Comment[ArrayExpressAccession]	E-GEOD-68967
MAGE-TAB Version	1.1					
Public Release Date	2015-05-19
Investigation Title	The rat lncRNA microarray analysis of the 8 samples from control and NNK treatment group					
Comment[Submitted Name]	The rat lncRNA microarray analysis of the 8 samples from control and NNK treatment group
Experiment Description	In order to assess the alteration in lncRNA expression in rat lung carcinogenesis induced by NNK, we determined the lncRNA expression profiles in 3 rat lung tumor samples and matched normal lung tissues and 2 blood samples from the control and NNK treatment group in the 95th week using Arraystar Rat lncRNA Microarray. We induced lung cancer using 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in a rat model and determined the lncRNA expression profiles in lung cancer tissues and rat blood samples.					
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl				
Person Last Name	Wu	Wu	Jiang			
Person First Name	Jianjun	Jianjun	Yiguo			
Person Email	wooland@126.com					
Person Affiliation	Guangzhou Medical University					
Person Address	School of Public Health, Guangzhou Medical University, Xinzao Town, Panyu District, Guangzhou, China					
Person Roles	submitter					
Protocol Name	P-GSE68967-1	P-GSE68967-4	P-GSE68967-5	P-GSE68967-2	P-GSE68967-3	P-GSE68967-6
Protocol Description	Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). After Quantile normalization of the raw data, lncRNAs and mRNAs that at least 1 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable lncRNAs and mRNAs expression pattern among samples. ID_REF =  VALUE = Normalized signal intensity	1 μg of total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies)	The labeled cRNAs were hybridized onto the Rat lncRNA Array (4x44K, ArrayStar)	Three lung tumor tissues and three matched normal lung tissues and two blood samples from the control and NNK treatment group in the 95th week were collected from a rat lung cancer model induced by NNK.	total RNA was extracted using Trizol reagent. The integrity of RNA can be assessed by electrophoresis on a denaturing agarose gel. Intact total RNA run on a denaturing gel will have sharp 28S and 18S rRNA bands (eukaryotic samples). The 28S rRNA band should be approximately twice as intense as the 18S rRNA band. This 2:1 intensity ratio indicates that the RNA is intact.The NanoDrop 1000 was used for accurately measuring RNA concentrations (OD260), protein contamination (ratio of OD260/OD280) and organic compound contamination (ratio of OD260/OD230). We typically ask our customers to provide total RNA with OD260/OD280 ratio higher than 1.8.	After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	organism part					
Experimental Factor Type	organism part					
Comment[SecondaryAccession]	GSE68967					
Comment[GEOReleaseDate]	2015-05-19					
Comment[ArrayExpressSubmissionDate]	2015-05-18					
Comment[GEOLastUpdateDate]	2015-05-19					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-68967.sdrf.txt