|
| Status |
Public on Nov 06, 2012 |
| Title |
TMAO vs. O2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild type grown under standard conditions
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
strain: NRC-1
genotype: wild type
growth condition: standard (O2)
|
| Treatment protocol |
Cells were chilled prior to nucleic acid extraction.
|
| Growth protocol |
Cells were grown to early log phase for all samples except the bat cultures, which were grown to log phase, in CM+ or modified CM+ media (see DasSarma, S., and E. M. Fleischmann. 1995. Halophiles. Cold Spring Harbor Laboratory Press, Plainview, N.Y.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated immediately after cell harvest using spin columns (Agilent, Palo Alto, Calif.).
|
| Label |
Cy3
|
| Label protocol |
Total RNA was combined with 500 ng of random hexamers (Qiagen) and reverse transcribed to Cy3- or Cy5-dCTP (Amersham Pharmacia)-labeled cDNA using SuperScript II RNase H_ reverse transcriptase (Invitrogen).
|
| |
|
| Channel 2 |
| Source name |
wild type grown with TMAO
|
| Organism |
Halobacterium salinarum NRC-1 |
| Characteristics |
strain: NRC-1
genotype: wild type
growth condition: TMAO
|
| Treatment protocol |
Cells were chilled prior to nucleic acid extraction.
|
| Growth protocol |
Cells were grown to early log phase for all samples except the bat cultures, which were grown to log phase, in CM+ or modified CM+ media (see DasSarma, S., and E. M. Fleischmann. 1995. Halophiles. Cold Spring Harbor Laboratory Press, Plainview, N.Y.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated immediately after cell harvest using spin columns (Agilent, Palo Alto, Calif.).
|
| Label |
Cy5
|
| Label protocol |
Total RNA was combined with 500 ng of random hexamers (Qiagen) and reverse transcribed to Cy3- or Cy5-dCTP (Amersham Pharmacia)-labeled cDNA using SuperScript II RNase H_ reverse transcriptase (Invitrogen).
|
| |
|
| |
| Hybridization protocol |
Labeled cDNA targets were mixed with hybridization buffer (Agilent) and hybridized to microarray slides, which were assembled into a hybridization chamber (Agilent) for 17 h at 65°C in the dark.
|
| Scan protocol |
Slides were scanned for the Cy3 and Cy5 fluorescent signals using an Agilent DNA microarray scanner.
|
| Description |
O2vsTMAO_left20PMT.txt: Cy3=O2, Cy5=TMAO
|
| Data processing |
Image processing was carried out using Agilent Feature Extraction software. Data from replicate arrays were analyzed using the Agilent microarray data analyzing software GeneSpring version 11.5.1. Green and red signal intensities of the probes were imported using a custom-created single-color technology.
|
| |
|
| Submission date |
May 31, 2012 |
| Last update date |
Nov 06, 2012 |
| Contact name |
Priya DasSarma |
| E-mail(s) |
[email protected]
|
| Phone |
410-234-8861
|
| Organization name |
UMB
|
| Department |
Microbiology
|
| Street address |
701 East Pratt Street, Suite 236
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21202 |
| Country |
USA |
| |
|
| Platform ID |
GPL15637 |
| Series (1) |
| GSE38374 |
Metabolic responses of the model archaeon Halobacterium sp. NRC-1 to oxygen limitation |
|
