Comment[ArrayExpressAccession]	E-GEOD-51401
MAGE-TAB Version	1.1						
Public Release Date	2013-10-19
Investigation Title	Expression data from tumor-associated endothelial cells of hepatocellular carcinoma						
Comment[Submitted Name]	Expression data from tumor-associated endothelial cells of hepatocellular carcinoma
Experiment Description	Primary uncultured CD31+ and CD105+ tumor endothelial cells (TEC), non-tumor endothelial cells (NEC) ,remnant cells from tumor (TC) and non-tumor liver tissue (NTC)of HCC tissues from patientswere isolated by magnetic-activated cell sorting. Affymetrix Human Gene ST Arrays were used to determine gene expression profiles of HCC cells and matched TEC and NEC cells. We use the gene expression profiling of the Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) to identify distinct genes of TEC and NEC. Patient specimens were collected immediately after removal from patients with pathologically proven HCC and positive alpha-fetoprotein (AFP), then washed 3 times by phosphate buffer solution (PBS). Single cell suspension was obtained from separated tumor and non-tumor liver tissues of surgical specimens following the protocol (http://www.miltenyibiotec.com), then CD31+ cells or CD105+ cells were isolated using CD31 antibody or CD105 antibody conjugated magnetic beads in autoMACSpro (Meltenyi biotec).After the sample preparation, the gene expression profiling was performed using the Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA) according to manufacturerM-bM-^@M-^Ys protocols at ShanghaiBio Corporation (Shanghai, China).						
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	Kong	Sun	Wang				
Person First Name	ling-qun	Hui-Chuan	Xin-Wei				
Person Email	konglingqun2008@gmail.com						
Person Affiliation	Zhongshan hospital affiliated to fudan university						
Person Address	Zhongshan hospital affiliated to fudan university, 180# Fenglin Road, Shanghai, shanghai, China						
Person Roles	submitter						
Protocol Name	P-GSE51401-1	P-GSE51401-5	P-GSE51401-6	P-GSE51401-2	P-GSE51401-3	P-GSE51401-4	P-GSE51401-7
Protocol Description	Slides were  Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). ID_REF =  VALUE = MAS 5.0	Total RNA were amplified, labeled and purified by using GeneChip 3M-bM-^@M-^YIVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturerM-bM-^@M-^Ys instructions to obtain biotin labeled cRNA.	Array hybridization and wash was performed using GeneChipM-. Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00M-bM-^@M-^P0331M-bM-^@M-^P220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00M-bM-^@M-^P0079, Affymetrix, Santa Clara, CA, US) followed the manufacturerM-bM-^@M-^Ys instructions	Single cell suspension was obtained from separated tumor and non-tumor liver tissues of surgical specimens following the protocol (http://www.miltenyibiotec.com), then CD31+ cells or CD105+ cells were isolated using CD31 antibody or CD105 antibody conjugated magnetic beads in autoMACSpro (Meltenyi biotec).	Patient specimens were collected immediately after removal from patients with pathologically proven HCC and positive -fetoprotein (AFP), then washed 3 times by phosphate buffer solution (PBS) ,and then processing into a single cell suspension	Lysis/Binding Bufferextraction of total RNA was performed according to the manufacturer's instructions.	Slides were scanned by GeneChipM-. Scanner 3000 (Cat#00M-bM-^@M-^P00212, Affymetrix, Santa Clara, CA, US)
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GENDER MALE OR FEMALE	AGE YEAR	ORGANISM PART				
Experimental Factor Type	gender male or female	age year	organism part				
Comment[SecondaryAccession]	GSE51401						
Comment[GEOReleaseDate]	2013-10-19						
Comment[ArrayExpressSubmissionDate]	2013-10-18						
Comment[GEOLastUpdateDate]	2013-10-25						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-51401.sdrf.txt