|
| Status |
Public on Dec 18, 2014 |
| Title |
E. coli alone_after treatment_rep.3 |
| Sample type |
RNA |
| |
|
| Source name |
Escherichia coli O103:H25 alone after treatment
|
| Organism |
Escherichia coli O103:H25 |
| Characteristics |
co-culture/in supernatant/alone: alone
treated/not treated: treated
|
| Growth protocol |
E. coli O103:H25 was grown individually or in co-culture with Bacteroides thetaiotaomicron to mid-log phase (OD 600nm 0.5) anaerobically in modified BHI media (Elay et al., J Med Microbiol. (1985), 19(2):195)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a Purelink RNA mini kit (Life technologies, Carlsbad, California). DNA was removed using a Turbo DNA-free kit (Invitrogen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
For labeling of the cDNA samples, the NimbleGen protocol was followed.
|
| |
|
| Hybridization protocol |
The hybridization of samples in randomized order to custom designed by NimbleGen arrays
|
| Scan protocol |
The samples were read with a GenePix 4000B scanner
|
| Description |
E. coli alone 3 hours after treatment with MMC. It is the third of three biological replicates.
|
| Data processing |
RMA was used as the normalization algorithm in accordance with Nimblegen recommendation. Batch correction was performed with the ComBat function of the SVA package.
|
| |
|
| Submission date |
Mar 08, 2013 |
| Last update date |
Dec 19, 2014 |
| Contact name |
Hildegunn Iversen |
| E-mail(s) |
[email protected]
|
| Phone |
004795147301
|
| Organization name |
Norwegian School of Veterinary Science
|
| Department |
Department of Food Safety and Infection Biology
|
| Lab |
Food Safety
|
| Street address |
P.O.Box 8146 Dep
|
| City |
Oslo |
| ZIP/Postal code |
0033 |
| Country |
Norway |
| |
|
| Platform ID |
GPL16737 |
| Series (1) |
| GSE44790 |
Transcription analysis of E. coli O103:H25 in co-culture with Bacteroides thetaiotaomicron CCUG 10774 |
|
