|
| Status |
Public on Mar 23, 2016 |
| Title |
30mM SCFA replicate 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
enterohemorrhagic E. coli_30mM short chain fatty acid mix
|
| Organism |
Escherichia coli |
| Characteristics |
e. coli subset: enterohemorrhagic E.coli
treated with: 30mM short chain fatty acid mix
|
| Treatment protocol |
overnight culture subcultured in either of the SCFA mixes (or the sodium chloride controls) at 37C, static with 5%CO2 to OD600 of 1
|
| Growth protocol |
overnight bacterial culture in Luria Broth at 37C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extracted using Trizol Extraction Protocol
|
| Label |
CY5
|
| Label protocol |
175 ng of each sample was used to generate 300 ng of cRNA with labelling protocol version GE2 v6.5
|
| |
|
| Channel 2 |
| Source name |
N30-4
|
| Organism |
Escherichia coli |
| Characteristics |
e. coli subset: enterohemorrhagic E.coli
treated with: 30mM NaCl
|
| Treatment protocol |
overnight culture subcultured in either of the SCFA mixes (or the sodium chloride controls) at 37C, static with 5%CO2 to OD600 of 1
|
| Growth protocol |
overnight bacterial culture in Luria Broth at 37C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extracted using Trizol Extraction Protocol
|
| Label |
CY3
|
| Label protocol |
175 ng of each sample was used to generate 300 ng of cRNA with labelling protocol version GE2 v6.5
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2505B-C scanner.
|
| Description |
S30-4
|
| Data processing |
Images were quantified and normalized using extraction protocol GE2_107_Sept09 and Agilent Feature Extraction Software (version 10.7.3.1).
|
| |
|
| Submission date |
Mar 22, 2016 |
| Last update date |
Mar 23, 2016 |
| Contact name |
Debora Eleanor Barnett Foster |
| E-mail(s) |
dfoster@ryerson.ca
|
| Phone |
416 912 7469
|
| Organization name |
Ryerson University
|
| Department |
Chemistry and Biology
|
| Street address |
350 Victoria Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5B 2K3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13359 |
| Series (1) |
| GSE79509 |
Enterohemorrhagic Escherichia coli: impact of short chain fatty acid treatment on virulence gene expression |
|
