Signal of Col-0 grown at 30ºC (mean of the intensities read on the ~50 pixels corresponding to each spot) |
| Cy3 Density (st.dev.) {A} |
Unbiased standard deviation (according to Microsoft Excel's nomenclature) of the Cy3 intensities read on the ~50 pixels corresponding to each spot |
| Cy5 Density (mean){A} |
Signal of Col-0 grown at 22ºC (mean of the intensities read on the ~50 pixels corresponding to each spot) |
| Cy5 Density (st.dev.) {A} |
Unbiased standard deviation (according to Microsoft Excel's nomenclature) of the Cy5 intensities read on the ~50 pixels corresponding to each spot |
