NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5444698 Query DataSets for GSM5444698
Status Public on Jul 13, 2024
Title DET_4_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 DET (4µM) 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 D1
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

Data table header descriptions
ID_REF
VALUE normalized intensities for each array

Data table
ID_REF VALUE
PH_mr_0000010 337.5
PH_mr_0000014 39
PH_mr_0000017 2696.68
PH_mr_0000023 83
PH_mr_0000029 36
PH_mr_0000042 1692.45
PH_mr_0000045 36
PH_mr_0000048 33
PH_mr_0000050 1817.22
PH_mr_0000058 34
PH_mr_0000062 68
PH_mr_0000071 33
PH_mr_0000073 41
PH_mr_0000076 53
PH_mr_0000079 36
PH_mr_0000080 39
PH_mr_0000092 36
PH_mr_0000093 70
PH_mr_0000096 34
PH_mr_0000097 40

Total number of rows: 2544

Table truncated, full table size 45 Kbytes.




Supplementary file Size Download File type/resource
GSM5444698_H005-3170700591.gpr.gz 445.2 Kb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap