|
| Status |
Public on Feb 14, 2008 |
| Title |
Complex I RNAi Mutant 4 |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans young adult whole worms complex RNAi mutant
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Genotype: ETC complex I mutant generated by feeding RNAi for Y56A3A.19 allele (MRC GeneService clone ID III-6K15) to N2 larvae for 2 generations on plates, then 3rd generation in liquid culture, all in presence of 5 mM IPTG.
Age: predominantly young adults (collected by sucrose gradient centrifugation)
|
| Treatment protocol |
Liquid cultures of each strain were washed free of bacteria and subjected to sucrose centrifugation to enrich for Adult-stage animals.
|
| Growth protocol |
C. elegans were grown for 2 generations on NGM agar 10 cm plates, spread with OP50, HT115, or RNAi-specific E. coli, as indicated in the description for each strain above. Worms were then transferred for 3rd generation growth in liquid culture in either
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent was used according to the manufacturer's instructions to extract total RNA from approximately 0.2-2.0 g of C. elegans whole worms grown in liquid culture. Following extraction, RNA from 3 biological replicates of each strain were combined
|
| 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 mutant 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 18, 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) |
| GSE9897 |
Expression data from 2 wildtype and 8 C. elegans ETC mutants |
| GSE9967 |
Expression data from wildtype and C. elegan mutants |
|
