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Sample GSM1488958 Query DataSets for GSM1488958
Status Public on Aug 20, 2015
Title NRCWE-030.28.54 Sample 40
Sample type RNA
 
Channel 1
Source name Mouse lung tisue, middle dose, day28
Organism Mus musculus
Characteristics sample id: 99
genetic background: C57BL/6
tissue: lung
dose: middle dose
time: day28
treatment: NRCWE-030
Treatment protocol each mouse received 18, 54, or 162 µg 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 18, 54, or 162 µg 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)
GSE60799 Transcriptional profiling to identify physical-chemical properties detrimental to nanomaterial-induced pulmonary response (part 3)
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_52_P616356 -0.004555998
A_52_P403405 0.02947284
A_52_P819156 -0.168697453
A_51_P331831 0.90677078
A_51_P430630 0.11428851
A_52_P502357 -0.169495429
A_52_P299964 0.044591244
A_51_P356389 0.167147164
A_52_P684402 -1.335004609
A_51_P414208 -0.019761758
A_51_P280918 -0.069528658
A_52_P613688 0.059661284
A_52_P258194 -0.729846842
A_52_P229271 -0.107623943
A_52_P579519 -0.722322081
A_52_P979997 -0.001229199
A_52_P453864 0.752149591
A_52_P655842 0.030511973
A_51_P282374 -0.11706159
A_52_P176013 -0.045742901

Total number of rows: 41174

Table truncated, full table size 1020 Kbytes.




Supplementary file Size Download File type/resource
GSM1488958_251486837700_201301300922_S01_GE2_1100_Jul11_1_1.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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