|
| Status |
Public on Jan 29, 2018 |
| Title |
Ciprofloxacin (3 ng/ml) exposed culture, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Ciprofloxacin (3 ng/ml) exposed MG1655 culture
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
genotype/variation: wild type
growth stage: logarithmic
treatment: ciprofloxacin
|
| Treatment protocol |
E. coli cells were grown with three different conditions namely (i) with 10 mM GSH (ii) with 3 ng/ml ciprofloxacin (sub-inhibitory antibiotic concentration) and (iii) with 10 mM GSH and 50 ng/ml ciprofloxacin (inhibitory antibiotic concentration). Control cultures were grown in LB with no exogenous GSH or ciprofloxacin added.
|
| Growth protocol |
Overnight grown E. coli were freshly diluted 1:100 in LB medium for collection of total RNA at mid-logarithmic stage (OD600 ~ 0.3-0.4).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained using the RNeasy Protect Bacteria Mini kit (Qiagen) according to the manufacturer's instructions. The purity, concentration, and integrity of RNA were confirmed by Agilent Bioanalyzer 2100 and agarose gel electrophoresis.
|
| Label |
Biotin
|
| Label protocol |
Total RNA was reverse transcribed, biotin labelled and purified using GeneChip® IVT express kit according to the manufacturer's instruction.
|
| |
|
| Hybridization protocol |
Fragmented, biotinylated cDNA generated using the GeneChip® IVT express kit was hybridized to Affymetrix GeneChip® E. coli genome 2.0 arrays for 16 h at 45°C and 60 r.p.m.
|
| Scan protocol |
Hybridized probe arrays were scanned on the GeneChip® Scanner 3000 7G to detect the patterns of hybridization.
|
| Description |
Cip 1
Gene expression data from ciprofloxacin (3 ng/ml) exposed logarithmically growing MG1655 cells.
|
| Data processing |
Original microarray data (CEL files) were preprocessed using RMA (Robust Multichip Average) algorithm in GeneSpring GX 12.0.
|
| |
|
| Submission date |
Jan 20, 2017 |
| Last update date |
Jan 29, 2018 |
| Contact name |
Manish Goswami |
| E-mail(s) |
manishbarc@gmail.com
|
| Phone |
91-22-25590386
|
| Organization name |
Bhabha Atomic Research Centre
|
| Department |
Molecular Biology Division
|
| Street address |
Mod Labs, trombay
|
| City |
MUMBAI |
| State/province |
Maharashtra |
| ZIP/Postal code |
400085 |
| Country |
India |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE93896 |
Transcriptome analysis of E. coli strain MG1655 on exposure to glutathione (GSH) and/or ciprofloxacin |
|
