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Sample GSM466106 Query DataSets for GSM466106
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.
 
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

Data table header descriptions
ID_REF
VALUE quantile normalized signal intensity of the log2 of the median signal intensity
Raw.Slide_12_Ref
Flag.Slide_12_Ref
Norm.Collapsed.Probe.Slide_12_Ref
Flag.Probe.Slide_12_Ref
Norm.Collapsed.miRNA.Slide_12_Ref
Flag.miRNA

Data table
ID_REF VALUE Raw.Slide_12_Ref Flag.Slide_12_Ref Norm.Collapsed.Probe.Slide_12_Ref Flag.Probe.Slide_12_Ref Norm.Collapsed.miRNA.Slide_12_Ref Flag.miRNA
1 NULL NULL NULL NULL NULL NULL NULL
2 NULL NULL NULL NULL NULL NULL NULL
3 NULL NULL NULL NULL NULL NULL NULL
4 NULL NULL NULL NULL NULL NULL NULL
5 NULL NULL NULL NULL NULL NULL NULL
6 NULL NULL NULL NULL NULL NULL NULL
7 NULL NULL NULL NULL NULL NULL NULL
8 NULL NULL NULL NULL NULL NULL NULL
9 NULL NULL NULL NULL NULL NULL NULL
10 NULL NULL NULL NULL NULL NULL NULL
11 NULL NULL NULL NULL NULL NULL NULL
12 NULL NULL NULL NULL NULL NULL NULL
13 NULL NULL NULL NULL NULL NULL NULL
14 NULL NULL NULL NULL NULL NULL NULL
15 NULL NULL NULL NULL NULL NULL NULL
16 NULL NULL NULL NULL NULL NULL NULL
17 NULL NULL NULL NULL NULL NULL NULL
18 NULL NULL NULL NULL NULL NULL NULL
19 NULL NULL NULL NULL NULL NULL NULL
20 NULL NULL NULL NULL NULL NULL NULL

Total number of rows: 15744

Table truncated, full table size 717 Kbytes.




Supplementary file Size Download File type/resource
GSM466106.txt.gz 1.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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