|
| Status |
Public on Jun 27, 2011 |
| Title |
Methanococcus maripaludis MM901 growth curve. Array 252330810004 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Methanococcus maripaludis MM901 [reference sample]
|
| Organism |
Methanococcus maripaludis S2 |
| Characteristics |
growth phase: mid-log phase (OD660=0.804)
|
| Biomaterial provider |
John A. Leigh, Univ. Washington
|
| Treatment protocol |
Samples were harvested through the sampling port by drawing out with a 20-ml syringe, aliquoted 1.5 ml each into microcentrifuge tubes, and centrifuged at 9800 rpm for 30 sec. Supernatant was removed and pellets were immediately frozen in an ethanol-dry ice bath and stored at -80°C.
|
| Growth protocol |
Methanococcus maripaludis MM901, wild type Methanococcus maripaludis S2 with an in frame deletion of the uracil phosphoribosyltransferase gene (Proc. Natl. Acad. Sci. U S A 107:11050-11055), was grown in a one-liter fermenter set up as described in (FEMS Microbiol. Lett. 238:85-91), using the modifications to the medium and gases for non-limiting conditions described in (BMC Microbiol. 9:149).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA 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 |
Methanococcus maripaludis MM901 growth curve [test sample]
|
| Organism |
Methanococcus maripaludis S2 |
| Characteristics |
growth phase: mid-log phase (OD660=0.402)
time: 334 min
replicate: 2
|
| Biomaterial provider |
John A. Leigh, Univ. Washington
|
| Treatment protocol |
Samples were harvested through the sampling port by drawing out with a 20-ml syringe, aliquoted 1.5 ml each into microcentrifuge tubes, and centrifuged at 9800 rpm for 30 sec. Supernatant was removed and pellets were immediately frozen in an ethanol-dry ice bath and stored at -80°C.
|
| Growth protocol |
Methanococcus maripaludis MM901, wild type Methanococcus maripaludis S2 with an in frame deletion of the uracil phosphoribosyltransferase gene (Proc. Natl. Acad. Sci. U S A 107:11050-11055), was grown in a one-liter fermenter set up as described in (FEMS Microbiol. Lett. 238:85-91), using the modifications to the medium and gases for non-limiting conditions described in (BMC Microbiol. 9:149).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA 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: Methanococcus maripaludis MM901 at OD660=0.804
ch2: Methanococcus maripaludis MM901 at OD660=0.402, t=334 min, Replicate 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 |
Jan 19, 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 |
GPL11621 |
| Series (2) |
| GSE26777 |
Methanococcus maripaludis S2 growth curve, tiling arrays |
| GSE26782 |
Parallel evolution of transcriptome structure during genome reorganization |
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