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Sample GSM1217157 Query DataSets for GSM1217157
Status Public on May 15, 2014
Title RNE-sham 2
Sample type RNA
 
Source name RNE-sham
Organism Rattus norvegicus
Characteristics gender: male
tissue: Nasal Cavity Respiratory Epithelium
tissue source: Nose
treatment: fresh air
treatment concentration [ug nicotine/l]: 0
treatment duration [days]: 28
daily exposure [hours]: 1
exposure path: nose-only
smoking regimen: --
Treatment protocol Animals were exposed to mainstream smoke smoke through nose-only inhalation for 28 days with varying doses (0, 8, 15, 23 ug nicotine/l) and different tobacco products (pMRTP and 3R4F).
Growth protocol na
Extracted molecule total RNA
Extraction protocol Whole tissue for nasal epithelia or laser microdissected (LCM) tissue for bronchi and lung parenchyma was used to extract total RNA using miRNAeasy Mini Kit (Qiagen).
Label biotin
Label protocol GeneChip(R) 3’ IVT Express Kit (Affymetrix, Santa Clara, USA) with 100 ng RNA.
 
Hybridization protocol The biotin-labeled RNA was hybridized on Affymetrix Rat230_2 microarrays. The wash and stain procedures were performed according to Affymetrix protocols (GeneChip(R) Expression Wash, Stain and ScanUser Manual, Affymetrix).
Scan protocol Cartridges were scanned using the GeneChip Scanner 3000 (Affymetrix). Scanned image files were visually inspected for artifacts and the generated Cel files was used as input for data analysis. The Affymetrix Command Console Software (AGCC, Affymetrix, Santa Clara, CA) was used to control the fluidics station and the scanner.
Description 910090-RNE
Data processing Data processing was implemented in the R statistical environment. Raw RNA expression data was analyzed using the affy and gcrma packages of the Bioconductor suite of microarray analysis tools available in the R statistical environment. GC Robust Microarray Analysis (GCRMA) (including background correction and quantile normalization) was used to generate probe set expression values.
 
Submission date Aug 27, 2013
Last update date May 15, 2014
Contact name Sam Ansari
E-mail(s) sam.ansari@pmi.com
Organization name Philip Morris Products SA
Department Research & Development
Lab Biological Systems Research
Street address Quai Jeanrenaud 5
City Neuchatel
State/province Neuchatel
ZIP/Postal code 2000
Country Switzerland
 
Platform ID GPL1355
Series (1)
GSE50254 Integration of toxicological end points with molecular measurements in a 28-day rat repeated dose inhalation study with cigarette smoke provides mechanistic understanding of smoke impact

Data table header descriptions
ID_REF
VALUE GCRMA normalized intensity (log2)

Data table
ID_REF VALUE
1367452_at 12.77633562
1367453_at 9.76739081
1367454_at 10.99763096
1367455_at 12.14549074
1367456_at 11.951709
1367457_at 11.23537497
1367458_at 7.401019264
1367459_at 12.7176271
1367460_at 12.9185396
1367461_at 10.78681617
1367462_at 10.40762839
1367463_at 11.21687132
1367464_at 10.57688798
1367465_at 12.17452448
1367466_at 10.52241284
1367467_at 11.91211116
1367468_at 9.096753106
1367469_at 13.79842813
1367470_at 10.7581294
1367471_at 10.51186531

Total number of rows: 31099

Table truncated, full table size 699 Kbytes.




Supplementary file Size Download File type/resource
GSM1217157_12871_IVT03.2_Rat230_2_90A.CEL.gz 2.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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