|
| Status |
Public on Mar 26, 2008 |
| Title |
C. elegans_Cd_4h_rep14 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Caenorhabditis elegans, N2 wild type
|
| Treatment protocol |
The Bristol N2 strain of C. elegans was cultured in S-medium with Escherichia coli OP50 as a food source. Total RNA was prepared from non-treated control nematodes and those exposed to 100 uM cadmium for 4 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To isolate total RNA, frozen nematode pellets were ground into fine powder using a liquid nitrogen-chilled mortar and pestle before homogenization in TRIzol (Invitrogen). Total RNA was subsequently purified using RNAeasy kits (Qiagen) prior to microarray experiments.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
4h treated
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Caenorhabditis elegans, N2 wild type
|
| Treatment protocol |
The Bristol N2 strain of C. elegans was cultured in S-medium with Escherichia coli OP50 as a food source. Total RNA was prepared from non-treated control nematodes and those exposed to 100 uM cadmium for 4 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To isolate total RNA, frozen nematode pellets were ground into fine powder using a liquid nitrogen-chilled mortar and pestle before homogenization in TRIzol (Invitrogen). Total RNA was subsequently purified using RNAeasy kits (Qiagen) prior to microarray experiments.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.
|
| Scan protocol |
Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (version A.7.5.1).
|
| Description |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (version A.7.5.1).
|
| Data processing |
GeneSpring GX per spot and per chip: intensity dependent (Lowess) normalization, natural log ratio Treated/Control
|
| |
|
| Submission date |
Apr 16, 2007 |
| Last update date |
Mar 26, 2008 |
| Contact name |
Yuxia Cui |
| E-mail(s) |
[email protected]
|
| Phone |
919-541-2679
|
| Fax |
919-541-5737
|
| Organization name |
NIEHS
|
| Department |
ETP, DIR
|
| Lab |
LMT
|
| Street address |
111 TW Alexander Dr.
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL2875 |
| Series (1) |
| GSE7535 |
Toxicogenomic Analysis of Caenorhabditis elegans Reveals Genes Involved in the Resistance to Cadmium Toxicity |
|
