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Sample GSM1281575 Query DataSets for GSM1281575
Status Public on Jan 01, 2014
Title sh1_shTEAD4
Sample type RNA
Source name LoVo_sh1_shTEAD4
Organism Homo sapiens
Characteristics cell type: LoVo colorectal cancer cells
genotype/variation: expressing sh1_shTEAD4
Growth protocol LoVo stable cells were cultured in the RPMI 1640 medium supplemented with 10% FBS.
Extracted molecule total RNA
Extraction protocol RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's
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 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 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 8x60k 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 of LoVo cells expressing sh1_shTEAD4
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 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
Submission date Dec 06, 2013
Last update date Apr 23, 2018
Contact name Chen-Ying Liu
Organization name Xinhua Hospital, Shanghai Jiao Tong University
Street address 1665 Kong Jiang Road
City Shanghai
ZIP/Postal code 200092
Country China
Platform ID GPL17077
Series (1)
GSE53063 Identification of TEAD4 target genes in colorectal cancer cells
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 16.892511
DarkCorner 2.185121
A_23_P117082 13.625191
A_33_P3246448 2.628467
A_33_P3318220 2.236908
A_33_P3236322 2.7826295
A_33_P3319925 4.648586
A_21_P0000509 14.926837
A_21_P0000744 7.7459283
A_24_P215804 7.997424
A_23_P110167 12.740884
A_33_P3211513 8.134479
A_23_P103349 2.1888413
A_32_P61480 2.1922958
A_33_P3788124 2.1889906
A_33_P3414202 8.146927
A_33_P3316686 7.361657
A_33_P3300975 6.1787453
A_33_P3263061 13.209317
A_33_P3261373 2.1664293

Total number of rows: 50739

Table truncated, full table size 1147 Kbytes.

Supplementary file Size Download File type/resource
GSM1281575_sh1.txt.gz 7.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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