|
| Status |
Public on Oct 18, 2010 |
| Title |
D_D21 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA, mouse liver, BaP exposure
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Median liver lobe
gender: Male
age: 27-30 days
strain: B6C3F1
exposure: 150 mg/kg Benzo(a)pyrene (CAS number 50-32-8)
time post exposure: 4 h
rna storage: <7 days at -80C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA containing the small fraction was isolated from each sample using the miRVana miRNA Isolation Kit (Ambion), Streetsville, ON, Canada). Quality was confirmed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 chips.
|
| Label |
Hy5
|
| Label protocol |
Labelling reactions were performed using Exiqon’s miRCURY LNA miRNA power labelling kit, according to the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
Pooled mouse reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
reference: Pooled total RNA (containing small fraction) derived from 10 mouse tissues
|
| Biomaterial provider |
Ambion, Streetsville, ON, Canada
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Purchased from Ambion
|
| Label |
Hy3
|
| Label protocol |
Labelling reactions were performed using Exiqon’s miRCURY LNA miRNA power labelling kit, according to the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Hy3 and Hy5 labelled samples were cohybridised to Exiqon multi-species miRCURY LNA miRNA array slides (version 11.0), containing ~1700 capture probes covering all human, mouse and rat miRNAs annotated in miRBase 11.0. Hybridisations were performed in SureHyb chambers (Agilent) for 16 h at 56oC and slides were washed according to manufacturer’s instructions.
|
| Scan protocol |
Arrays were scanned at a resolution of 5 um using an Agilent G2505B scanner.
|
| Description |
no additional information
|
| Data processing |
Data were acquired using Agilent Feature Extraction software version 9.5.3.1, using an FE protocol available on-demand from Exiqon. Technical replicates were averaged using the median removing probes flagged as population background outliers. The averaged signal intensities were then quantile normalized. Data was flagged if the averaged signal intensity signal intensity was less than the mean plus three standard deviations of the negative controls (hsa_negative_control_1).
Sample Data table header definitions:
RawHy5 and RawHy3 is the average (over the technical replicates) of the median signal intensities for the Hy5 and Hy3 channels.
NormHy5 and NormHy3 is the quantile normalized signal intensity (log2).
Flag indicates whether the averaged signal intensity included a spot that had a median signal intensity within the background (mean plus three standard deviations of the negative controls).
Ratio (i.e., VALUE) is the log2 of the Ratio Hy3/Hy5.
|
| |
|
| Submission date |
Oct 28, 2009 |
| Last update date |
Oct 18, 2010 |
| Contact name |
Andrew Williams |
| Organization name |
Health Canada
|
| Street address |
50 Columbine
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1A OK9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7723 |
| Series (2) |
| GSE18782 |
MicroRNA expression profiling in adult mouse liver following benzo(a)pyrene (BaP) treatment [Exiqon miRNA array] |
| GSE18841 |
Adult mouse liver following benzo(a)pyrene (BaP) treatment: miRNA and mRNa profiling |
|
