|
| Status |
Public on Mar 31, 2016 |
| Title |
3 hour after dark time in the first day |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
3 hour after dark time in the first day
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
sample type: test
|
| Treatment protocol |
50 mL of cluture was collected every two hours in two diurnal cycles with steps of spinning down, frozen by liquid nitrogen, and holding in -80°C freezer.
|
| Growth protocol |
Synechocystis sp. PCC 6803 cells cultured in BG11 medium were diuluted 100-fold after a week growth under 12h/12h light/dark cycles condition, and this new culture was hold in 30°C with bubbling by air for another four days for sampling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by using RNAwiz reagent (Ambion) according to the manufacturer’s instructions and quantified with the NanoDrop ND-1000 UVVIS Spectrophotometer.
|
| Label |
Cy5
|
| Label protocol |
Total RNA (2.5 µg) was labeled directly with Cy3 and Cy5 dyes by using the Micromax ASAP RNA labeling kit (Perkin–Elmer Life and Analytical Sciences) according to the manufacturer’s instruction.
|
| |
|
| Channel 2 |
| Source name |
An equimolar mixture of RNA from all time points
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
sample type: reference
|
| Treatment protocol |
50 mL of cluture was collected every two hours in two diurnal cycles with steps of spinning down, frozen by liquid nitrogen, and holding in -80°C freezer.
|
| Growth protocol |
Synechocystis sp. PCC 6803 cells cultured in BG11 medium were diuluted 100-fold after a week growth under 12h/12h light/dark cycles condition, and this new culture was hold in 30°C with bubbling by air for another four days for sampling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by using RNAwiz reagent (Ambion) according to the manufacturer’s instructions and quantified with the NanoDrop ND-1000 UVVIS Spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (2.5 µg) was labeled directly with Cy3 and Cy5 dyes by using the Micromax ASAP RNA labeling kit (Perkin–Elmer Life and Analytical Sciences) according to the manufacturer’s instruction.
|
| |
|
| |
| Hybridization protocol |
The microarrays were hybridized at MoGene by using 750 ng of RNA and a specific activity of 50 pmol for each dye.
|
| Scan protocol |
Technology: Agilent.SingleColor.17371
|
| Data processing |
The data from each microarray were independently normalized to correct for variations in labeling intensities between channels. The background signal for each measurement was subtracted from the raw signal. A LOWESS curve was fit to the training set by using a window length of 25% the number of points fit. The signals were then normalized with the fit LOWESS curve by using linear interpolation to correct points that fell between two points in the training set.
|
| |
|
| Submission date |
Mar 30, 2016 |
| Last update date |
Mar 31, 2016 |
| Contact name |
Himadri Pakrasi |
| E-mail(s) |
pakrasi@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Biology
|
| Lab |
Himadri Pakrasi
|
| Street address |
One Brookings Dr.
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63130 |
| Country |
USA |
| |
|
| Platform ID |
GPL21668 |
| Series (1) |
| GSE79714 |
Oscillating profiles of global genes in Synechocystis sp. PCC 6803 in diurnal light/dark cyles. |
|
