|
| Status |
Public on Apr 30, 2007 |
| Title |
D1 chloromethane treated sample biological replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
Nitrosomonas europaea culture at late exponential phase.
|
| Organism |
Nitrosomonas europaea |
| Characteristics |
strain ATCC 19718
|
| Treatment protocol |
cells grown to late exponential phase were washed and innoculated into medium with 5 mM (NH4)2SO4, placed on the orbital shaker. Cells were treated with 3.2 mM chloromethane for one hour. 150 mls of cells were collected for RNA extraction by centrifugation.
|
| Growth protocol |
Nitrosomonas europaea cells grown in batch cultures with 25 mM (NH4)2SO4, to OD600 close to 0.07
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's protocol. RNA extracts were further purified using RNeasy Mini kit (QIAGEN), and on-column DNase digestion was performed.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA according to the Affymetrix prokaryotic target preparation protocol
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Nitrosomonas Genome Array in Affymetrix geneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GenChip Scanner 3000
|
| Description |
Gene expression data from chloromethane treated cells
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
|
| |
|
| Submission date |
Dec 21, 2006 |
| Last update date |
Mar 27, 2007 |
| Contact name |
barbara gvakharia |
| Organization name |
OSU
|
| Department |
Botany and Plant Pathology
|
| Street address |
Cordley Hall 4097
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL4617 |
| Series (1) |
| GSE6594 |
Nitrosomonas europaea cells treated with chloromethane for one hour and compared to untreated cells |
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