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Sample GSM929435 Query DataSets for GSM929435
Status Public on May 02, 2013
Title High Dose Day 28, Sample.18
Sample type RNA
 
Channel 1
Source name Heart tissue, high-dose Printex 90, day 28
Organism Mus musculus
Characteristics strain: C57BL/6
gender: female
tissue: heart
treatment: Printex 90 carbon black nanoparticles
dose: 162 ug
time point: day 28
sampleID: 340
Treatment protocol Female C57BL/6 mice (Taconic, Denmark) were acquired at 5-6 weeks of age and given food (Altromin no 1324; Christian Petersen, Denmark) and water ad libitum. Printex 90 was suspended by sonication in 0.9% NaCl MilliQ water containing 10% v/v acellular bronchial alveolar lavage fluid from C57BL/6 mice. A 40 µl suspension was instilled followed by 150 μl air.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the mirVana Isolation kit (Ambion, Canada).
Label Cy5
Label protocol Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).
 
Channel 2
Source name Universal Mouse Reference RNA
Organism Mus musculus
Characteristics sample type: reference
Extracted molecule total RNA
Extraction protocol Material was purchased as total RNA (Universal Mouse Reference RNA) from Stratagene (CA, USA).
Label Cy3
Label protocol Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).
 
 
Hybridization protocol Agilent Mouse G4852A Microarrays (containing approximately 44,000 probes) were hybridized with 300 ng Cy5-labelled heart RNA and 300 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays. Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.
Scan protocol Arrays were scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 10.7.3.1.
Description Sample.18
Data processing The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities, were normalized using lowess using the transform.madata function in the maanova library in R.
 
Submission date May 09, 2012
Last update date May 02, 2013
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 GPL13912
Series (2)
GSE37887 Cardiac gene expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles (set 2)
GSE37891 Cardiac gene and miRNA expression (random section containing both ventricles) in C57BL/6 mice intratracheally instilled with Printex 90 carbon black nanoparticles

Data table header descriptions
ID_REF
VALUE Lowess-normalized log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
1 null
2 null
3 null
4 0.001678329
5 -0.000135199
6 -0.006251453
7 -0.380899139
8 1.383104742
9 -1.121688832
10 0.172602741
11 0.031165386
12 0.0337947
13 0.158460505
14 0.059732582
15 0.426396649
16 0.018291574
17 0.040093428
18 -0.493819985
19 -0.374894621
20 0.099295342

Total number of rows: 62976

Table truncated, full table size 1096 Kbytes.




Supplementary file Size Download File type/resource
GSM929435_US22502706_252800512930_S01_GE2_1010_Sep10_1_2.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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