|
| Status |
Public on Dec 17, 2008 |
| Title |
E.coli_15min_AE_1 |
| Sample type |
RNA |
| |
|
| Source name |
E.coli_15min_aerobic
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
Escherichia coli MG1655
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The hot-phenol method was used to extract total RNA from two independent cultures of cells grown aerobically
|
| Label |
Biotin
|
| Label protocol |
RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip E. coli Genome 2.0 Arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 1.5 ug of cDNA was fragmented with DNase and end-labeled (GeneChip® WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.
|
| |
|
| Hybridization protocol |
1 µg of end-labeled, fragmented cDNA was used in a 80-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0006; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G controlled by Affymetrix GeneChip Operating Software version 1.4. All arrays were scaled to a target value of 500.
|
| Description |
not applicable
|
| Data processing |
Scanned arrays were analyzed with Affymetrix GCOS 1.4 software to obtain Detection calls and Expression values based on MAS 5.0 algorithms. All arrays were scaled to a target value of 500.
|
| |
|
| Submission date |
Dec 15, 2008 |
| Last update date |
Dec 16, 2008 |
| Contact name |
Lígia Santos Nobre |
| E-mail(s) |
lnobre@itqb.unl.pt
|
| Organization name |
Instituto de Tecnologia Quimica e Biologica
|
| Lab |
Molecular Genetics of Microbial Resistance
|
| Street address |
Av. da Republica (EAN)
|
| City |
Oeiras |
| ZIP/Postal code |
2780-157 Oeiras |
| Country |
Portugal |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE13982 |
Effect of CORM-2 on E. coli transcriptome |
|
