|
| Status |
Public on Mar 21, 2012 |
| Title |
PLB3 |
| Sample type |
RNA |
| |
|
| Source name |
All C. elegans strains were obtained from the Caenorhabditis Genetic Center, University of Minnesota
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: Bristol N2
genotype: wild-type
protocol: grown and maintained at room temperature (22 to 24°C) on Nematode Growth Media (NGM) containing 2.1% agar with E. coli strain OP50 as a food source. Age-synchronized populations were obtained by collecting the eggs laid by fertile adults over 5 to 7 hours and allowing them to develop to the young adult stage before transfer to treatment plates
agent: 100 µM plumbagin
|
| Biomaterial provider |
All C. elegans strains were obtained from the Caenorhabditis Genetic Center, University of Minnesota
|
| Treatment protocol |
Approximately 1,000 age-synchronized young adults were treated for two days with 100 µM plumbagin(Sigma-Aldrich Co., St. Louis, MO), washed three times in M9 and flash frozen with dry ice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Absolutely RNA Miniprep Kit (Agilent Technologies, USA). RNA concentration and quality was assessed with an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies, USA).
|
| Label |
Cy5
|
| Label protocol |
Total RNA was used in the labeling reaction with the QuickAmp labeling Kit, (Agilent Technologies, USA) according to manufacturer’s protocols. In short, 1000ng of total RNA was used to generate double stranded cDNA from mRNA and containing a T7 RNA polymerase binding site. Then Cy-5 labeled cRNA was generated from this cDNA template using T7 RNA polymerase.
|
| |
|
| Hybridization protocol |
The labeled Cy5 probe (825 ng) was applied to the C. elegans 4x44K Oligo Microarray (Agilent Technologies, USA). Slides were hybridized in a rotating chamber overnight at 60°C, and then washed in 6X SSC, 0.005% Triton X-102 for 10 minutes, and then in 0.1X SSC, 0.005% Triton X-102 for 5 minutes on ice. Slides were dried using a nitrogen-filled air gun, and scanned using an Agilent array scanner.
|
| Scan protocol |
Arrays were scanned at a 5um resolution using the extended dynamic range setting on an Agilent Scanner(G2565AA) .
|
| Description |
PLB3
|
| Data processing |
Data from the Cy-5 channel was extracted using the Agilent Feature Extractor Software, Version 9.5.1.1, then each array was z-normalized. In short, the natural logs of all raw intensities were used to find the avg and std of each array and the z-score normalization was calculated: Z-score = (Natural Log raw value - avg)/std. Complete data on all spots will be included in the supplemental files.
|
| |
|
| Submission date |
Mar 31, 2011 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL7727 |
| Series (1) |
| GSE28301 |
Extension of lifespan in C. elegans by naphthoquinones that act through stress hormesis mechanisms |
|
