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Sample GSM2338005 Query DataSets for GSM2338005
Status Public on Aug 21, 2017
Title Patient1_HGIN
Sample type RNA
Source name gastroscopic biopsy, patient1, HGIN
Organism Homo sapiens
Characteristics individual: Patient 1
tissue: gastroscopic biopsy
age: 45
gender: Male
pathological stage: high-grade intraepithelial neoplasia (HGIN)
Extracted molecule total RNA
Extraction protocol RNA was extracted using an RNeasy Mini Kit (Qiagen, MD, United States) following the manufacturers instructions. RNA concentration and integrity were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, USA) and an Agilent 2100 Bioanalyser (Agilent, CA, United States), respectively.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen, MD, United States). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 600 ng 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 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 SurePrint G3 Human GE 8x60K Microarray (G4851B) 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).
Scan protocol Slides were scanned immediately after washing on Agilent SureScan Microarray Scanner (G2600D) using default settings for 8x60k array slides.
Description Gene expression after gastroscopic biopsy
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol: GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalized signal intensity using GeneSpring GX v12.6.1 (Silicon Genetics, CA, USA) by its default settings.
Submission date Oct 05, 2016
Last update date Aug 21, 2017
Contact name li cheng Zhang
Organization name National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College
Street address No. 17 Panjiayuan Nanli, Chaoyang District
City Beijing
State/province Beijing
ZIP/Postal code 100021
Country China
Platform ID GPL17077
Series (1)
GSE87666 Gene expression profiling of human gastric tissues at different pathological stages

Data table header descriptions
VALUE Normalized signal intensity using GeneSpring GX v12.6.1 (Silicon Genetics, CA, USA) by its default settings.

Data table
A_23_P117082 -1.9730923
A_33_P3246448 -2.06064
A_33_P3318220 0.6941986
A_33_P3236322 1.0243399
A_33_P3319925 0.6737189
A_21_P0000509 -0.9665866
A_21_P0000744 -2.11384
A_24_P215804 0.10175657
A_23_P110167 0.07532263
A_33_P3211513 0.10658479
A_23_P103349 1.0068178
A_32_P61480 0.24686861
A_33_P3788124 0.8684621
A_33_P3414202 -0.031793356
A_33_P3316686 -0.72736835
A_33_P3300975 -2.9225116
A_33_P3263061 -0.6721587
A_33_P3261373 2.271366
A_24_P278460 0.4558127
A_21_P0013109 1.5717402

Total number of rows: 50656

Table truncated, full table size 1196 Kbytes.

Supplementary file Size Download File type/resource
GSM2338005_P1H.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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