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Sample GSM2079831 Query DataSets for GSM2079831
Status Public on Mar 15, 2016
Title TFK-1 cell-TSA-rep3
Sample type RNA
Source name TFK-1 cell, TSA, replicate 3
Organism Homo sapiens
Characteristics cell line: TFK-1
cell type: cholangiocarcinoma
Treatment protocol TFK-1 cells treated by TSA in indicated concentration (IC50) 48 hours as the experiment sample and no TSA as the control sample.
Growth protocol TFK-1 Cells were cultured in RPMI-1640 containing 10% fetal calf serum
Extracted molecule total RNA
Extraction protocol RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions
Label Cy3
Label protocol 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.
Hybridization protocol 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.
Scan protocol 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%).
Description Gene expression after TSA treated in TFK-1 cell
Data processing The scanned images were analyzed with Feature Extraction Software (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.
Submission date Mar 03, 2016
Last update date Apr 23, 2018
Contact name wei -- yao
Organization name Tongji hospital
Street address NO.1095 of jiefang stree
City wuhan
ZIP/Postal code 430030
Country China
Platform ID GPL17077
Series (1)
GSE78867 The anti-tumor core molecular targets of TSA in cholangiocarcinoma
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 15.210948
DarkCorner 2.4358058
A_23_P117082 11.764556
A_33_P3246448 2.0895092
A_33_P3318220 2.084858
A_33_P3236322 2.0776696
A_33_P3319925 4.186537
A_21_P0000509 15.281875
A_21_P0000744 7.7164097
A_24_P215804 3.4443703
A_23_P110167 10.326773
A_33_P3211513 5.6874566
A_23_P103349 1.1077538
A_32_P61480 2.0260255
A_33_P3788124 2.0205894
A_33_P3414202 4.6677294
A_33_P3316686 6.5040703
A_33_P3300975 7.157399
A_33_P3263061 9.647333
A_33_P3261373 1.9726422

Total number of rows: 50739

Table truncated, full table size 1152 Kbytes.

Supplementary file Size Download File type/resource
GSM2079831_A3.txt.gz 6.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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