Comment[GEAAccession]	E-GEAD-367
MAGE-TAB Version	1.1
Investigation Title	Analysis of gene expression change after TUG1-ASO treatment in BxPC3
Experiment Description	we investigated gene expression change after TUG1-ASO treatment in BxPC3
Experimental Design	compound treatment design
Experimental Factor Name	treatment
Experimental Factor Type	treatment
Person Last Name	tasaki
Person First Name	yoshihiko
Person Affiliation	Cancer Biology, Nagoya University Graduate School of Medicine
Person Roles	submitter
Public Release Date	2021-01-15
Protocol Name	P-GEAD-489	P-GEAD-490	P-GEAD-491	P-GEAD-492	P-GEAD-493	P-GEAD-494
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	BxPC-3 was transfected with 50 nM TUG1-ASO or CTRL-ASO. After fourty-eight hours, we collected samples.	After transfecting, we collected samples. Total RNA was isolated from BxPC-3 cells with TRIzol reagent.	Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 Spectrophotometer.	600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60 degree C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K array slides (G4851B, Agilent Technologies) at 65 degree C with rotation at 10 rpm for 17 hours in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37 degree C GE Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.	Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA, Agilent Technologies) using one color scan setting for 8x60k array slides.	Expression data were centered on a median with the use of the GeneSpring normalisation option with no substantial difference in results.
SDRF File	E-GEAD-367.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEOD-21185
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB9640
Comment[Last Update Date]	2021-01-15