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Sample GSM612732 Query DataSets for GSM612732
Status Public on Oct 19, 2011
Title Sample 17
Sample type RNA
 
Source name liver
Organism Mus musculus
Characteristics tissue: part of liver
gender: male
age: 25 weeks
strain: transgenic mouse strain 40.6
date of exposure: March 2-30
exposure: Exposed to 75 mg/kg Bap
time post exposure: 3 days
Treatment protocol 25-week old male Muta™Mouse (i.e., transgenic mouse strain 40.6) were dosed daily via oral gavage for 28-days with BaP dissolved in olive oil (25, 50 and 75 mg/kg body weight/day) purchased from Sigma-Aldrich (Oakville, ON, Canada). Each dose group contained 5 animals; 5 animals were also dosed with a vehicle (olive oil) control. Following a 3 day expression period after the last treatment, mice were euthanized with isofluorane followed by cervical dislocation. Liver was then excised, flash-frozen in liquid nitrogen, and stored at -80ºC until use.
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 Cyanine 3-pCp
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.
Data processing Data were extracted from scanned images using Agilent Feature Extraction software version 10.7.3.1. Median signal intensities were cyclic lowess normalized. Technical replicates for each 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.
 
Submission date Oct 25, 2010
Last update date Oct 19, 2011
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 GPL8824
Series (2)
GSE24909 Lack of hepatic response of microRNA in mice following chronic benzo(a)pyrene exposure (miRNA)
GSE24910 Lack of hepatic response of microRNA in mice following chronic benzo(a)pyrene exposure

Data table header descriptions
ID_REF
VALUE Cy3 is the median of the miRNA technical replicates of the log2 of the cyclic lowess normalized data
Flag Flag indicates whether the median of the miRNA technical replicates was within the background(mean plus three standard deviations of the negative controls).

Data table
ID_REF VALUE Flag
DarkCorner NULL NULL
dmr_285 NULL NULL
dmr_3 NULL NULL
dmr_308 NULL NULL
dmr_316 NULL NULL
dmr_31a NULL NULL
dmr_6 NULL NULL
hur_1 NULL NULL
hur_2 NULL NULL
hur_4 NULL NULL
hur_5 NULL NULL
hur_6 NULL NULL
mghv-miR-M1-1 5.783172734 1
mghv-miR-M1-2 6.093536077 0
mghv-miR-M1-3 5.683450143 1
mghv-miR-M1-4 5.706897719 1
mghv-miR-M1-5 5.697811655 1
mghv-miR-M1-6 5.7470278 1
mghv-miR-M1-7-3p 5.802848622 1
mghv-miR-M1-7-5p 5.636413254 1

Total number of rows: 605

Table truncated, full table size 15 Kbytes.




Supplementary file Size Download File type/resource
GSM612732.txt.gz 636.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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