|
| Status |
Public on Dec 07, 2007 |
| Title |
Whole Daphnia_20microg/LCadmium_48hr_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Whole body, unexposed
|
| Organism |
Daphnia pulex |
| Characteristics |
Daphnia pulex, strain: Log52
Age: 15 days
|
| Biomaterial provider |
Laboratory colonies
|
| Treatment protocol |
48-hr Unexposed
|
| Growth protocol |
Genetically homogeneous Daphnia pulex were cultured in modified COMBO (Kilham et al. 1998) and kept at 20 degree C in an environmental chamber with a 16-h light/ 8-h dark cycle. The D. pulex were fed daily Ankistrodesmus falcatus at a rate of 75,000 cells/mL. Stock culture medium were renewed and neonates seperated from adults three times weekly.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiashredder columns (QIAGEN) and RNeasy Kit (QIAGEN) according to manufacturers recommendations followed by Dnase digestion (Ambion).
|
| Label |
Alexa Fluor 647
|
| Label protocol |
cDNA was labeled using amino-allyl labeling methods as given by The Institute for Genome Research (TIGR; Hedge et al. 2000).
|
| |
|
| Channel 2 |
| Source name |
Whole body, 20microg/L cadmium exposure, 48 hr
|
| Organism |
Daphnia pulex |
| Characteristics |
Daphnia pulex, strain: Log52
Age: 15 days
|
| Biomaterial provider |
Laboratory colonies
|
| Treatment protocol |
48-h exposure to 20 microg/L cadmium as cadmium chloride
|
| Growth protocol |
Genetically homogeneous Daphnia pulex were cultured in modified COMBO (Kilham et al. 1998) and kept at 20 degree C in an environmental chamber with a 16-h light/ 8-h dark cycle. The D. pulex were fed daily Ankistrodesmus falcatus at a rate of 75,000 cells/mL. Stock culture medium were renewed and neonates seperated from adults three times weekly.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiashredder columns (QIAGEN) and RNeasy Kit (QIAGEN) according to manufacturers recommendations followed by Dnase digestion (Ambion).
|
| Label |
Alexa Fluor 555
|
| Label protocol |
cDNA was labeled using amino-allyl labeling methods as given by The Institute for Genome Research (TIGR; Hedge et al. 2000).
|
| |
|
| |
| Hybridization protocol |
Hybridization followed recommendations given by The Institute for Genome Research (TIGR; Hedge et al. 2000). Samples were dried and resuspended in hybridization buffer (50% formamide, 5X SSC, 0.1% SDS, 20 microg SSDNA and 20 microg of poly(A)-DNA). The hybridization solution was placed on microarray and hybridization was accomplished overnight at 42 degrees C. Following hybridization, the glass slides were washed successively in a low stringency solution (0.1X SSC, 0.2% SDS) at room temperature for 4 minutes, twice in 0.1X SSC for 2.5 minutes, dipped in water, dried and immediately scanned.
|
| Scan protocol |
Images were quantified using GenePix Professional 3000 with GenePix Pro software (version 5.1).
|
| Description |
None
|
| Data processing |
Signal intensities determined by GenePix Pro software version 5.1 (Axon Instruments, Union City, CA).
|
| |
|
| Submission date |
Dec 02, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Joseph R Shaw |
| E-mail(s) |
joeshaw@indiana.edu
|
| Organization name |
Indiana University
|
| Department |
The School of Public and Environmental Affairs
|
| Lab |
Shaw Lab
|
| Street address |
1315 E. Tenth Street
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL6195 |
| Series (1) |
| GSE9746 |
Whole Daphnia_20microg/L Cadmium_48hr |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
averaged normalized log 2 ratio (experimental/reference) determined by Genepix but with flagged values removed |
| F635 Mean |
averaged mean signal intensity of Alexa Fluor 647 |
| B635 Mean |
averaged mean background signal intensity of Alexa Fluor 647 |
| F532 Mean |
averaged mean signal intensity of Alexa Fluor 555 |
| B532 Mean |
averaged mean background signal intensity of Alexa Fluor 555 |
| FLAGS |
"-" good spot, "null" means the spot was flagged |
| UNF_VALUE |
averaged normalized log 2 ratio (experimental/reference) determined by Genepix |
