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| Status |
Public on Feb 01, 2016 |
| Title |
CHB 6 |
| Sample type |
RNA |
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| Source name |
Serum
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| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Chronic hepatitis B (CHB)
gender: Male
age: 54
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| Extracted molecule |
total RNA |
| Extraction protocol |
For serum preparation, peripheral blood was subjected to centrifugation at 400×g for 10 min. The supernatant was transferred into 1.5 ml tubes and centrifuged at 1,800×g for 10 min to remove any remaining cellular debris. Total RNA from 200 μl sera was extracted using mirVana miRNA Isolation Kit (Cat No. AM1560, Ambion/Applied Biosystems, Foster City, CA) according to the manufacturer’s protocol.
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| Label |
FAM
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| Label protocol |
TaqMan Megaplex RT and pre-amplification reactions (Applied Biosystems, Foster City, CA) were performed using equal volumes of input RNA. QPCR on 754 human miRNAs was then conducted in the Applied Biosystems 7900HT Real-Time PCR System using the TaqMan Array Human MicroRNA A+B Cards Set v3.0 (Applied Biosystems, Foster City, CA).
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| Hybridization protocol |
n/a
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| Scan protocol |
n/a
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| Description |
Control
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| Data processing |
Cycle threshold (Ct) values were processed and exported using SDS v2.4 software (Applied Biosystems, Foster City, CA). MiRNAs with Ct>35 across all samples were removed from subsequent analysis. The data from different plates were calibrated as follows: plate A and plate B were calibrated to each other according to the average Ct value of U6 snRNA with four replicates in each plate. Four methods, including NormFinder, geNorm, limma quantile and mean-centering restricted (MCR), were used for data normalization.
Matrix normalized worksheets report normalized signal according to the corresponding normalization methods. Fold Change worksheet reports HCC_average/CHB_average ratios.
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| Submission date |
Feb 06, 2015 |
| Last update date |
Feb 01, 2016 |
| Contact name |
Xue-Jia Lin |
| E-mail(s) |
[email protected]
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| Organization name |
Sun Yat-sen University
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| Street address |
Xin Gang Xi Road 135#
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
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| Platform ID |
GPL16850 |
| Series (1) |
| GSE65708 |
Identification of the serum microRNAs (miRNAs) displaying differential levels between hepatocellular carcinoma (HCC) patients and chronic hepatitis B (CHB) controls |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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