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Sample GSM490165 Query DataSets for GSM490165
Status Public on Dec 13, 2010
Title Nano-titanium Lung 9 (miRNA)
Sample type RNA
 
Source name Total RNA enriched with small RNA species from mouse lungs labeled with Cyanine-5 (red)
Organism Mus musculus
Characteristics tissue: part of lung
gender: female
age: 11-13 weeks
strain: C57BL/6
date of exposure: 2008-11-01
exposure: Exposed to 40 mg nanoTiO2/m3 for one hour/day for 11 consecutive days and were sacrificed 5 days following the last exposure.
time post exposure: 5 days
set: Hybridization Block 1
Treatment protocol Briefly, fortyfive time-mated, nulliparous, young adult female mice at GD 3 were housed in cages under controlled environmental conditions with 12 h light–dark cycles. Food and tap water were provided ad libitum. Exposure was performed by whole-body inhalation to 42.4 ± 2.9 (SEM) mg nanoTiO2/m3 or to the filtered air for 1 h/day from GD 8–18. Seventeen of the time-mated mice (“NP3 females” in Hougaard et. al, submitted) that had not conceived, as evidenced by lack of pups and absence of interuterine implantation sites were used in the present study as a group of adult females. Animals were sacrificed by cardiac puncture five days after the last exposure. The lungs and livers were dissected, weighed, and snap frozen. Samples were stored at -80°C until analysis. All procedures complied with EC Directive 86/609/EEC and Danish law regulating experiments on animals (permission 2006/561-1123).
Extracted molecule total RNA
Extraction protocol The mirVana miRNA Isolation Kit (Ambion, Streetsville, ON, Canada) was used to prepare total RNA enriched with small RNA species from randomly selected left lung sections. All RNA samples showing A260/280 ratios between 2.0 and 2.1 were further analysed by Agilent 2100 Bioanalyzer (Agilent Technologies Inc.,) to determine RNA integrity. Only high quality RNA (28S/18S > 1.8) was used for further analysis.
Label Cy3
Label protocol Freshly isolated individual total lung RNA samples from 8 controls and 8 treated groups were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Technologies, Inc.,). Briefly, 100 ng of total RNA was dephosphorylated by incubation with calf intestinal phosphatase at 37ºC for 30 min, denatured using 100 % DMSO at 100ºC for 5 min, then labelled with pCp-Cy3 using T4 ligase by incubation at 16ºC for 1 hour.
 
Hybridization protocol The labelled RNA samples were hybridised to an individual array on 8 x 15K format Agilent mouse miRNA array slides. Hybridizations were performed in SureHyb chambers (Agilent) at 55ºC for 20 hours.
Scan protocol Arrays were washed, scanned at a resolution of 5 m using an Agilent G2505B scanner and data were acquired using Agilent Feature Extraction software version 9.5.3.1.
Description Total RNA enriched with small RNA species
Data processing Non-background subtracted raw data were quantile normalized (Bolstad et al. 2003). Present calls were determined as signals that were greater than 3 trimmed SDs above the trimmed mean of the the (-)3xSLv1 probes on the array. Probes with technical replicates for a miRNA were averaged using the median signal intensity.
 
Submission date Dec 24, 2009
Last update date Dec 13, 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 GPL8824
Series (1)
GSE19487 Lungs of mice exposed to subtoxic doses of nano-titanium dioxide particles by inhalation

Data table header descriptions
ID_REF
VALUE quantile normalized signal
Flag Flag indicates whether the median of the miRNA technical replicates was within the background. (mean plus three standard deviations of the negative controls). 1-yes, 0-no

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 5.681171843 1
mghv-miR-M1-2 6.114896812 0
mghv-miR-M1-3 5.469758401 1
mghv-miR-M1-4 5.561203552 1
mghv-miR-M1-5 5.538339546 1
mghv-miR-M1-6 5.614071707 1
mghv-miR-M1-7-3p 5.824545402 1
mghv-miR-M1-7-5p 5.483812721 1

Total number of rows: 599

Table truncated, full table size 15 Kbytes.




Supplementary file Size Download File type/resource
GSM490165_251911910805_200908111303_S01_miRNA-v1_10_Apr08_1_1.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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