|
| Status |
Public on May 31, 2016 |
| Title |
Lab C T6 |
| Sample type |
RNA |
| |
|
| Source name |
liver
|
| Organism |
Pimephales promelas |
| Characteristics |
tissue: liver
treatment: EE2
|
| Treatment protocol |
Males exposed to 25 ng/L EE2 for 96 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol protocol for total RNA following manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
Agilent one color protocol for Cy3 following manufacturer's protocol
|
| |
|
| Hybridization protocol |
Agilent Technologies One-Color Microarray-Based Gene Expression Analysis Protocol was used.
|
| Scan protocol |
Microarrays were kept in the dark until scanned at 5 um, channel G, Agilent HD (61x21.6mm) using the Agilent DNA Microarray Scanner with SureScan High ResolutionTechnology.
|
| Data processing |
BG correction (in a smooth monotonic transformation of the background subtracted intensities such that all the corrected intensities are positive), between-array quantile normalization, and averaging duplicated spots (both items were done using limma package)
filtering out control probes and low expressed probes. To get an idea of how bright expression probes should be, we compute the 95% percentile of the negative control probes on each array. We keep probes that are at least 10% brighter than the negative controls on at least 7 arrays ( there are 8 biological replicates per condition)
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
Nov 13, 2022 |
| Contact name |
Christopher Martyniuk |
| E-mail(s) |
[email protected]
|
| Phone |
3523173905
|
| Organization name |
University of Florida
|
| Street address |
8891 SW 79th Avenue
|
| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32608 |
| Country |
USA |
| |
|
| Platform ID |
GPL15775 |
| Series (2) |
| GSE81348 |
Interlab microarray comparison Lab C |
| GSE81544 |
Interlab microarray comparison |
|
