|
| Status |
Public on Jun 04, 2011 |
| Title |
Heat Killed E coli #2 |
| Sample type |
RNA |
| |
|
| Source name |
Heat Killed E coli #2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
infection: Heat Killed E coli
|
| Treatment protocol |
Young adult C. elegans were added to 10-cm plates containing 20-mL of BHI agar (with 45 μg of kanamycin/ ml) and live C. albicans, heat-killed C. albicans or heat-killed E. coli. Three separate biological replicates of nematodes were exposed to these conditions for 4 hours at 25°C.
|
| Growth protocol |
N2 animals were synchronized by hypochlorite treatment. Arrested L1s were plated on 10-cm NGM plates seeded with E. coli OP50 and grown at 20°C until they were young adults.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRI Reagent (Molecular Research Center) according to the manufactures instructions and purified using an RNeasy column (Qiagen).
|
| Label |
biotin
|
| Label protocol |
RNA samples were prepared and hybridized to Affymetrix full-genome GeneChips for C. elegans at the Harvard Medical School Biopolymer Facility following previously described protocols and instructions from Affymetrix.
|
| |
|
| Hybridization protocol |
Affymetrix standard scan protocol
|
| Scan protocol |
Affymetrix standard scan protocol
|
| Data processing |
Data were analyzed using Resolver Gene Expression Data Analysis System, version 5.1 (Rosetta Inpharmatics). Three biologic replicates per condition were normalized using the Resolver intensity error model for single color chips. Conditions were compared using Resolver to determine the fold-change between conditions for each probe set and to generate a P value using a modified t-test. Probe sets were considered differentially expressed if the fold change was 2-fold or greater (P<0.01).
|
| |
|
| Submission date |
Feb 18, 2011 |
| Last update date |
Jun 04, 2011 |
| Contact name |
Read Pukkila-Worley |
| E-mail(s) |
[email protected]
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Molecular Biology and Medicine
|
| Lab |
Ausubel and Mylonakis
|
| Street address |
55 Fruit Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE27401 |
Caenorhabditis elegans infection with Candida albicans |
|
