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Sample GSM3754779 Query DataSets for GSM3754779
Status Public on Mar 15, 2020
Title B0344-2: GastricLowGradeIntraepithelialNeoplasia
Sample type RNA
Source name GastricLowGradeIntraepithelialNeoplasia
Organism Homo sapiens
Characteristics tissue: gastric
gender: Male
age: 54
Treatment protocol Biopsy forceps were used to clamp the tissue from the suspected gastric mucosa and adjacent normal gastric mucosa that were at least 5 cm from the lesion location. Gastroscopic biopsy tissues were rapidly immersed in RNA later after being isolated and transferred to a -80° C refrigerator for long-term storage after overnight storage at 4° C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen tissues using the RNeasy Mini Kit (Cat No. 74106, Qiagen, Germany) according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop ND-2000 Spectrophotometer (NanoDrop Technologies, Wilmington, USA), and RNA integrity was evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Label Cy3
Label protocol CTP-cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Agilent, version 6.6) according to manufacturer's instructions, followed by RNeasy column purification (RNeasy Mini kit, QIAGEN). Dye incorporation and cRNA yield and quality were checked by spectrophotometry (Nanodrop ND1000, Labtech) and with the Agilent 2100 Bioanalyser.
Hybridization protocol 600 ng of CTP-Cy3-labelled cRNA (specific activity > 10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µl containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2 x Agilent hybridization buffer were added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v2 8x60K (Agilent) for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief passage in acetonitrile.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides: scan area was 61x21.6 mm, scan resolution 3 µm, dye channel was set to Green, Tiff file dynamic range was 20 bits and Green PMT was set to 100 %.
Description LGIN
Data processing The raw data were normalized using GeneSpring GX software, version 11.5 (Silicon Genetics, Redwood City, CA, USA). The expression value for a particular gene was determined as the median value of all probes mapping to this gene.
Submission date May 07, 2019
Last update date Mar 16, 2020
Contact name Yajing Zhang
Phone 8618800193022
Organization name Peking Union Medical College
Street address no.17 Panjiayuan Nanli
City Beijing
State/province Beijing
ZIP/Postal code 100021
Country China
Platform ID GPL17077
Series (1)
GSE130823 Dissecting Expression Profiles of Gastric Precancerous Lesions and Early Gastric Cancer to Explore Crucial Molecules in Intestinal-type Gastric Cancer Tumorigenesis

Data table header descriptions
VALUE Normalized signal intensity

Data table
GE_BrightCorner 0.04469776
DarkCorner -0.046946764
A_23_P117082 -0.31251144
A_33_P3246448 -0.46964788
A_33_P3318220 -0.063795805
A_33_P3236322 0.4075098
A_33_P3319925 0.34347892
A_21_P0000509 -0.2919817
A_21_P0000744 -1.1416421
A_24_P215804 1.14835
A_23_P110167 0.28605175
A_33_P3211513 -0.031654835
A_23_P103349 -0.055214643
A_32_P61480 -0.06572819
A_33_P3788124 0.8838918
A_33_P3414202 0.13228321
A_33_P3316686 0.12531424
A_33_P3300975 -0.093621254
A_33_P3263061 -0.33946896
A_33_P3261373 -0.21765876

Total number of rows: 50739

Table truncated, full table size 1234 Kbytes.

Supplementary file Size Download File type/resource
GSM3754779_B0344.2.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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