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Sample GSM1489060 Query DataSets for GSM1489060
Status Public on Aug 20, 2015
Title NRCWE-032.1.54 Sample 49
Sample type RNA
 
Channel 1
Source name Mouse lung tissue, low dose, day 28
Organism Mus musculus
Characteristics sample id: L405
genetic background: C57BL/6
tissue: lung
dose: low dose
time: day 28
treatment: NRCWE-032
Treatment protocol each mouse received 54, 162 or 486 µg of sanding dusts of paint consisting of TiO2NPs or only the vehicle via single intratracheal instillation. Mice were anaesthetised and intratracheally instilled with particle suspensions as described previously (Saber et al 2012, Particle and Fiber Toxicology). Whole lung tissues were collected 24 h and 28 d post exposure, flash frozen in liquid nitrogen and stored at -80°C until the analysis.
Extracted molecule total RNA
Extraction protocol In brief, a small frozen section of lung tissue was homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) using the Retsch Mixer MM 400. RNA was isolated using chloroform, precipitated using isopropyl alcohol and purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada). All RNA showed high integrity with a A260/280 ratio between 2.0 and 2.2 and RNA integrity number above 7.0.
Label Cy5
Label protocol Agilent Linear Amplification Kit (Agilent Technologies Inc., Mississauga, ON, Canada) was used to synthesize cDNA and labelled cRNA from 200 ng of total RNA derived from each individual mouse lungs and commercially available Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada). Cyanine-labelled cRNA was in vitro transcribed using T7 RNA polymerase and purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada). Experimental samples were labelled with Cyanine-5 and the UMRR was labelled with Cyanine-3.
 
Channel 2
Source name Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)
Organism Mus musculus
Characteristics sample type: Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada)
Treatment protocol each mouse received 54, 162 or 486 µg of sanding dusts of paint consisting of TiO2NPs or only the vehicle via single intratracheal instillation. Mice were anaesthetised and intratracheally instilled with particle suspensions as described previously (Saber et al 2012, Particle and Fiber Toxicology). Whole lung tissues were collected 24 h and 28 d post exposure, flash frozen in liquid nitrogen and stored at -80°C until the analysis.
Extracted molecule total RNA
Extraction protocol In brief, a small frozen section of lung tissue was homogenized in Trizol (Invitrogen, Carlsbad, CA, USA) using the Retsch Mixer MM 400. RNA was isolated using chloroform, precipitated using isopropyl alcohol and purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada). All RNA showed high integrity with a A260/280 ratio between 2.0 and 2.2 and RNA integrity number above 7.0.
Label Cy3
Label protocol Agilent Linear Amplification Kit (Agilent Technologies Inc., Mississauga, ON, Canada) was used to synthesize cDNA and labelled cRNA from 200 ng of total RNA derived from each individual mouse lungs and commercially available Universal Mouse Reference RNA (UMRR, Stratagene, Mississauga, ON, Canada). Cyanine-labelled cRNA was in vitro transcribed using T7 RNA polymerase and purified using RNeasy Mini Kits (Qiagen, Mississauga, ON, Canada). Experimental samples were labelled with Cyanine-5 and the UMRR was labelled with Cyanine-3.
 
 
Hybridization protocol Equal amount (300 ng) of labelled cRNA from each experimental sample was hybridized to Agilent Sureprint G3 Mouse GE 4x44K microarrays (agilent Technologies Inc., Mississuaga, ON, Canada) at 65°C for 17 hours in the Agilent SureHyb Hybridization chamber.
Scan protocol Scanned on an Agilent G2565AA scanner.
Data processing Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.
 
Submission date Aug 26, 2014
Last update date Aug 20, 2015
Contact name Andrew Williams
Organization name Health Canada
Street address 50 Colombine Dr
City Ottawa
State/province ON
ZIP/Postal code K1A0K9
Country Canada
 
Platform ID GPL7202
Series (2)
GSE60800 Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 4)
GSE60801 Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3) representing Sample/reference

Data table
ID_REF VALUE
A_51_P100021 0.166898013
A_51_P100034 0.938421086
A_51_P100052 0.078929247
A_51_P100063 0.252412141
A_51_P100084 -0.022014416
A_51_P100099 -0.104359292
A_51_P100155 -0.295984446
A_51_P100174 0.306241024
A_51_P100181 -0.281498865
A_51_P100218 -0.029216651
A_51_P100227 -1.028668916
A_51_P100238 -0.118328221
A_51_P100246 -0.343937822
A_51_P100289 -0.50686532
A_51_P100298 -0.12297363
A_51_P100309 0.182857667
A_51_P100327 -0.338589148
A_51_P100347 0.122650208
A_51_P100379 -0.02060981
A_51_P100428 0.119858621

Total number of rows: 41174

Table truncated, full table size 1022 Kbytes.




Supplementary file Size Download File type/resource
GSM1489060_251486838030_201304251152_S01_GE2_1100_Jul11_1_2.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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