|
| Status |
Public on Aug 11, 2016 |
| Title |
fer-1_72h_E. coli OP50_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
fer-1, uninfected, 72h
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: HH142
genotype: fer-1(b232ts)
hours: 72h
diet: E. coli OP50
condition: uninfected
|
| Treatment protocol |
For recovery, 200ug/ml Neomycin in M9 was used to rinse worms and Streptomycin was included in plates at 50ug/ml.
|
| Growth protocol |
Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 72 hours. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 72 hours and then exposed to P. aeruginosa PA14 for 4 hours. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 72 hours, exposed to P. aeruginosa PA14 for 4 hours, and then treated with Neomycin and shifted to E. coli OP50 plus Streptomycin plates for 6, 12, or 24 hours to resolve the infection. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 82 hours. Synchronized L1 fer-1(b232ts) animals were grown on E. coli OP50 for 76 hours and then treated with Neomycin and shifted to E. coli OP50 plus Streptomycin plates for 6 hours. Animals were kept at 25dC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Life Technologies) and the RNeasy Plus Universal Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Total RNA was converted to Cy-3-labeled, linearly amplified cRNA using the Low Input Quick Amp (LIQA) One-Color Microarray-Based Gene Expression Analysis Kit (Agilent)
|
| |
|
| Hybridization protocol |
Hybridization was performed in the Agilent Rotisserie Hybridization Oven (Agilent) for 17 hours.
|
| Scan protocol |
Agilent B scanner according to standard Agilent protocols (Agilent).
|
| Description |
72hOP1
|
| Data processing |
Log2 transformation and quantile normalization using Partek Genomics Suite (Partek).
|
| |
|
| Submission date |
May 18, 2016 |
| Last update date |
Aug 12, 2016 |
| Contact name |
Brian P Head |
| E-mail(s) |
[email protected]
|
| Phone |
919-668-2449
|
| Organization name |
Duke University Medical Center
|
| Department |
Molecular Genetics and Microbiology
|
| Lab |
Alejandro Aballay
|
| Street address |
Box 3580 DUMC
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL11346 |
| Series (1) |
| GSE81592 |
C. elegans gene expression in response to acute Pseudomonas aeruginosa infection (Part 1) and recovery (Part 2) by Neomycin/Streptomycin treatment |
|
