|
| Status |
Public on Dec 31, 2011 |
| Title |
young adult_24hr Benzene exposure_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mRNA isolated from wildtype young adult, benzene
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype: wildtype
gender: hemaphrodite
developmental stage: young adult
treatment: benzene
treatment time: 24 hours
|
| Treatment protocol |
From stock solutions, experimental concentrations of benzene, toluene, formaldehyde and BTF mix were prepared in k-media (0.032 M KCl and 0.051M NaCl; 28). For toxicity tests, worms were incubated at 20°C for 24 hr without a food source and then subjected to each type of analysis.
|
| Growth protocol |
C. elegans were grown in Petri dishes on nematode growth medium (NGM) and fed OP50 strain Escherichia coli and young adults (3 days) from an age-synchronized culture were used in all the experiments. To produce age-synchronized cultures, at 2 to 3 days, eggs from mature adults were isolated using a 10% hypochlorite solution, followed by a rinse with M9 buffer, and the eggs allowed to hatch on agar plates with a food source, resulting in synchronized adult worm populations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was prepared from the exposed and control worms according to the standard protocol of the RNeasy Mini kit (Qiagen, Hilden, Germany).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip® 3’ IVT Express Kit User Manual Affymetrix, P/N 702646 Rev. 1).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on the GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Genechip Array scanner 3000 7G.
|
| Description |
Gene expression data from Caenorhabditis elegans young adults.
C.elegans-Benzene
|
| Data processing |
Affymetrix data were normalized, and summarized with the robust multi-average (RMA) method implemented in the Affymetrix Expression Console 1.1. To reduce noise for the significance analysis, the probesets called Absent by the MAS5 detection call on all arrays were filtered out.
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| |
|
| Submission date |
Jul 19, 2010 |
| Last update date |
Dec 31, 2011 |
| Contact name |
jinhee choi |
| E-mail(s) |
jinhchoi@uos.ac.kr
|
| Phone |
82-2-2210-5622
|
| Organization name |
University of Seoul
|
| Department |
College of Urban Science
|
| Lab |
Faculty of Environmental Engineering
|
| Street address |
90 Jeonnong-dong, Dongdaemun-gu
|
| City |
seoul |
| ZIP/Postal code |
130-743 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL200 |
| Series (2) |
| GSE23013 |
mRNA microarray analysis on young adult Caenorhabditis elegans exposed to benzene, toluene, formaldehyde and a BTF mix |
| GSE24923 |
mRNA microarray analysis on young adult Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio exposed to benzene, toluene, and formaldehyde |
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