Dataset features

Specifications


Dataset type: Expression profiling by array, transcription profiling by array, Transcriptome or Gene expression
Number of samples: 8
Release date: Sep 15 2008
Last update date: Mar 17 2012
Access: Public
Chemicals: Phosphates
Dataset link Genome-wide transcriptional response of an Avian Pathogenic Escherichia coli (APEC) Pst Mutant

Experimental Protocol


RNA extraction was performed onto the chi7122 and K3 strains on four biological replicates. 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. RNA extractions were performed on four different days (the chi7122 and K3 RNA were extracted at the same time) and a total of eight hybridizations were performed. Hybridization was carried out at McGill University & Genome Quebec Innovation Centre according to the Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4). GeneChip scan was carried out at McGill University & Genome Quebec Innovation Centre according to the Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4), and data were processed using the FlexArray software (Michal Blazejczyk, Mathieu Miron, Robert Nadon (2007). FlexArray: A statistical data analysis software for gene expression microarrays. 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.

Repositories


GEO

GSE9178

ArrayExpress

E-GEOD-9178

BioProject

PRJNA102743

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Contact


Sébastien Crépin
Sébastien Crépin