|
| Status |
Public on Dec 25, 2009 |
| Title |
Salmonella 48C Treatment Rep1-1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Salmonella Control Cy3
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: ATCC 14028
|
| Treatment protocol |
S. Typhimurium ATCC 14028 was grown until mid-log phase at 30°C and maintained at 30°C for 30 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following incubation, cultures were resuspended immediately in RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA). Total RNA was extracted using RNeasy Protect Bacteria Mini Kit (Qiagen Inc.) and DNA removed using RNase-Free DNase Set (Qiagen Inc.) and used further for microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
Following the reverse transcriptase reaction, the cDNA was labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences) using the LabelStar kit (Qiagen Inc.) and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO).
|
| |
|
| Channel 2 |
| Source name |
Salmonella 48C Treatment Cy5
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: ATCC 14028
|
| Treatment protocol |
S. Typhimurium ATCC 14028 was grown until mid-log phase at 30°C and heat shocked at 48°C for 30 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following incubation, cultures were resuspended immediately in RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA). Total RNA was extracted using RNeasy Protect Bacteria Mini Kit (Qiagen Inc.) and DNA removed using RNase-Free DNase Set (Qiagen Inc.) and used further for microarray analysis.
|
| Label |
Cy5
|
| Label protocol |
Following the reverse transcriptase reaction, the cDNA was labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences) using the LabelStar kit (Qiagen Inc.) and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO).
|
| |
|
| |
| Hybridization protocol |
Microarray hybridizations were performed by cross hybridization of treatment and control samples. Along with the hybridizations, technical replications (dye swaps) were also performed.
|
| Scan protocol |
Images were captured using a Genepix 4000B (Molecular Devices Corporation, Union City, CA) laser scanner and images processed using GenePix 6.0 software (Molecular Devices Corporation).
|
| Description |
Isolated from pools of heart and liver from 4-week-old chickens
Analyses were performed using Acuity 4.0 software. Slides were normalized using standard settings (ratio based so that the mean of the ratio of means, of all features, were equal to 1.0).
|
| Data processing |
All spots were manually evaluated, and bad, low signal, absent, or unfound features were not included. To obtain the final data provided, it was required that elements on each array and on each dye-swap (after mathematical conversion x’ = -x) provided agreement and showed statistically significant similarity, based upon a student t-test, at the p < 0.05 level. Genes were included in the final dataset that exhibit at least 2.0 fold regulations.
|
| |
|
| Submission date |
Sep 12, 2009 |
| Last update date |
Sep 29, 2009 |
| Contact name |
Arunachalam Muthaiyan |
| Organization name |
University of Arkansas
|
| Department |
Food Science
|
| Street address |
2435 N Hatch Ave
|
| City |
Fayetteville |
| State/province |
AR |
| ZIP/Postal code |
72704 |
| Country |
USA |
| |
|
| Platform ID |
GPL9181 |
| Series (1) |
| GSE18089 |
Influence of Microbial and Host Cell Sublethal Heat Stress on S. Typhimurium Gene Expression |
|
