|
| Status |
Public on Sep 15, 2008 |
| Title |
Pst mutant K3 exp. 1 |
| Sample type |
RNA |
| |
|
| Source name |
Pst mutant (K3) strain experiment 1
|
| Organism |
Escherichia coli |
| Characteristics |
E. coli serotype O78:K80:H9, K3 strain grown in LB media [LB broth, per liter, is composed of 10 g of Bacto tryptone, 5 g of yeast extract, 10 g of NaCl and the pH is adjusted to 7.5 by 10 N of NaOH]
|
| Extracted molecule |
total RNA |
| Extraction protocol |
An overnight culture grown at 37°C was diluted 100-fold into 5 ml of LB broth and was allowed to grow to mid-log phase (OD600 0,6). Cultures were centrifuged and RNAs were isolated by using the RiboPure™-Bacteria Kit (Ambion, Austin, TX), according to the manufacturer’s recommendations, with the exception that the DNAse 1 treatment was performed twice.
|
| Label |
biotin
|
| Label protocol |
Fragmented cDNA was 3’ biotynylated using GeneChip DNA Labelling Reagent, 7.5 mM (Affymetrix, Santa Clara, CA) and 60 U of Terminal Deoxynucleotidyl Transferase (Promega, Madison, WI) at 37°C for 60 min, as recommended by Affymetrix (www.affymetrix.com). The reaction was stopped by adding 2 µl of 0.5 M EDTA (Sigma) to the reaction mix.
|
| |
|
| Hybridization protocol |
Hybridization was carried out at McGill University & Genome Quebec Innovation Centre according to Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).
|
| Scan protocol |
Scan procedure was carried out at McGill University & Genome Quebec Innovation Centre according to Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).
|
| Description |
The cDNA of the K3 strain from experience 1 was hybridized onto the GeneChip.
|
| Data processing |
Data were processed using the FlexArray software (Blazejczyk, M., M. Miron and R. Nadon. 2007. FlexArray: A statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada. Genome Quebec, Montreal, Canada). Raw data were normalized using the RMA algorithm and log2 were generated. The expression value was generated by subtracting the mean value of each replicate of the mutant strain by wild-type strain.
|
| |
|
| Submission date |
Sep 26, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Sébastien Crépin |
| E-mail(s) |
sebastien.crepin@umontreal.ca
|
| Organization name |
Université de Montréal
|
| Department |
Microbiologie et pathologie
|
| Lab |
Josée Harel
|
| Street address |
3200 Sicotte
|
| City |
St-Hyacinthe |
| State/province |
Québec |
| ZIP/Postal code |
J2S7C6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE9178 |
Genome-wide transcriptional response of an Avian Pathogenic Escherichia coli (APEC) Pst Mutant |
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