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Sample GSM1488824 Query DataSets for GSM1488824
Status Public on Aug 20, 2015
Title Indoor-R 28d-L3
Sample type RNA
 
Channel 1
Source name Mouse lung tissue, 54 ug, day 28
Organism Mus musculus
Characteristics genetic background: C57BL/6
tissue: lung
treatment: Indoor-R
time: 28d
Treatment protocol Each mouse received 54, 162 or 486 µg of sanding dusts of paints 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 paints 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)
GSE60797 Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 1)
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 0.18608387
A_51_P100034 1.079516189
A_51_P100052 -0.01191016
A_51_P100063 0.532125815
A_51_P100084 -0.226665854
A_51_P100099 -0.197772467
A_51_P100155 -0.454020784
A_51_P100174 -0.01405436
A_51_P100181 -0.358523535
A_51_P100218 0.159394141
A_51_P100227 -1.311135973
A_51_P100238 -0.02775881
A_51_P100246 -0.833800415
A_51_P100289 0.017431954
A_51_P100298 -0.046881001
A_51_P100309 0.094068103
A_51_P100327 0.002714815
A_51_P100347 -0.19304444
A_51_P100379 -0.107246757
A_51_P100428 -0.073438069

Total number of rows: 41174

Table truncated, full table size 1022 Kbytes.




Supplementary file Size Download File type/resource
GSM1488824_251486831194_201303211114_S01_GE2_1100_Jul11_1_3.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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