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Sample GSM1217193 Query DataSets for GSM1217193
Status Public on May 15, 2014
Title Parenchyma-med-3R4F 3
Sample type RNA
 
Source name Parenchyma-med-3R4F
Organism Rattus norvegicus
Characteristics gender: male
tissue: Parenchyma
tissue source: Left Lung
treatment: 3R4F
treatment concentration [ug nicotine/l]: 15
treatment duration [days]: 28
daily exposure [hours]: 1
exposure path: nose-only
smoking regimen: Health Canada
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 910091-Paren
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 11.50949553
1367453_at 10.35846897
1367454_at 10.47860783
1367455_at 11.45838088
1367456_at 12.1362434
1367457_at 10.82939036
1367458_at 6.593855809
1367459_at 11.91450117
1367460_at 13.85285269
1367461_at 9.457224304
1367462_at 10.66235263
1367463_at 9.962803231
1367464_at 10.36505128
1367465_at 10.71371309
1367466_at 10.30609385
1367467_at 11.92525273
1367468_at 8.52610666
1367469_at 13.55587195
1367470_at 10.42707493
1367471_at 10.9000189

Total number of rows: 31099

Table truncated, full table size 699 Kbytes.




Supplementary file Size Download File type/resource
GSM1217193_12871_IVT_04_Rat230_2_91E.CEL.gz 2.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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