|
| Status |
Public on Jun 27, 2011 |
| Title |
Sulfolobus solfataricus P2 growth curve. Array 252331010016 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Sulfolobus solfataricus P2 growth curve [test sample]
|
| Organism |
Saccharolobus solfataricus P2 |
| Characteristics |
growth phase: mid-log phase (OD600=0.923)
time: 74h
replicate: 1
|
| Biomaterial provider |
Steven M. Yannone, Lawrence Berkeley National Laboratory, Berkeley, CA
|
| Treatment protocol |
Samples of 1 x 10^9 cells were taken every 6 hours by pipette, immediately chilled on ice and the cells collected by centrifugation at 1400 x g for 10 minutes at 4°C. Aspirated cell pellets were immediately plunged into liquid nitrogen and stored at -80°C until RNA extraction.
|
| Growth protocol |
Cells were grown aerobically at 80°C in liquid mineral medium pH=3.0 (Arch. Mikrobiol. 84:54-68) containing 0.2% tryptone and 0.1% yeast extract (Difco). One-liter culture flasks containing 400 ml media were inoculated with log phase cells and maintained under constant agitation (230 RPM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using mirVana miRNA isolation kit (Applied Biosystems, Austin, TX) following manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
1.5 µg of total RNA were directly labeled with 1.5 µl of Kreatech dye (Cy3 or Cy5) at 95°C for 5 min, then put it on ice. The solutions were purified by KREApure column.
|
| |
|
| Channel 2 |
| Source name |
Sulfolobus solfataricus P2 [reference sample]
|
| Organism |
Saccharolobus solfataricus P2 |
| Characteristics |
growth phase: mid-log phase (OD600=0.312)
|
| Biomaterial provider |
Steven M. Yannone, Lawrence Berkeley National Laboratory, Berkeley, CA
|
| Treatment protocol |
Samples of 1 x 10^9 cells were taken every 6 hours by pipette, immediately chilled on ice and the cells collected by centrifugation at 1400 x g for 10 minutes at 4°C. Aspirated cell pellets were immediately plunged into liquid nitrogen and stored at -80°C until RNA extraction.
|
| Growth protocol |
Cells were grown aerobically at 80°C in liquid mineral medium pH=3.0 (Arch. Mikrobiol. 84:54-68) containing 0.2% tryptone and 0.1% yeast extract (Difco). One-liter culture flasks containing 400 ml media were inoculated with log phase cells and maintained under constant agitation (230 RPM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using mirVana miRNA isolation kit (Applied Biosystems, Austin, TX) following manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
1.5 µg of total RNA were directly labeled with 1.5 µl of Kreatech dye (Cy3 or Cy5) at 95°C for 5 min, then put it on ice. The solutions were purified by KREApure column.
|
| |
|
| |
| Hybridization protocol |
7.5 µg of labeled sample RNA and 7.5 µg of labeled reference RNA were fragmented in total 250 µl mixture (50 µl of 10X blocking agent, 10 µl of 25X fragmentation buffer, H2O) at 60°C for 30 min, then put it on ice for 1 min. 250 µl of fragmentation mix and 250 µl of GE hybridization buffer HI-RPM were mixed and spinned for 1 min at RT at 13,000 rpm, and put on ice. 490 µl of the hybridization mix was applied to the slide in chamber, and put in a hybridization oven at 65°C for 17 hrs. After hybridization, the slide was washed sequentially in GE wash buffer 1 (twice) and 2.
|
| Scan protocol |
The arrays were scanned by ScanArray (Perkin Elmer).
|
| Description |
ch1: Sulfolobus solfataricus P2 at OD600=0.923, t=74h, Replicate 1
ch2: Sulfolobus solfataricus P2 at OD600=0.312
|
| Data processing |
Signal intensities and local backgrounds were determined by Feature Extraction software (Agilent Technologies). Cy3 and Cy5 intensities were normalized by scaling so that the 75th percentile in the Cy3 and Cy5 channels were equal.
|
| |
|
| Submission date |
Jan 20, 2011 |
| Last update date |
Jun 27, 2011 |
| Contact name |
Sung Ho Yoon |
| Organization name |
Konkuk University
|
| Department |
Department of Bioscience and Biotechnology
|
| Street address |
120 Neungdong-ro, Gwangjin-gu
|
| City |
Seoul |
| ZIP/Postal code |
05029 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL11623 |
| Series (2) |
| GSE26779 |
Sulfolobus solfataricus P2 growth curve, tiling arrays |
| GSE26782 |
Parallel evolution of transcriptome structure during genome reorganization |
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