|
| Status |
Public on Feb 27, 2009 |
| Title |
L1 larvae 3 hr after hatching in the absence of food |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans 3 hr L1 arrest
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
wild-type; starved
3 hr after hatching
|
| Treatment protocol |
Worms were briefly pelleted in a clinical centrifuge, fed samples were washed three times in S-complete. All but 100 microliters of buffer was removed, and the pelleted worms were frozen in liquid nitrogen.
|
| Growth protocol |
C. elegans strain N2 was grown in S-complete at a density of 1 worm/microliter with or without 25 mg/ml E. coli HB101 at 20C. Cultures were 10 ml volume (10,000 larvae).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions except 50 micrograms of linear polyacrylamide was added as a carrier (Sigma). After TRIzol extraction, the RNA pellet was dissolved in Rnase-free water and further purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol and eluted in 14 μl RNAse-free water.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard protocol for MessageAmp II-Biotin Enhanced kit (Ambion) starting with 100 ng total RNA.
|
| |
|
| Hybridization protocol |
12.5 micrograms of biotin-labeled cRNA was fragmented and hybridized according to the Affymetrix protocol.
|
| Scan protocol |
Arrays were scanned using the Affymetrix GeneChip 3000 scanner.
|
| Description |
Gene expression data from larvae hatched in the presence or absence of food.
|
| Data processing |
Data were processed using Rosetta Resolver version 7.1 (Rosetta Biosoftware); the Affymetrix-Rosetta – Intensity Profile and Experiment Builder pipelines were used. Data processing resulted in average expression values and associated errors as well as a statistic reporting whether the target transcript was detected above background. The processing pipelines used include a global error model for the Affymetrix platform that specifies the typical error associated with an expression measurement of a given magnitude. For each average expression value, the larger of the model-based error and empirical error was reported.
|
| |
|
| Submission date |
Apr 04, 2008 |
| Last update date |
Feb 27, 2009 |
| Contact name |
L. Ryan Baugh |
| E-mail(s) |
ryan.baugh@duke.edu
|
| Phone |
919-613-8179
|
| Organization name |
Duke University
|
| Department |
Biology
|
| Lab |
Baugh
|
| Street address |
4314 French Family Science Center
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708-0338 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (2) |
| GSE11055 |
Temporal expression analysis of C. elegans larvae hatching in the presence and absence of food. |
| GSE14009 |
Nutritional control of gene expression during C. elegans L1 arrest and recovery |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM279206_N2-2_-_3hr.CEL.gz |
1.9 Mb |
(ftp)(http) |
CEL |
| GSM279206_N2-2_-_3hr.CHP.gz |
124.8 Kb |
(ftp)(http) |
CHP |
| GSM279206_N2-2_-_3hr.EXP.gz |
362 b |
(ftp)(http) |
EXP |
| GSM279206_N2-3_-_3hr.CEL.gz |
2.0 Mb |
(ftp)(http) |
CEL |
| GSM279206_N2-3_-_3hr.CHP.gz |
123.3 Kb |
(ftp)(http) |
CHP |
| GSM279206_N2-3_-_3hr.EXP.gz |
362 b |
(ftp)(http) |
EXP |
| GSM279206_N2-4_-_3hr.CEL.gz |
2.1 Mb |
(ftp)(http) |
CEL |
| GSM279206_N2-4_-_3hr.CHP.gz |
122.3 Kb |
(ftp)(http) |
CHP |
| GSM279206_N2-4_-_3hr.EXP.gz |
359 b |
(ftp)(http) |
EXP |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
