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Sample GSM2251207 Query DataSets for GSM2251207
Status Public on Jul 26, 2016
Title Tumor sample obtained from patient 4
Sample type RNA
Source name Tumor sample obtained from patient 4
Organism Homo sapiens
Characteristics cancer status: tumor sample
tissue: stomach
gender: male
Treatment protocol All clinical samples were quickly stored in liquid nitrogen after surgical resection.
Growth protocol All cancer samples and paired normal samples obtained from GC patients with primary GC from Zhongshan hospital, Fudan University.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cancer cells using TRIzol Reagent (Invitrogen, Shanghai, China), and cDNA was synthesized using a PrimeScript RT reagent kit (Takara, Kusatsu, Shiga, Japan).
Label Cy3
Label protocol The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using a Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).
Hybridization protocol 1.5 ug of Cy3-labelled cDNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human Gene Expression 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 (G2505B).
Description lncRNA expression
Data processing Feature Extraction software (version, Agilent Technologies) was used to analyze array images to obtain raw data. GeneSpring software (version 12.5, Agilent Technologies) was employed to finish the basic analysis of the raw data. Initially, the raw data were normalized using the quantile algorithm. The probes with at least 100 percent of samples in any 1 condition out of 2 conditions having flags that indicate “Detected” were chosen for further data analysis. Differentially expressed lncRNAs were then identified through fold change, and p values were calculated using t-tests. The thresholds set for up- and down-regulated genes were a fold change ≥ 2.0 and a p value ≤ 0.05.
Submission date Jul 25, 2016
Last update date Apr 23, 2018
Contact name Jianjun Zhang
Phone 86-13817312207
Organization name Shanghai Jiaotong University
Street address No.639, Zhizaoju road
City Shanghai
State/province Shanghai
ZIP/Postal code 200011
Country China
Platform ID GPL17077
Series (1)
GSE84787 Human gastric cancer_Tumor samples_Paired normal samples_10 replicates
Reanalyzed by GSE113533

Data table header descriptions
VALUE log2 Normalized signal intensity

Data table
GE_BrightCorner 10162.34196
DarkCorner 0.864514349
A_23_P117082 1023.883427
A_33_P3246448 31.41529277
A_33_P3318220 1.031218444
A_33_P3236322 1.47384801
A_33_P3319925 3.706710769
A_21_P0000509 274.5198802
A_21_P0000744 64.9652236
A_24_P215804 7.426030065
A_23_P110167 659.2465229
A_33_P3211513 114.5711555
A_23_P103349 0.829937504
A_32_P61480 1.041064838
A_33_P3788124 1.041108273
A_33_P3414202 61.39965406
A_33_P3316686 128.7434177
A_33_P3300975 105.6624412
A_33_P3263061 479.33286
A_33_P3261373 1.03869669

Total number of rows: 50739

Table truncated, full table size 1259 Kbytes.

Supplementary file Size Download File type/resource
GSM2251207_Tumor_4.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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