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| Status |
Public on Oct 16, 2014 |
| Title |
MicroRNA Profiles and Differential Expression in Normal Skin Samples from the Uyghur and Han Populations in Xinjiang |
| Platform organisms |
Homo sapiens; Human alphaherpesvirus 1; Human alphaherpesvirus 2; Cytomegalovirus; Lymphocryptovirus; Rhadinovirus; JC polyomavirus; Human immunodeficiency virus 1; Merkel cell polyomavirus; Betapolyomavirus hominis; Betapolyomavirus macacae |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
This study investigated the microRNA (miRNA) expression profiles in normal skin samples from the Uyghur and Han populations in Xinjiang and analyzed the miRNA expression differences between the two populations. The 7th generation miRCURYTM LNA Array kit (containing 3100 probes) was used to detect the miRNA expression in 10 Uyghur and 10 Han normal skin samples and to compare the miRNA expression differences between the two populations. A total of 2041 miRNAs were present in normal Uyghur and Han skin samples. In particular, 2039 miRNAs were present in normal Uyghur skin, of which 295 miRNAs were expressed more than 2.0-fold and 1461 miRNAs were expressed less than 0.5-fold of the average value. Moreover, 2041 miRNAs were expressed in normal Han skin, of which 279 miRNAs were expressed more than 2.0-fold and 1414 miRNAs were expressed less than 0.5-fold of the average value. Considering both populations together, 228 miRNAs were expressed more than 2.0-fold and 1353 miRNAs were expressed less than 0.5-fold of the average value. In the Han population, 76 miRNAs were upregulated and 171 miRNAs were downregulated compared with the Uyghur population (p < 0.05). A total of 13 miRNAs had fold changes that were greater than 10, and 9 miRNAs had fold changes that were between 3 and 10. The upregulated miRNAs were miR-1, miR-106b-5p, miR-1915-5p, miR-200c-3p, miR-221-3p, miR-222-3p, miR-3139, miR-4802-3p, miR-507, miR-541-3p, miR-876-3p, and kshv-miR-K12-2-5p. The downregulated miRNAs were miR-1207-3p, miR-206, miR-2116-5p, miR-3667-5p, miR-374b-3p, miR-4423-5p, miR-4450, miR-4468, miR-542-3p, miR-548ao-3p, and miR-553. Specific miRNA expression patterns were observed in normal Uyghur and Han skin samples, and the miRNA expression patterns differed significantly between the two populations.
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| Overall design |
All 20 normal skin tissues were obtained from surgical specimens immediately after resection from Jan 2012 to Sep 2013 in the Department of Dermatology, People’s Hospital of the Xinjiang Uyghur Autonomous Region, China. The samples were flash frozen in liquid nitrogen and stored at -180℃ until RNA extraction. RNA labeling and hybridization were completed by KangChen Bio-tech Inc. (Shanghai, China) according to the manufacturer's instructions. Briefly, Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions. After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0) which contains probes for 3100 mature miRNA. Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner. Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.
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| Contributor(s) |
Wu X, Pu X |
| Citation(s) |
29443776 |
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| Submission date |
Oct 15, 2014 |
| Last update date |
Aug 26, 2019 |
| Contact name |
Xiu-Juan Wu |
| E-mail(s) |
xjwuxj@sina.com
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| Phone |
86-991-8563351
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| Organization name |
People’s Hospital of Xinjiang, Uygur Autonomous Region
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| Department |
Department of Dermatology
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| Street address |
91 Tianchi Road
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| City |
Urumqi |
| State/province |
Xinjiang |
| ZIP/Postal code |
830001 |
| Country |
China |
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| Platforms (1) |
| GPL19128 |
Exiqon miRCURY LNA microRNA array; 7th generation - hsa, mmu & rno (miRBase 18.0) |
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| Samples (20)
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| Relations |
| BioProject |
PRJNA263896 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62354_RAW.tar |
19.9 Mb |
(http)(custom) |
TAR (of GPR) |
| GSE62354_normalized.txt.gz |
280.7 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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