|
| Status |
Public on Nov 28, 2012 |
| Title |
acrylamide_low_expose-4h_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: L4 larvae
exposure chemical: Acrylamide
exposure concentration (mg/l): 100
exposure length (hours): 4
|
| Treatment protocol |
Nematode populations were synchrnoized to the same developmental stage by treating the gravid adults with bleach and sodium hydroxide. This dissolves the adults, but allows the less sensitive embryos to remain viable. Following bleaching, embryos were maintained in an aqueous salt solution to allow larval nematodes to emerge and proceed into the first larval stage. Development is arrested at this time until the larvae are supplied with an adequate source of nutrition to support further development. Synchronized nematodes were then transferred to CeHR medium and allowed to proceed to mid L4 larval stage before the study compound was added. The study compounds were incorporated into the CeHR medium. Incubation under exposure conditions was at 22.5 °C for 4 and 8 hours. A single flasks of worms was harvested prior to beginning the exposure as the 0 h control.
|
| Growth protocol |
C. elegans cultures were grown in CeHR medium at 22.5 °C in T-75 tissue culture flasks with shaking at 70 rpm.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Flash frozen worms were pulverized under liquid nitrogen in a Spex 6750 Freezer Mill. RNA was extracted from pulverized worms with Trizol followed by an additional purification step using RNeasy Midi columns. PolyA RNA was then isolated using OligoTex. All steps were performed following manufacturers recommendations.
|
| Label |
Biotin
|
| Label protocol |
cDNA was synthesized using SuperScript Choice kit and a T24T7 primer following the manufacturer's protocol. Biotin labeled cRNA was synthesized using the Enzo BioArray High Yield Kit following the manufacturer's protocol. cRNA was purified from unincorporated nucleotides and other reaction components using the RNeasy Mini Kit (Qiagen).
|
| |
|
| Hybridization protocol |
Biotin labeled cRNA was fragmented and hybridized to Affymetrix C. elegans whole genome GeneChips as recommended by Affymetrix.
|
| Scan protocol |
Hybridized Affymetrix C. elegans whole genome GeneChips were then scanned as recommended by Affymetrix.
|
| Description |
gene expression data from L4 larvae
551-005-003
|
| Data processing |
The data were analyzed with MAS 5.0 using Affymetrix default analysis settings.
|
| |
|
| Submission date |
Nov 28, 2012 |
| Last update date |
Nov 28, 2012 |
| Contact name |
John A. Lewis |
| E-mail(s) |
john.a.lewis1@us.army.mil
|
| URL |
http://usacehr.amedd.army.mil
|
| Organization name |
U.S. Army Center for Environmental Health Research
|
| Department |
Biomarkers Program
|
| Street address |
568 Doughten Drive
|
| City |
Ft. Detrick |
| State/province |
MD |
| ZIP/Postal code |
21702-5010 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE42592 |
Alterations in gene expression in Caenorhabditis elegans associated with exposure to several classes of toxic industrial chemicals/materials. |
|
