|
| Status |
Public on Jun 05, 2012 |
| Title |
HN12 cell, mesenchymal phenotype and high invasive capacity cell |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
HN12 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HN12
cell type: mesenchymal phenotype and high invasive capacity cell, derived from a nodal metastasis in the patient from whom the HN4 cells originated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the miRNA isolation kit . The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
|
| Label |
Hy5
|
| Label protocol |
One µg total RNA from sample and reference was labeled with Hy5™ and Hy3™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
common reference pool
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Multiple
gender: Mixed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the miRNA isolation kit . The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.
|
| Label |
Hy3
|
| Label protocol |
One µg total RNA from sample and reference was labeled with Hy5™ and Hy3™ fluorescent label, respectively, using the miRCURY™ LNA Array power labeling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
Hybridization of the mix of Hy5™-labeled sample and Hy3™-labeled reference RNAs to the arrays at 56 ºC for 16 hours followed by washing was performed by Exiqon® (Vedbaek, Denmark) on an HS Pro instrument (Tecan®, Männedorf, Switzerland). The 6th generation miRCURY™ LNA microRNA arrays (Exiqon®, Vedbaek,Denmark) that were used have approx. 2383 locked nucleic acid oligonucleotide probes on quadruplicate 100 µM-sized probe-spots to detect all human, mouse and rat microRNAs, respectively, of miRbase v.16.respectively, of miRbase v.16.
|
| Scan protocol |
Arrays were scanned, after hybridization and washing, using the G2505B scanning system (Agilent®, Santa Clara, USA) by Exiqon® (Vedbaek, Denmark).
|
| Description |
natural mesenchymal phenotype and high invasive capacity cell, derived from a nodal metastasis in the patient from whom the HN4 cells originated
|
| Data processing |
Data processing was done in R (version 2.12.1) using the limma (version 3.4.5) Bioconductor package. The 'normexp' method with offset=10 was used for background-correction, and followed with within-array global 'loess' normalization, with span=1/3 and values from probe-spots with flag-values >1 ignored, and then, between-array 'Rquantile' normalization. For probe-set summarization, the median of the values from multiple spots was used when the ratio of the maximum and minimum values was > 1.5; else, the mean was used. The ratios of the summarized normalized Hy5/Hy3 (test/reference) signal-intensities were log2-transformed.
|
| |
|
| Submission date |
Jun 04, 2012 |
| Last update date |
Jun 05, 2012 |
| Contact name |
zhiyuan zhang |
| E-mail(s) |
zhangzhiyuanmailbox@yahoo.cn
|
| Organization name |
Shanghai Jiaotong University
|
| Street address |
639 zhizaoju Road
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL11434 |
| Series (1) |
| GSE38459 |
miRNA profiles in head and neck natural epithelial - mesenchymal phenotype cell line pair, and in TGF-β induced EMT models |
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