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Sample GSM2282072 Query DataSets for GSM2282072
Status Public on May 01, 2017
Title vehicle (PBS) aspiration 4days + 24h UT1
Sample type RNA
 
Source name UT1
Organism Mus musculus
Characteristics exposure: Untreated
exposure method: inhalation
time: 4d + 24h
Treatment protocol mice lung tissue samples collected 24h after final exposure. Tissue samples stored in RNAlater in -80ºC
Growth protocol Female C57BL/6 mice (7-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.
Extracted molecule total RNA
Extraction protocol RNA isolation from the lung samples was done with TRIsure (phenol-chloroform extraction) and the quantity and purity was determined by NanoDrop spectrophotometer. Further quality check of the total RNA was performed with the Agilent BioAnalyzer, according to the manufacturer's recommendations.
Label Cy3
Label protocol Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.
 
Hybridization protocol Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays, , according to the manufacturer's recommendations.
Scan protocol Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.
Data processing Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.
 
Submission date Aug 16, 2016
Last update date May 01, 2017
Contact name Dario Greco
E-mail(s) dario.greco@tuni.fi
Organization name Tampere University
Department Faculty of Medicine and Health Technology
Lab Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
Street address Arvo ylpön Katu 34
City Tampere
ZIP/Postal code 33520
Country Finland
 
Platform ID GPL13912
Series (1)
GSE85711 Inhalation and oropharyngeal aspiration exposure to rod-like carbon nanotubes induces highly similar airway inflammation and biological pathways in mouse lungs

Data table header descriptions
ID_REF
VALUE Log2 transformation and quantile normalization

Data table
ID_REF VALUE
1 14.4609557395084
2 5.44312665989574
3 5.52380840375981
4 5.49758843630589
5 6.34369490240927
6 5.66150317661839
7 6.08078125490293
8 11.1266041479405
9 5.81923799831414
10 5.91407534221377
11 6.21754898919956
12 5.57162941226238
13 7.91708350960489
14 12.0106390937524
15 6.18029304824719
16 5.78364953550185
17 10.2442691249514
18 7.34167165168409
19 10.873912687269
20 12.7171536282164

Total number of rows: 62976

Table truncated, full table size 1398 Kbytes.




Supplementary file Size Download File type/resource
GSM2282072_Pool5+Pool6_US23502401_252800516533_S01_GE2_1100_Jul11_1_3.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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