Comment[ArrayExpressAccession]	E-GEOD-78867
MAGE-TAB Version	1.1						
Public Release Date	2016-03-15
Investigation Title	The anti-tumor core molecular targets of TSA in cholangiocarcinoma						
Comment[Submitted Name]	The anti-tumor core molecular targets of TSA in cholangiocarcinoma
Experiment Description	Firstly our study demonstrated that TSA can inhibits cell proliferation, induces cell apoptosis and cell cycle arrest in CCA cell lines in vitro. To identify the target transcripts of TSA to suppress CCA tumorigenesis, mRNA expression profiles were determined by microarray analysis. We chose TFK-1 cells treated by TSA in indicated concentration (IC50) 48 hours for the microarray. Then we found out TACC3 was downregulated, and demonstrated that TACC3 was high expression and may played a role as an target of TSA in inhibiting CCA cells proliferation and migration via in vitro and vivo experiments. We chose TFK-1 cells treated by TSA in indicated concentration (IC50) 48 hours as the experiment sample and without TSA as the control sample to do this microarray  analysis for three times. Then regulated genes would be tested to investigate the potential roles in CCA tumorigenesis,						
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	yao	He	Yao				
Person First Name	wei	Junchuang	Wei				
Person Mid Initials	--						
Person Email	373161341@qq.com						
Person Affiliation	Tongji hospital						
Person Address	Tongji hospital, NO.1095 of jiefang stree, wuhan, China						
Person Roles	submitter						
Protocol Name	P-GSE78867-1	P-GSE78867-5	P-GSE78867-6	P-GSE78867-2	P-GSE78867-3	P-GSE78867-4	P-GSE78867-7
Protocol Description	The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained. ID_REF =  VALUE = Normalized signal intensity	Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.	0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.	TFK-1 cells treated by TSA in indicated concentration (IC50) 48 hours as the experiment sample and no TSA as the control sample.	TFK-1 Cells were cultured in RPMI-1640 containing 10% fetal calf serum	RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions	Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE78867						
Comment[GEOReleaseDate]	2016-03-15						
Comment[ArrayExpressSubmissionDate]	2016-03-03						
Comment[GEOLastUpdateDate]	2016-03-18						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-78867.sdrf.txt