|
| Status |
Public on Mar 29, 2016 |
| Title |
CFT073_6_A |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
2 dpf zebrafish embryos infected with E. coli CFT073
|
| Organism |
Danio rerio |
| Characteristics |
agent: E. coli CFT073
hours post inoculum: 6
|
| Treatment protocol |
48 hpf zebrafish embryos were inoculated with ~1000 CFU of E. coli strain CFT073, F11, or an equivalent volume of sterile PBS as a control.
|
| Growth protocol |
Wildtype AB zebrafish were maintained as breeding colonies on a 14h/10h light/dark cycle. Embryos were collected as mixed egg clutes and raised at 28.5C in E3 medium. Bacterial strains were grown statically in modified M9 minimal medium at 37C for 24 hrs. 1000 ul culture was spun down, washed in sterile PBS, and then resuspended ~800-1200 ul sterile PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pools of 18-20 2 dpf zebrafish embryo were manually homogonized and RNA extracted using the Rneasy Plus Universal Kit (Qiagen)
|
| Label |
Cy3
|
| Label protocol |
Fluorescently labeled cRNA was synthesized using the Two-Color Low RNA Input Linear Amplifliciation Kit (Agilent)
|
| |
|
| Channel 2 |
| Source name |
2 dpf zebrafish embryos injected with sterile PBS
|
| Organism |
Danio rerio |
| Characteristics |
inoculated with: Sterile PBS
hours post inoculum: 6
|
| Treatment protocol |
48 hpf zebrafish embryos were inoculated with ~1000 CFU of E. coli strain CFT073, F11, or an equivalent volume of sterile PBS as a control.
|
| Growth protocol |
Wildtype AB zebrafish were maintained as breeding colonies on a 14h/10h light/dark cycle. Embryos were collected as mixed egg clutes and raised at 28.5C in E3 medium. Bacterial strains were grown statically in modified M9 minimal medium at 37C for 24 hrs. 1000 ul culture was spun down, washed in sterile PBS, and then resuspended ~800-1200 ul sterile PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pools of 18-20 2 dpf zebrafish embryo were manually homogonized and RNA extracted using the Rneasy Plus Universal Kit (Qiagen)
|
| Label |
Cy5
|
| Label protocol |
Fluorescently labeled cRNA was synthesized using the Two-Color Low RNA Input Linear Amplifliciation Kit (Agilent)
|
| |
|
| |
| Hybridization protocol |
Fluroescently labeled cRNA (825 ng) was then fragemented, combined with Hi-RPM Hybridization Buffer (Agilent), and hybridized using a SureHyb Hybridization chamber (Agilent)
|
| Scan protocol |
Slides were scanned in a G2505C Microarray Scanner (Agilent)
|
| Data processing |
TIFF files of scanned microarrays were processed using Feature Extraction Software version 10.6 (Agilent). Array data was then log2 transformed, Lowess-normalized, and median centered.
Fold changes were calculated by comparing samples to mock-infected (PBS-injected) controls from the same clutch of embryos.
|
| |
|
| Submission date |
Mar 28, 2016 |
| Last update date |
Mar 29, 2016 |
| Contact name |
Amelia E Barber |
| Organization name |
Leibniz-HKI
|
| Department |
Fungal Informatics
|
| Street address |
Adolf-Reichwein-Straße 23
|
| City |
Jena |
| State/province |
Thuringia |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13390 |
| Series (1) |
| GSE79665 |
Host response to systemic bacterial challenge (sepsis) with E. coli strains CFT073 and F11 at 6 and 12 hours post inoculum |
|
