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Sample GSM2338008 Query DataSets for GSM2338008
Status Public on Aug 21, 2017
Title Patient3_LGIN
Sample type RNA
 
Source name gastroscopic biopsy, patient3, LGIN
Organism Homo sapiens
Characteristics individual: Patient 3
tissue: gastroscopic biopsy
age: 60
gender: Male
pathological stage: low-grade intraepithelial neoplasia (LGIN)
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 10.5.1.1 (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
E-mail(s) zhang.chengli@163.com
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
ID_REF
VALUE Normalized signal intensity using GeneSpring GX v12.6.1 (Silicon Genetics, CA, USA) by its default settings.

Data table
ID_REF VALUE
A_23_P117082 -0.42105365
A_33_P3246448 1.7310529
A_33_P3318220 1.5609372
A_33_P3236322 0.6925297
A_33_P3319925 0.7117555
A_21_P0000509 1.972681
A_21_P0000744 -1.2454424
A_24_P215804 0.97034407
A_23_P110167 0.48860073
A_33_P3211513 0.5016391
A_23_P103349 1.5381479
A_32_P61480 1.115299
A_33_P3788124 1.2011788
A_33_P3414202 0.23973393
A_33_P3316686 0.87779427
A_33_P3300975 -0.1304729
A_33_P3263061 0.069169044
A_33_P3261373 1.5195279
A_24_P278460 -1.3713152
A_21_P0013109 1.0642989

Total number of rows: 50656

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM2338008_P3L.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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