|
| Status |
Public on May 03, 2013 |
| Title |
MM901 formate-excess(380 mM sodium formate) N-limiting(2 mM NH4Cl) rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ss HighFormate noH2 LowN
|
| Organism |
Methanococcus maripaludis S2 |
| Characteristics |
strain: MM901
treatment: formate-excess(380 mM sodium formate) N-limiting(2 mM NH4Cl)
|
| 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 |
bulk from a mid-log phase culture(OD660=0.804)
|
| Organism |
Methanococcus maripaludis S2 |
| Characteristics |
strain: MM901
treatment: none
|
| 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 Microarray Scanner (Agilent Technologies, Santa Clara, CA).
|
| Description |
Technical replicate 2 of 2
|
| 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 |
Nov 07, 2012 |
| Last update date |
May 03, 2013 |
| 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 |
GPL15063 |
| Series (1) |
| GSE42111 |
Steady-state samples of Methanococcus maripaludis MM901 grown on formate under hydrogen limited conditions |
|
