|
| Status |
Public on Jul 15, 2008 |
| Title |
Ecoli_untreated_-5min_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Untreated E. coli -5 minute
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
MG1655
|
| Treatment protocol |
Antibiotics were added to final concentration of 10 ug/ml cefsulodin and 0.03 ug/ml mecillinam when the culture reached an OD of approximately 0.2. In the case of the combination treatment the same concentrations were used but the antibiotics were measured and mixed prior to addition.
|
| Growth protocol |
Cultures of MG1655 were grown overnight at 37°C for 14-16 hours Cultures of SEA113 (MG1655) were grown in LB at 37°C overnight (14-18 hrs) with rotation. The overnight cultures were diluted in fresh media to an OD600 of 0.02 and grown at 37°C with shaking in a gyrotary water bath until an OD600 of 0.2, at which point antibiotics were added.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected from both the treated and untreated cultures 5 minutes before treatment as well as 5, 20 and 40 minutes after treatment. The 40 minute time point was immediately before cell growth slowed due to antibiotic treatment. 10 ml of culture was added to an ice-cold 5% phenol/ethanol solution to stop further transcription. RNA was extracted using the hot phenol method of extraction.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual).
|
| |
|
| Hybridization protocol |
Labeled cDNA was hybridized according to the Affymetrix manual for E. coli Antisense chips and were washed and stained in the GeneChip Fluids Station 400
|
| Scan protocol |
Chips were scanned with the GCS3000 scanner
|
| Description |
Gene expression data from untreated E. coli cells
|
| Data processing |
The data were analyzed with the robust multichip averaging (RMA) program in the Simpleaffy package for the Bioconductor statistics environment. Genes with significant changes in gene expression were identified using the significance analysis of microarrays (SAM) program using two-way paired comparison with a false discovery rate of 0.958 % for cef/mec.
|
| |
|
| Submission date |
Jan 12, 2008 |
| Last update date |
Jan 12, 2008 |
| Contact name |
Mary Elizabeth Laubacher |
| E-mail(s) |
mel23@psu.edu
|
| Phone |
814-863-1075
|
| Organization name |
Pennsylvania State University
|
| Department |
Biochemistry Microbiology and Molecular Biology
|
| Lab |
Ades
|
| Street address |
317 S Frear
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL199 |
| Series (2) |
| GSE10158 |
Expression of Escherichia coli treated with cefsulodin and mecillinam, alone and in combination |
| GSE10160 |
Expression of Escherichia coli treated with cefsulodin and mecillinam |
|
