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Sample GSM2282065 Query DataSets for GSM2282065
Status Public on May 01, 2017
Title Untreated inhalation control 4 days + 24h UT3
Sample type RNA
 
Source name UT3
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 Cy5
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 14.5921408162454
2 5.66656251430738
3 5.70697645847432
4 5.69730566869396
5 6.25077153950432
6 5.83398446251221
7 6.16047827791846
8 11.3397974258463
9 5.77971028026087
10 5.9253709152008
11 5.9253709152008
12 5.46884825604233
13 8.00117393585146
14 12.160068589768
15 6.30981075877519
16 5.53692195510997
17 10.3856625397384
18 7.47735879175751
19 11.15241236815
20 12.5001606238225

Total number of rows: 62976

Table truncated, full table size 1398 Kbytes.




Supplementary file Size Download File type/resource
GSM2282065_Pool15+Pool16_US23502401_252800516533_S01_GE2_1100_Jul11_2_4.txt.gz 6.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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