|
| Status |
Public on Apr 21, 2011 |
| Title |
wt, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Wild-type animals infected with P. aeruginosa PA14 for 4 hours at 25°C (total transcripts)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animals
genotype: wild type
developmental stage: L4 animals
infection: P. aeruginosa PA14
genetic background: N2
|
| Treatment protocol |
Animals were collected and washed with M9 buffer before transferring to NGM plates containing P. aeruginosa PA14 for 4 hours at 25°C.
|
| Growth protocol |
Gravid adult wild-type and tag-24/octr-1 animals were lysed using a solution of sodium hydroxide and bleach (ratio of 5:2), washed and the eggs were synchronized for 22 hours in S basal liquid medium at room temperature. Synchronized L1 larval animals were placed onto NGM plates seeded with E. coli OP50 and grown at 20°C until the animals had reached the L4 larval stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After 4 hours, animals were collected and washed with M9 buffer, and RNA was extracted using TRIzol reagent (Invitrogen). Residual genomic DNA was removed by DNase treatment (Ambion Austin, TX).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from L4 animals
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
|
| |
|
| Submission date |
Mar 09, 2011 |
| Last update date |
Apr 21, 2011 |
| Contact name |
Alejandro Aballay |
| Organization name |
Duke University
|
| Department |
Molecular Genetics and Microbiology
|
| Lab |
Aballay
|
| Street address |
268 Jones
|
| City |
Durham |
| State/province |
North Carolina |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE27867 |
Expression data from C. elegans (wild type vs. tag-24) |
|
