|
| Status |
Public on May 16, 2007 |
| Title |
Pooled glp-1 C elegans old adults_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Pooled glp-1 C elegans 6-day-old adults.
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Pool of ~3000-5000 age-matched 6-day-old (“old”) adults, Strain: JK1107, Genotype: glp-1(q224) III
|
| Biomaterial provider |
Caenorhabditis Genetics Center
|
| Treatment protocol |
Normal culturing conditions.
|
| Growth protocol |
Eggs obtained from adults raised at 15ºC were hatched in M9 buffer overnight at 20ºC, transferred as L1s to OP50-seeded K agar plates, and raised at 25ºC (to prevent germ cell proliferation) until 6 days post-L4 stage. Worms were transferred to fresh plates every 2 days by washing off in K medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
6-day-old adults were rinsed off plates with K medium and allowed to settle by gravity. They were washed twice with K medium over ~30 minutes, and after the final wash were resuspended in ~500ul K medium and dripped into liquid nitrogen using a glass pasteur pipette. The resulting pellets were ground in liquid nitrogen, and the powder dissolved in lysis buffer with proteinase K and RNase A from the RNEasy extraction kit (Qiagen); subsequent extraction was per the Qiagen protocol.
|
| Label |
biotin
|
| Label protocol |
Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.
|
| |
|
| Hybridization protocol |
15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.
|
| Scan protocol |
Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
|
| Description |
Gene expression analysis was conducted using C. Elegans Genome Genechip® arrays (Affymetrix, Santa Clara, CA). Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol. For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Slides were stained and washed as indicated in the Antibody Amplification Stain for Eukaryotic Targets protocol using the Affymetrix Fluidics Station FS450. Arrays were then scanned with an Affymetrix Scanner 3000. Data was obtained using the Genechip® Operating Software (Version 1.2.0.037).
|
| Data processing |
Data were processed using the Rosetta Resolver® system (version 5.1), as described in Weng (2004). Weng, L. (2004). Data processing and analysis methods in the Rosetta Resolver system, Rosetta Biosoftware Technical Note, http://www.rosettabio.com/tech/default.htm
|
| |
|
| Submission date |
Apr 24, 2006 |
| Last update date |
Jul 06, 2007 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
microarray@niehs.nih.gov, liuliw@niehs.nih.gov
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE4766 |
Decline of Nucleotide Excision Repair Capacity in Aged Caenorhabditis elegans |
|
