|
| Status |
Public on Feb 14, 2008 |
| Title |
Wildtype, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Wildtype C. elegans young adult whole worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Genotype: N2 (Bristol) wildtype
Age: young adults (confirmed by Biosort sorting)
|
| Treatment protocol |
Adult animals of each strain were sorted based on time of flight gated by size using an automated sorter (COPAS Biosort, Union Biometrica) to collect 5 biological replicates each consisteing of 1000 living adult worms.
|
| Growth protocol |
C. elegans were grown on NGM agar 10 cm plates spread with standard OP50 E. coli. Synchrony was obtained by bleaching gravid adults, plating the recovered eggs on unspread NGM plates overnight, after which L1-stage arrested animals were transferred to NGM plates spread with standard OP50 E. coli.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent was used according to the manufacturer's instructions to extract total RNA from aliquots of 500 to 1,000 sorted adult worms
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Revision 5, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.
|
| Description |
Gene expression data from wildtype C. elegans
|
| Data processing |
Probe-level measurements were normalized, summarized and log2-transformed by dCHIP software using perfect-match-only and invariant-set methods.
|
| |
|
| Submission date |
Dec 14, 2007 |
| Last update date |
Nov 14, 2016 |
| Contact name |
Marni J Falk |
| E-mail(s) |
falkm@email.chop.edu
|
| Phone |
215-590-4564
|
| Organization name |
CHOP
|
| Department |
Pediatrics/ Human Genetics
|
| Lab |
ARC 1002c
|
| Street address |
3615 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (2) |
| GSE9896 |
Expression data from wildtype and gas-1 mitochondrial mutant C. elegans |
| GSE9967 |
Expression data from wildtype and C. elegan mutants |
|
