|
| Status |
Public on Aug 02, 2012 |
| Title |
60_DMSO_2 [exiqon] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
zebrafish embryos,60 hours post-fertilization
|
| Organism |
Danio rerio |
| Characteristics |
strain: wildtype TL strain
tissue: zebrafish embryos
developmental stage: 60 hours post-fertilization
treatment: DMSO
|
| Treatment protocol |
Zebrafish embryos at 30 hours post-fertilization were exposed to DMSO or TCDD for 1 hour and sampled at 36 hpf and 60 hpf for miRNA expression profiling
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAGEN miRNeasy kit. Total RNA was assessed for quality using Bioanalyzer.
|
| Label |
Hy3
|
| Label protocol |
miRCURY™ LNA Array Power labeling kit was used.
|
| |
|
| Channel 2 |
| Source name |
Universal Reference RNA
|
| Organism |
Danio rerio |
| Characteristics |
strain: wildtype TL strain
reference: pool of individual RNA samples
|
| Treatment protocol |
Zebrafish embryos at 30 hours post-fertilization were exposed to DMSO or TCDD for 1 hour and sampled at 36 hpf and 60 hpf for miRNA expression profiling
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAGEN miRNeasy kit. Total RNA was assessed for quality using Bioanalyzer.
|
| Label |
Hy5
|
| Label protocol |
miRCURY™ LNA Array Power labeling kit was used.
|
| |
|
| |
| Hybridization protocol |
Hybridization and washing steps were carried out using Tecan hybridization stations.
|
| Scan protocol |
Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.
|
| Description |
Universal Reference RNA is a pool of individual RNA samples
|
| Data processing |
The data was normalized by Exiqon using LOESS method and log2 transformation. Depending on the experimental setup and the size of the project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA). The "1_Exiqon_" raw data files correspond to the Hy3-labelled test RNA, while the "0_Exiqon_" raw data files correspond to the Hy5-labelled reference RNA.
|
| |
|
| Submission date |
Aug 01, 2012 |
| Last update date |
Aug 02, 2012 |
| Contact name |
Neelakanteswar Aluru |
| E-mail(s) |
naluru@whoi.edu
|
| Phone |
508-289-3607
|
| Organization name |
Woods Hole Oceanographic Institution
|
| Department |
Biology
|
| Lab |
Aluru Lab
|
| Street address |
45 Water Street
|
| City |
Woods Hole |
| State/province |
MA |
| ZIP/Postal code |
02543 |
| Country |
USA |
| |
|
| Platform ID |
GPL7724 |
| Series (2) |
| GSE38839 |
MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [agilent and exiqon array data] |
| GSE39809 |
MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos |
|
