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Sample GSM378791 Query DataSets for GSM378791
Status Public on Mar 09, 2010
Title HONE1_rep2
Sample type RNA
 
Source name epithelial biopsies of carcinoma
Organism Homo sapiens
Characteristics tissue: nasopharynx
cell line: HONE1
disease state: carcinoma
Growth protocol The TW01 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS). The HONE1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS. The NP460hTert cells were maintained in culture medium as previously described (H.M. Li et al., 2006).
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted with RNeasy mini kit (Qiagen) according to the manufacturer’s introduction. The integrity of the RNA samples was verified using the RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA, USA).
Label Cy3
Label protocol The Agilent’s low RNA input linear amplification / one-color labeling kit were used for target preparation essentially followed the protocol recommended by Agilent Technologies. Briefly, 1000 ng of total RNA was reverse transcribed into cDNA using the T7 promoter primer. Cyanine 3-dCTP labeled cRNA was synthesized from the cDNA by using the T7 RNA polymerase. To remove unincorporated nucleotides, the labeled cRNA was purified using the RNeasy mini kit (Qiagen).
 
Hybridization protocol Array hybridization was performed in 100 ul of a hybridization mixture containing cRNA probes at 65℃ for 17 hrs.
Scan protocol Slides were scanned immediately after washing on the Agilent G2565BA DNA microarray scanner using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression of HONE1, biological replicate 2 of 2.
Data processing Fluorescence intensities of spots were quantified, background subtracted, and dye normalized by Feature Extraction software, version 8.1.1 (Agilent Technologies). The data were then imported and analyzed using GeneSpring GX (Agilent Technologies) to generate gene lists of differentially expressed (change in expression with fold change > 2).
 
Submission date Mar 10, 2009
Last update date Mar 09, 2010
Contact name Chia Huei Lee
E-mail(s) chlee124@nhri.edu.tw
Organization name Taiwan National Health Research Institute
Department National Institute of Cancer Research
Street address 35, Keyan Rd.
City Zhunan Miaoli County
ZIP/Postal code 114
Country Taiwan
 
Platform ID GPL6480
Series (2)
GSE15170 Expression profiling of nasopharyngeal carcinoma cell lines
GSE15191 Nasopharyngeal carcinoma cell lines TW01 and HONE1: transcriptomic and genomic analyses

Data table header descriptions
ID_REF
VALUE Genespring-processed, normalized log2 signal intensity

Data table
ID_REF VALUE
GE_BrightCorner -1.2358437
DarkCorner -0.090987206
A_24_P66027 0.06253958
A_32_P77178 -1.4513292
A_23_P212522 -0.15308332
A_24_P934473 -0.65224934
A_24_P9671 0.35899734
A_32_P29551 0.022680283
A_24_P801451 0.5023837
A_32_P30710 -0.093342304
A_32_P89523 -0.05073166
A_24_P704878 1.712707
A_32_P86028 0.13475561
A_24_P470079 0.11686611
A_23_P65830 0.067988396
A_23_P109143 -0.115728855
A_24_P595567 -1.7982483
A_24_P391591 -1.2414751
A_24_P799245 -0.3519168
A_24_P932757 -0.3090334

Total number of rows: 41078

Table truncated, full table size 956 Kbytes.




Supplementary file Size Download File type/resource
GSM378791.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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