|
| 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 |
| E-mail(s) |
zhangyajing932011@163.com
|
| 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 |
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