|
| Status |
Public on Oct 01, 2009 |
| Title |
drh-3 tiling array |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA from drh-3(ne4253)
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: gravid adult
genotype: drh-3(ne4253)
|
| Growth protocol |
Synchronous populations were grown in triplicate on E. coli OP50 at 20°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using TRI-Reagent (MRC Laboratories). Instead of pelleting and resuspending the RNA (as described in the TRI Reagent protocol), RNA was recovered, washed and eluted using the RiboPure total RNA isolation kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
Reverse transcritption was performed on 7µg of each sample using the GeneChip WT Double-Stranded cDNA Synthesis Kit. The dsDNA was then purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified. 7.5µg of each dsDNA sample were used for the subsequent fragmentation and labeling reactions, using the GeneChip WT Double Stranded DNA Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization to the arrays was made using standard Affymetrix protocols and reagents
|
| Scan protocol |
Scanning was done with GeneChip Scanner 3000 7G at the University Massachusetts Medical School’s Genomics Core Facility
|
| Description |
n/a
|
| Data processing |
Probe signals were calculated using Affymetrix Tiling Analysis Software 1.1.2 (bandwidth: 30; intensities: PM/MM) with three replicates each drh-3(ne4253) (experimental) and wild-type (control). Affymetrix probe coordinates (release WS170) were converted to release WS192 coordinates using a Perl script. Gene expression values were defined as the geometric mean of all probe signals within a gene that had a P-value of <0.1 and were present in both datasets. Actin was used to normalize expression values prior to comparison.
_signal.bar files are log10; _pvalue.bar are -10Log10
|
| |
|
| Submission date |
Sep 23, 2009 |
| Last update date |
Sep 23, 2009 |
| Contact name |
Craig Mello |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Craig Mello
|
| Street address |
368 Plantatoin Street, Suite AS5-2047
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL5634 |
| Series (2) |
| GSE18230 |
Expression comparison between C. elegans drh-3(ne4253) and wild-type |
| GSE18231 |
WAGO pathway |
|
