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Status |
Public on Sep 30, 2015 |
Title |
primary tumor_stage 3_#3 |
Sample type |
RNA |
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Source name |
colorectal primary tumor, stage 3
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Organism |
Homo sapiens |
Characteristics |
tissue: colorectal primary tumor histology: G1,Well differentiated age: 65 Sex: Female Stage: 3
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Extracted molecule |
total RNA |
Extraction protocol |
On average, 100-150mg of flash frozen sample tissue were prepared for the extraction of total RNA. TRIZOL Reagent (Invitrogen ) were used to extract total RNA according to manufacturer's protocol
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Label |
Cy5
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Label protocol |
1 μg total RNA was labeled using a miRCURY LNA™ microRNA Hy3/Hy5 power labeling kit (Exiqon).
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Hybridization protocol |
Chips with labeled samples were hybridized at 56°C for overnight in a heat-shrunk hybridization bag (Phalanx), and then washed using a miRCURY LNA™ washing buffer kit (Exiqon).
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Scan protocol |
Slides were scanned using a Genepix 4000B laser scanner (Axon, New York) and fluorescent intensities were extracted from the generated images by Genepix Pro 6.0 software (Axon).
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Data processing |
The repeatability of the microarray within each class ( normal, stage1,2,3 and 4) were examined by correlation analysis. Only those data with over 50% of intra-class correlation coefficient greater than 0.8 were selected for further analysis(Chen et al., 2007). Data filter: > 50% of the arrays and gene signal > 50 were selected. Normalization was done using per chip median normalization and median array method(Liu et al.,2004) .RVM F-test was applied to screen the dynamic differentially expressed miRNA for the normal and different TNM group(Wright et al., 2003).
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Submission date |
Sep 19, 2012 |
Last update date |
Sep 30, 2015 |
Contact name |
xiayu li |
E-mail(s) |
lixiayu@163.com
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Organization name |
Xiangya third hospital
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Department |
department of gastroenterology
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Lab |
Provincial key lab of non-resolving inflammation and cancer
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Street address |
Yuelu district, Tongzipo road #138
|
City |
Changsha |
State/province |
Hunan |
ZIP/Postal code |
410013 |
Country |
China |
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Platform ID |
GPL7724 |
Series (2) |
GSE41012 |
Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer (miRNA) |
GSE41015 |
Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer |
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