|
| Status |
Public on Jul 13, 2024 |
| Title |
vehicle_technical repeat 1 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: triple-negative breast cancer cell line
treatments: 1 h vehicle (0.5% DMSO) treatment
molecule subtype: small RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 1 million of treated MDA-MB-231 cells in each experimental group using the TRIzol® Reagent (Invitrogen,Carlsbad, CA) according to the manufacturer’s instructions. RNA quantity and purity was assessed using NanoDrop ND-1000 while RNA integrity number (RIN) was assessed using Agilent RNA 6000 Nano assay. A260/A280 ≥ 1.6 and A260/A230 ≥ 1 indicate acceptable RNA purity, while RIN value ≥ 5 indicates acceptable RNA integrity. All the samples meet the above criteria with A260/A280 ranging from 1.78-1.83, A260/A230 ranging from 1.21-1.53, and RIN ranging from 9.7-10.0.
|
| Label |
Cy5
|
| Label protocol |
Fluorescent targets were prepared from 2 μg total RNA samples using miRNA ULSTM Labeling Kit (Kreatech Diagnostics, The Netherlands). Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA).
|
| |
|
| Hybridization protocol |
Enriched labeled miRNA targets were hybridized to the Human miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber. After 16 h of hybridization, non-specific binding targets were washed away using wash buffer (2× saline sodium citrate solution).
|
| Scan protocol |
The arrays were scanned using a DNA Microarray Scanner (Model 4000B, Molecular Devices, Sunnyvale, CA, USA). The Cy5 fluorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).
|
| Description |
V1
|
| Data processing |
GPR files were loaded into R version 2.12.1 to process data analysis. Probes that all replicates within with flags equal to “-50” of all chips were filtered out. Intensity values from repeated probes within one chip are combined by median. CVs (coefficient of variance) of miRNA from repeated probes within one chip are calculated and the intensity values are calculated by median. Intensities were normalized with invariant set normalization method (Cheng Li et al., Genome Biology 2001), then took average of repeated data from the same sample. Selection criteria to identify differentially expressed genes were established at log 2 |Fold change| ≥ 0.8 and P < 0.05.
Average ratios and significant values for each miRNA were calculated based on the normalized intensities by pairwise comparison.
|
| |
|
| Submission date |
Jul 13, 2021 |
| Last update date |
Jul 13, 2024 |
| Contact name |
Lie-Fen Shyur |
| E-mail(s) |
lfshyur@ccvax.sinica.edu.tw
|
| Organization name |
Academia Sinica
|
| Street address |
No. 128, Sec. 2, Academia Road
|
| City |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL30415 |
| Series (1) |
| GSE180000 |
Redox-associated miRNAs regulated by anti-TNBC compounds DET and DETD-35 in MDA-MB-231 cells |
|
