|
| Status |
Public on Sep 30, 2015 |
| Title |
distant normal_stage 3_#2 |
| Sample type |
RNA |
| |
|
| Source name |
colorectal distant normal mucosa, stage 3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal distant normal mucosa
histology: Normal mucosa
age: 53
Sex: female
paired_tumor_stage: 3
|
| 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
|
| Label |
Cy5
|
| Label protocol |
5-μg total RNA was used for Cy5-labeled aRNA preparation using a MessageAmp™ aRNA amplification kit (Ambion, Austin, TX).
|
| |
|
| Hybridization protocol |
Chips with labeled samples were hybridized at 50°C for overnight in a heat-shrunk hybridization bag (Phalanx), and then washed successively with 2×SSPE/0.2% SDS at 42°C for 5 min, 2×SSC at 42°C for 5 min, 2×SSC at room temperature for 5 min and 0.2×SSC at room temperature for 15 min.
|
| 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).
|
| Description |
matched distant normal mucosa come from the same patient marked with identical sample name(I,II,III and IV stands for TNM stage 1,2,3 and 4,respectively, ca stands for tumor, n stands for normal mucosa);sample name with identical stage and number represent the same patient(for example, I-n-2 and I-ca-2 represent the normal mucosa and tumor from patient #2 of stage I,respectively).
|
| Data processing |
The repeatability of the microarray within each class ( normal, stageI,II,II and IV) 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 > 0 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
|
| Organization name |
Xiangya third hospital
|
| Department |
department of gastroenterology
|
| Lab |
Provincial key lab of non-resolving inflammation and cancer
|
| Street address |
Yuelu district, Tongzipo road #138
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410013 |
| Country |
China |
| |
|
| Platform ID |
GPL6254 |
| Series (2) |
| GSE41011 |
Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer (gene expression) |
| GSE41015 |
Dynamic Transcriptome Analysis Reveal New Prognosis Biomarker in Colorectal Cancer |
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