|
| Status |
Public on Apr 14, 2012 |
| Title |
DMSO I |
| Sample type |
RNA |
| |
|
| Source name |
DMSO I
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
treatment: DMSO
tissue: whole organism
strain: N2
|
| Treatment protocol |
Animals were incubated for 15 hours at 15°C in 2 mL of liquid S-basal complete medium containing 70 μM RPW-24 or DMSO and supplemented with E. coli OP50. The final concentration of DMSO in both samples was 1%.
|
| Growth protocol |
N2 C. elegans 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 the late L4 larval stage.
|
| 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 protocol
|
| Scan protocol |
Affymetrix standard protocol
|
| Data processing |
Data were analyzed with freely available GenePattern version 2.0 Software on the BROAD public Server using CEL files as input. Data were processed using ExpressionFileCreator with GC-RMA and quantile normalization. Data were then preprocessed using MultiplotPreprocess (no replicate FC, no random data, no outlier elimination, but with Stats), analyzed using Multiplot and means calculated from 3 independent biological replicates were visualized with scatter plots. Probability of differential expression was calculated by Multiplot from 3 independent biological replicates per sample using student t-tests and a probability of ≤ 0.025 was considered significant.
|
| |
|
| Submission date |
Apr 13, 2012 |
| Last update date |
Apr 18, 2012 |
| 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) |
| GSE37266 |
Stimulation of Host Immune Defenses by a Small Molecule Protects C. elegans from Bacterial Infection |
|
