|
| Status |
Public on Apr 16, 2012 |
| Title |
Control Replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
whole worms wild type
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
treatment: control
developmental stage: L3
|
| Treatment protocol |
LC10 at 5.9 mg/L of 4-nm citrate coated Au-NP for 12 hrs in 50% K-medium, the exposure solutions were replaced with 50% K-medium and left for another 12 hrs.
|
| Growth protocol |
C. elegans were maintained on NGM plates at 20 ⁰C. Age-synchronized nematodes at L3 stage were used for the experiment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from each of the replicates using Trizol (Invitrogen) followed by purification with Qiagen RNeasy Kit (Qiagen, Chatsworth, CA). Repeated freeze-thaw cycles (at -80 and 37⁰C) were used to lyse the cells.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared from 2 microgram total RNA according to standard protocol in the Affymetrix GeneChip Expression Analysis Manual.
|
| |
|
| Hybridization protocol |
Following Fragmentation, 13 microgram of cRNA were hybridized to Affymetrix C. elegans genome array for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
The microarray chips were scanned using Affymetrix GCS 3000 7G scanner
|
| Data processing |
The data were normalized using RMA algorithm followed by quantile normalization implemented in Partek Genomics Suite 6.4 (Partek, Inc, St Louis, MO).
|
| |
|
| Submission date |
Sep 30, 2011 |
| Last update date |
Apr 16, 2012 |
| Contact name |
Olga Tsyusko |
| E-mail(s) |
[email protected]
|
| Phone |
859-257-1777
|
| Organization name |
University of Kentucky
|
| Department |
Plant and Soil Sciences
|
| Street address |
1100 S. Limestone St
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40546 |
| Country |
USA |
| |
|
| Platform ID |
GPL200 |
| Series (1) |
| GSE32521 |
Toxicogenomic responses of C. elegans to gold nanoparticles |
|
