|
| Status |
Public on Jan 18, 2013 |
| Title |
GlnD mutation grown in MMNH4 biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
GlnD mutation grown in MMNH4
|
| Organism |
Sinorhizobium meliloti |
| Characteristics |
strain: Rm1021
phenotype in plant: Fix+Eff-
|
| Treatment protocol |
Cell processes were halted by addition of 1/9th sample volume of 5% buffer equilibrated phenol (pH 7.4) in ethanol, and cultures were harvested by centrifugation at 15000rpm for 1 minute. Total RNA was processed according to the Affymetrix User Guide, Prokaryotic Sample and Array Processing.
|
| Growth protocol |
Liquid cultures were grown at 30C with agitation at 250rpm to mid-log phase (0.5-0.6 OD600)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed using the Qiagen RNeasy Kit according to the protocol published by Barnett et al. (2004).
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was end labeled with biotin using the GeneChip DNA Labeling Reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega).
|
| |
|
| Hybridization protocol |
Following fragmentation, labeled cDNA was hybridized at 48C for 16 hr in the GeneChip Hybridization Oven 640 according to the manufacturer's recommendations. Hybridized arrays were washed and stained using the GeneChip Fluidics Station 450.
|
| Scan protocol |
Processed arrays were scanned using a 121 GeneChip 3000 7G scanner.
|
| Description |
Gene expression data from GlnD mutation grown in MMNH4
|
| Data processing |
Array quality was assessed, and images were quantified using GeneChip Operating Software v1.2 (Affymetrix). The data were viewed and analyzed using Partek Genomic Suite 6.5 beta software (Partek Incorporated). The genes with absolute expression ratio ≥2 (p < 0.05) were considered induced or repressed. The list of differentially expressed genes was created using analysis of variance (ANOVA).
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| |
|
| Submission date |
Jan 17, 2013 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Jennifer Rice |
| E-mail(s) |
[email protected]
|
| Organization name |
WSU
|
| Street address |
100 Dairy Road
|
| City |
Pullman |
| State/province |
WA |
| ZIP/Postal code |
99164-6340 |
| Country |
USA |
| |
|
| Platform ID |
GPL9757 |
| Series (1) |
| GSE43570 |
Expression data from wild type Sinorhizobium meliloti and mutants in the NSR grown under conditions of high and low nitrogen availability |
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