|
| Status |
Public on Sep 08, 2012 |
| Title |
E. coli O157:H7 at 2 h control biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
E. coli O157:H7 control, sampled at 2h of treatment
|
| Organism |
Escherichia coli O157:H7 |
| Characteristics |
strain: 06:0627
treatment: control
time: 2h
|
| Treatment protocol |
Exponential phase culture was used to incoculate duplicate flasks with or without 200 mg/l cinnamaldehyde and incubated at 37ºC for ≤ 4h. The Samples from each flask were collected at 2 and 4 h for total RNA extraction.
|
| Growth protocol |
An Overnight culture of E. coli O157:H7 was used to inoculate Brain heart infusion broth (BHIB) and incubated at 37ºC to get exponential phase cultures with absorbance at 600 nm (A600) between 0.6 to 0.7.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were centrifuged and pellet was treated with TRIzol® reagent. Total RNA was extracted according to the TRIzol® manufacturer's protocol.The RNA pellet digested with DNase I and cleaned-up using RNeasy mini columns (Qiagen Sciences, Germantown, MD, US) according to the manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
Labelling was performed according to the Affymetrix protocol (Affymetrix, Santa Clara, CA, US). Fragmented cDNAs were mixed with GeneChip® DNA labelling reagent at 7.5 mM (Affymetrix), reaction buffer and 60 U of terminal deoxynucleotidyl transferase (Promega, Madison, WI, US), and incubated at 37 oC for 60 min. The reaction was terminated by adding 2 µl of 0.5 M EDTA.
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| |
|
| Hybridization protocol |
Hybridization of the cDNAs was conducted at Genome Québec Innovation Centre (McGill University, Montréal, QC, Canada) using Affymetrix Genechip® E. coli Genome 2.0 Array (Affymetrix) as described by the manufacturer.
|
| Scan protocol |
Scan procedure was carried out at McGill University & Genome Quebec Innovation Centre according to Affymetrix recommendation.
|
| Description |
Gene expression data from control at 2 h
|
| Data processing |
Raw microarray data was imported into FlexArray 1.6.1 software and statistical tests were performed (Blazejczyk M, Miron M, Nadon R. 2007. FlexArray: A statistical data analysis software for gene expression microarrays. Genome Quebec, Montreal, Canada)
Data normalization, background correction and expression value calculation were done using the robust multi-array average algorithm (RMA). The expression fold change (FC), treatment minus control value ≥ 1.5 log2 with a p value ≤ 0.05 was considered as a cut-off point to determine differentially expressed genes
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| |
|
| Submission date |
Sep 07, 2012 |
| Last update date |
Sep 08, 2012 |
| Contact name |
Richard A Holley |
| E-mail(s) |
[email protected]
|
| Fax |
0012044747630
|
| Organization name |
University of Manitoba
|
| Department |
Department of Food Science
|
| Street address |
250 Ellis Building
|
| City |
Winnipeg |
| State/province |
Manitoba |
| ZIP/Postal code |
R3T 2N2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE40693 |
Transcriptional response of Escherichia coli O157:H7 to cinnamaldehyde |
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