Comment[ArrayExpressAccession]	E-GEOD-58828
MAGE-TAB Version	1.1				
Public Release Date	2014-06-26
Investigation Title	Human gastric mucosa: 3 paired hTERT-negative para cancerous tissue (Control) vs. hTERT-positive gastric cancer tissue				
Comment[Submitted Name]	Human gastric mucosa: 3 paired hTERT-negative para cancerous tissue (Control) vs. hTERT-positive gastric cancer tissue
Experiment Description	The lncRNA expression profiles in three pairs of hTERT-positive gastric cancer tissue sand hTERT-negative para-cancerous tissues. The para-cancerous tissue is at least 5cm away from the cancer tissue. The expression of hTERT of identified by immunohistochemistry before RNA extraction for lncRNA assay. LncRNAs/mRNAs in 3 gastric cancer tissue and 3 paired para-cancerous tissue (Control) by microarray using Arraystar Human LncRNA Microarray v2.0				
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	Lv	Shiming	LM-CM-<		
Person First Name	Muhan	Y	M		
Person Mid Initials			H		
Person Email	2394412@SINA.COM				
Person Affiliation	Southwest Hospital of Third Military Medical University				
Person Address	Southwest Hospital of Third Military Medical University, No.30 Gaotanyan Street, Shapingba District, Chongqing, China				
Person Roles	submitter				
Protocol Name	P-GSE58828-1	P-GSE58828-3	P-GSE58828-4	P-GSE58828-2	P-GSE58828-5
Protocol Description	Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (M-bM-^@M-^\All Targets ValueM-bM-^@M-^]) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method. Differentially expressed lncRNAs/mRNAs were identified as those with fold change >= 2; p <= 0.05 ID_REF =  VALUE = Normalized signal intensity	Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy Mini Kit (Qiagen p/n 74104). The concentration and specific activity of the labeled cRNAs (pmol Cy3/M-NM-<g cRNA) were measured by NanoDrop ND-1000 Spectrophotometer.	1 M-NM-<g of each labeled cRNA was fragmented by adding 11 M-NM-<l 10 M-CM-^W Blocking Agent and 2.2 M-NM-<l of 25 M-CM-^W Fragmentation Buffer, then heated the mixture at 60 M-0C for 30 min, finally 55 M-NM-<l 2 M-CM-^W GE Hybridization buffer was added to dilute the labeled cRNA. 100 M-NM-<l of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65M-0C in an Agilent Hybridization Oven.	RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturerM-bM-^@M-^Ys protocol. Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.	Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	TISSUE CANCER STATUS	SEX			
Experimental Factor Type	tissue cancer status	sex			
Comment[SecondaryAccession]	GSE58828				
Comment[GEOReleaseDate]	2014-06-26				
Comment[ArrayExpressSubmissionDate]	2014-06-25				
Comment[GEOLastUpdateDate]	2014-06-26				
Comment[AEExperimentType]	transcription profiling by array				
SDRF File	E-GEOD-58828.sdrf.txt