|
| Status |
Public on Dec 31, 2017 |
| Title |
TUNC3 |
| Sample type |
RNA |
| |
|
| Source name |
Human laryngeal squamous carcinoma cells TU177 negative control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: squamous carcinoma cells
cell line: TU177
transfection: Negative control
|
| Treatment protocol |
TU177 cells were transfected with Hsa-miR-145-5p mimic and negative control oligo at a final concentration of 50 nM by using lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions for 48 h, respectively.
|
| Growth protocol |
TU177 cells were maintained in RPMI1640 supplimented with 10% FBS under 37 ℃, 5% CO2 and 100% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer.
|
| |
|
| Hybridization protocol |
Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).
|
| Scan protocol |
Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).
|
| Description |
This sample is of negative control transfected TU177. It is the third of three negative control biological replicates.
|
| Data processing |
Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.
|
| |
|
| Submission date |
Dec 21, 2016 |
| Last update date |
Dec 31, 2017 |
| Contact name |
Yongyan Wu |
| E-mail(s) |
wu-yongyan@163.com
|
| Organization name |
Shanxi Medical University
|
| Department |
Department of Otolaryngology Head & Neck Surgery, The First Hospital
|
| Lab |
Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer
|
| Street address |
No.85 South Jiefang Road, Taiyuan, Shanxi, China
|
| City |
Taiyuan |
| State/province |
Shanxi |
| ZIP/Postal code |
030001 |
| Country |
China |
| |
|
| Platform ID |
GPL18943 |
| Series (1) |
| GSE92678 |
Expression analysis of Hsa-miR-145-5p overexpressed laryngeal squamous carcinoma cell line TU177 |
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