|
| Status |
Public on Feb 20, 2017 |
| Title |
4.63 um - replicate 1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Zebrafish fibroblast cells exposed to 4.63 um atrazine for 72 hours
|
| Organism |
Danio rerio |
| Characteristics |
agent: atrazine
dose: 4.63 um
cell type: fibroblast
|
| Treatment protocol |
Cells were exposed to either 0, 0.463, 4.63, or 46.3 um atrazine for 72 hours.
|
| Growth protocol |
7.5 x 10^5 cells were initially seeded into each petri dish. After set-up, petri dishes were placed in an incubator at 28°C and 5% CO2 for 72 hours (the equivalent of 1.5 cell cycle lengths).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 72 hours, cells were harvested and genomic DNA was isolated following a standard phenol:chloroform isolation method.
|
| Label |
Cy5
|
| Label protocol |
Labeling was performed following Agilent's protocol (version 7.3) for two color hybridization. Test DNA was labeled with Cy5 and the control treatment labeled with Cy3.
|
| |
|
| Channel 2 |
| Source name |
Zebrafish fibroblast cells exposed to 0 um atrazine
|
| Organism |
Danio rerio |
| Characteristics |
agent: control
cell type: fibroblast
|
| Treatment protocol |
Cells were exposed to either 0, 0.463, 4.63, or 46.3 um atrazine for 72 hours.
|
| Growth protocol |
7.5 x 10^5 cells were initially seeded into each petri dish. After set-up, petri dishes were placed in an incubator at 28°C and 5% CO2 for 72 hours (the equivalent of 1.5 cell cycle lengths).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 72 hours, cells were harvested and genomic DNA was isolated following a standard phenol:chloroform isolation method.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed following Agilent's protocol (version 7.3) for two color hybridization. Test DNA was labeled with Cy5 and the control treatment labeled with Cy3.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed following Agilent's protocol (version 7.3) for two color hybridization.
|
| Scan protocol |
Arrays were scanned on a SureScan microarray scanner (Agilent Technologies, Santa Clara, CA) at 3 microns.
|
| Description |
72 hours = ~1.5 cell cycle lengths
4.63_R1
|
| Data processing |
Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Microarray analysis was performed following MIAME guidelines. aCGH analysis was completed using Agilent Genomic Workbench 7.0.4 following the aberration detection method 2 (ADM2) algorithm. ADM2 identifies all aberrant intervals in a given sample with consistently high or low log ratios based on statistical score. The ADM2 algorithm searches for intervals in which a statistical score based on the average quality weighted log ratio of the sample and reference channels exceeds a user specific threshold and reports contiguous genomic regions as aberrant regions.
Calls were determined which contained at least six consecutive probes to obtain a high degree of confidence (Agilent Technologies, Santa Clara, CA).
|
| |
|
| Submission date |
Jan 14, 2017 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Jennifer Freeman |
| E-mail(s) |
[email protected]
|
| Organization name |
Purdue University
|
| Department |
School of Health Sciences
|
| Street address |
550 Stadium Mall Drive
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL22921 |
| Series (1) |
| GSE93635 |
Atrazine Exposure Elicits Copy Number Alterations in the Zebrafish Genome |
|
