|
| Status |
Public on Oct 04, 2011 |
| Title |
M9_TMP5_THY_Ad_AA_10min |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
E. coli MG1655 10 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media
|
| Organism |
Escherichia coli |
| Characteristics |
strain: MG1655
|
| Treatment protocol |
Time-point samples were taken every 15-30 minutes from 15 minutes to 2 hours post treatment.
|
| Growth protocol |
Overnight cultures were resuspended in fresh medium and TMP was added when the optical density (O.D. 600 nm) of the culture reached 0.3-0.4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were purified using the Qiagen RNeasy kit (Chatsworth, CA) according to the manufacturer’s protocol.
|
| Label |
Cy5
|
| Label protocol |
Fluorescence DNA probes were synthesized from 10~15 μg of total RNA with random hexamers and Cy-5 dUTP or Cy-3 dUTP dyes.
|
| |
|
| Channel 2 |
| Source name |
E. coli MG1655 mid-log phase in M9 media
|
| Organism |
Escherichia coli |
| Characteristics |
strain: MG1655
|
| Treatment protocol |
Time-point samples were taken every 15-30 minutes from 15 minutes to 2 hours post treatment.
|
| Growth protocol |
Overnight cultures were resuspended in fresh medium and TMP was added when the optical density (O.D. 600 nm) of the culture reached 0.3-0.4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were purified using the Qiagen RNeasy kit (Chatsworth, CA) according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
Fluorescence DNA probes were synthesized from 10~15 μg of total RNA with random hexamers and Cy-5 dUTP or Cy-3 dUTP dyes.
|
| |
|
| |
| Hybridization protocol |
Relative mRNA levels were determined by parallel two color hybridization at single-gene resolution to whole-genome E. coli K-12 MG1655 spotted DNA microarrays
|
| Scan protocol |
Images were scanned using Axon GenePix scanner.
|
| Description |
E. coli MG1655 10 min after TMP+thymine+adenine+glycine+methionine treatment in M9 media
|
| Data processing |
Raw fluorescence intensity data were normalized in R (http://cran.r-project.org/) using the Limma (Bioconductor) package
|
| |
|
| Submission date |
Oct 03, 2011 |
| Last update date |
Oct 04, 2011 |
| Contact name |
Dipen Sangurdekar |
| E-mail(s) |
dps@genomics.princeton.edu
|
| Organization name |
Princeton University
|
| Department |
Lewis-Sigler Institute for Integrative Genomics
|
| Street address |
132 Carl Icahn laboratory, Princeton University
|
| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
| |
|
| Platform ID |
GPL3503 |
| Series (1) |
| GSE32562 |
Trimethoprim response in Escherichia coli in bacteriostatic and bactericidal conditions |
|
