|
| Status |
Public on Feb 21, 2012 |
| Title |
wild-type 1 |
| Sample type |
RNA |
| |
|
| Source name |
mixed stages of C. elegans
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: wild-type
|
| Growth protocol |
N2 and outcrossed tdp-1(ok803lf) C. elegans were grown under standard conditions, and mixed stages of worms were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with TRIzol (Invitrogen) from triplicates of C. elegans and purified with the RNeasy kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
The RNAs were labeled using the 3’ IVT Express Labeling protocol described by Affymetrix.
|
| |
|
| Hybridization protocol |
15 µg of the labeled aRNA was fragmented and hybridized to the Affymetrix C. elegans genome array. Affymetrix Fluidics Station 450 was used to wash and stain the chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated aRNA. The staining was further amplified using a biotinilated anti-streptavidin antibody, followed by a second staining step with a streptavidin-phycoerythrin conjugate.
|
| Scan protocol |
Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 3.4 (AGCC v3.4) software from Affymetrix.
|
| Description |
N2-1
|
| Data processing |
Data were extracted from the CEL files, RMA normalized and converted to Log2 notation with Partek Genomics Suite (Partek, Missouri, USA). These values were labeled as to genotype and the groups compared with a standard 1-way ANOVA, Student's t-test.
|
| |
|
| Submission date |
Dec 02, 2011 |
| Last update date |
Feb 21, 2012 |
| Contact name |
Jiou Wang |
| Organization name |
Johns Hopkins University
|
| Street address |
615 N. Wolfe St.
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE34113 |
Expression Profiling of Caenorabditis elegans tdp-1 loss-of-function mutant |
|
