|
| Status |
Public on Oct 18, 2010 |
| Title |
Reference_1_Slide 12 |
| Sample type |
RNA |
| |
|
| Source name |
Total RNA, mouse liver, pooled 6 control + 6 BaP treated
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Median liver lobe
gender: Male
age: 27-30 days
strain: B6C3F1
reference: Pooled mouse reference RNA (equal proportions all samples)
rna storage: 6-8 weeks at -80C
time post exposure: 4 h
|
| 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 |
Cy3
|
| Label protocol |
Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).
|
| |
|
| Hybridization protocol |
Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.
|
| Description |
Pool
|
| Data processing |
Data were extracted from scanned images using Agilent Feature Extraction software version 9.5.3.1. Median signal intensities for the 4th and 24hr time points were quantile normalized separately. Technical replicates for Probe level and miRNA level were averaged using the median. Data was flagged if the raw signal intensity was less than the mean plus three standard deviations of the negative controls or if the median of the technical replicates was flagged to be in the background.
Sample Data table header definitions:
Raw is the median signal intensity.
Norm (i.e., VALUE) is the quantile normalized signal intensity of the log2 of the median signal intensity.
Flag indicates whether the raw signal intensity for the spot is within the background (mean plus three standard deviations of the negative controls).
Norm.Collapsed.Probe is the median of the probe technical replicates.
Flag.Probe indicates whether the median of the probe technical replicates was within the background.
Norm.Collapsed.miRNA is the median of the miRNA technical replicates.
Flag.miRNA indicates whether the median of the miRNA technical replicates was within the background.
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| |
|
| 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 |
GPL7732 |
| Series (2) |
| GSE18786 |
MicroRNA expression profiling in adult mouse liver following benzo(a)pyrene (BaP) treatment [Agilent miRNA array] |
| GSE18841 |
Adult mouse liver following benzo(a)pyrene (BaP) treatment: miRNA and mRNa profiling |
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