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Sample GSM465964 Query DataSets for GSM465964
Status Public on Oct 18, 2010
Title C_D06
Sample type RNA
 
Channel 1
Source name Total RNA, mouse liver
Organism Mus musculus
Characteristics tissue: Median liver lobe
gender: Male
age: 27-30 days
strain: B6C3F1
exposure: 0 mg/kg BaP
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

Data table header descriptions
ID_REF
VALUE log2 (Hy3/Hy5) ratio
RawHy5.814
RawHy3.814
Flag.814
NormHy5.814
NormHy3.814

Data table
ID_REF VALUE RawHy5.814 RawHy3.814 Flag.814 NormHy5.814 NormHy3.814
-1 NULL NULL NULL NULL NULL NULL
1100 NULL NULL NULL NULL NULL NULL
3320 NULL NULL NULL NULL NULL NULL
3980 NULL NULL NULL NULL NULL NULL
4040 NULL NULL NULL NULL NULL NULL
4390 NULL NULL NULL NULL NULL NULL
4610 NULL NULL NULL NULL NULL NULL
4700 NULL NULL NULL NULL NULL NULL
5250 NULL NULL NULL NULL NULL NULL
5560 NULL NULL NULL NULL NULL NULL
5730 NULL NULL NULL NULL NULL NULL
5740 NULL NULL NULL NULL NULL NULL
6880 NULL NULL NULL NULL NULL NULL
9578 NULL NULL NULL NULL NULL NULL
9938 NULL NULL NULL NULL NULL NULL
10138 NULL NULL NULL NULL NULL NULL
10306 NULL NULL NULL NULL NULL NULL
10482 NULL NULL NULL NULL NULL NULL
10618 NULL NULL NULL NULL NULL NULL
10899 -0.749892134 10375.5 11193.25 0 13.77056337 13.02067124

Total number of rows: 2001

Table truncated, full table size 74 Kbytes.




Supplementary file Size Download File type/resource
GSM465964.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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