|
| Status |
Public on Apr 01, 2016 |
| Title |
KU216 grown at 60˚C, replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
KU216 at 60°C
|
| Organism |
Thermococcus kodakarensis |
| Characteristics |
genotype: ∆pyrF
growth condition: The cells were grown in ASW-YT media supplemented with elemental sulfur at 60˚C for mid-logarithmic phase
|
| Treatment protocol |
The grown cells were freezed at -80°C prior to RNA extraction.
|
| Growth protocol |
KU216 strain was individually cultivated at 85°C and 60°C in the rich media supplemented with elemental sulfur. Cells were harvested in the mid-logarithmic phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
10 µg of total RNA was annealed with random hexamers, and reverse transcription was performed in solutions containing CyDye-labeled dUTP (GE Healthcare). RNA was subsequently degraded with RNase H, and the labeled cDNA was purified by using a QiaQuick PCR purification kit (Qiagen).
|
| |
|
| Channel 2 |
| Source name |
KU216 at 85°C
|
| Organism |
Thermococcus kodakarensis |
| Characteristics |
genotype: ∆pyrF
growth condition: The cells were grown in ASW-YT media supplemented with elemental sulfur at 85°C for mid-logarithmic phase
|
| Treatment protocol |
The grown cells were freezed at -80°C prior to RNA extraction.
|
| Growth protocol |
KU216 strain was individually cultivated at 85°C and 60°C in the rich media supplemented with elemental sulfur. Cells were harvested in the mid-logarithmic phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
10 µg of total RNA was annealed with random hexamers, and reverse transcription was performed in solutions containing CyDye-labeled dUTP (GE Healthcare). RNA was subsequently degraded with RNase H, and the labeled cDNA was purified by using a QiaQuick PCR purification kit (Qiagen).
|
| |
|
| |
| Hybridization protocol |
The labeled cDNA was dissolved in hybridization buffer (30 µl) containing 6×SSC (1×SSC is 0.1 M NaCl, 0.015 M sodium citrate), 0.2% Sodium lauryl sulfate, 5×Denhard's solution (Sigma-Aldrich), and 0.1 mg/ml denatured salmon sperm DNA. Hybridization was perfomed under a coverslip (Spaced cover glass XL, Takara bio) in a humidity chamber at 65˚C for 15 h. After hybridiztion, the microarray plates were washed four times with 2×SSC and 0.2% SDS at 55˚C for 5 min, rinsed in 0.05×SSC, and dried by centrifugation.
|
| Scan protocol |
The intensities of the Cy3 and Cy5 dyes were measured by using an Affymetrix 428 array scanner (Affymetrix)
|
| Description |
Technical replicate 2 of 2. KU216 grown at 60°C
|
| Data processing |
The microarray image analysis was processed by ImaGene 5.5 software (Biodiscovery) using a local background correction. For normalization of data, global intensity normalization was performed.
|
| |
|
| Submission date |
Aug 12, 2015 |
| Last update date |
Apr 01, 2016 |
| Contact name |
Ryota Hidese |
| E-mail(s) |
rhidese0830@gmail.com
|
| Organization name |
Kwansei-Gakuin University
|
| Department |
School of Science and Technology
|
| Lab |
Fujiwara lab.
|
| Street address |
Gakuen 2-1
|
| City |
Sanda |
| State/province |
Hyogo |
| ZIP/Postal code |
669-1337 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17565 |
| Series (1) |
| GSE71987 |
Microarray analysis of the hyperthermophilic archaeon Thermococcus kodakarensis grown at lowest growth temperature |
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