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Sample GSM2079475 Query DataSets for GSM2079475
Status Public on Mar 03, 2016
Title DU145-shHIC1
Sample type RNA
Source name DU145-shHIC1
Organism Homo sapiens
Characteristics cell line: DU145
treatment: HIC1 silencing
Growth protocol C4-2B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (Invitrogen Corp, Carlsbad, CA). DU145 cells was cultured in DMEM medium with 10% FBS.
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using Trizol (Invitrogen) following the manufacturer's recommendations. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) 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 was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression Microarrays (G2505C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan slides immediately to minimize the impact of environmental oxidants on signal intensities..
Scan protocol Slides were scanned immediately after washing on the Agilent Human Gene Expression Microarrays (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% (Hi) and 10% (Lo)).
Data processing The scanned images were analyzed with Agilent Feature Extraction (FE) software using default parameters and set FE Project Properties to export data to txt.
Submission date Mar 02, 2016
Last update date Apr 23, 2018
Contact name Mingang Hao
Organization name Shanghai Jiao Tong University School of Medicine
Department Department of Biochemistry and Molecular & Cell Biology
Street address NO. 280 South Chongqing Road
City Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL17077
Series (1)
GSE78850 Gene expression in human prostate cancer (PCa) cell lines upon HIC1 silencing
Reanalyzed by GSE113533

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P117082 12.622932
A_33_P3246448 1.9712443
A_33_P3318220 1.967277
A_33_P3236322 1.964198
A_33_P3319925 3.8031275
A_21_P0000509 13.130297
A_21_P0000744 11.178336
A_24_P215804 7.8378553
A_23_P110167 1.986429
A_33_P3211513 8.734803
A_23_P103349 2.150767
A_32_P61480 3.8258138
A_33_P3788124 1.9358476
A_33_P3414202 5.9397087
A_33_P3316686 8.469139
A_33_P3300975 10.371601
A_33_P3263061 11.847273
A_33_P3261373 1.9196026
A_24_P278460 10.82588
A_21_P0013109 1.9128041

Total number of rows: 50737

Table truncated, full table size 1147 Kbytes.

Supplementary file Size Download File type/resource
GSM2079475_DU145-shHIC1.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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