Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 15
Release date: Jun 1 2016
Last update date: Jun 19 2016
Access: Public
Diseases: Carcinoma, Squamous Cell, Infection, Neoplasms, Tongue Diseases
Chemicals: 5-Methylcytosine
Dataset link A minimal DNA 5-methylcytosine signature of oral tongue squamous cell carcinoma [HumanHT-12 V4.0]

Experimental Protocol


Whole-genome gene expression profiling was carried out with Illumina HumanHT12 v4 expression BeadChip (Illumina, San Diego, CA) with 21 tumors and their matched adjacent normal tissues. Total RNA was extracted using PureLink RNA mini kit (Invitrogen) and RNA quality was checked on the bioanalyzer using RNA Nano6000 chip (Agilent). RNA samples with poor RIN numbers (≤7) on the bioanalyzer chip, indicating partial degradation of RNA were processed using Illumina WGDASL assay and the ones with good RIN numbers (>7) were labelled using Illumina TotalPrep RNA Amplification kit (Ambion) as per the manufacturer’s recommendations. Targets were used to hybridize arrays and arrays were processed according to the manufacturer’s recommendations. Arrays were scanned using HiScan, Illumina, and the data collected were analyzed with GenomeStudio V2011.1 Gene Expression module 1.9.0 (Illumina) to check for the assay quality control probes. Raw signal intensities were exported from GenomeStudio for transformation, normalization and differential expression analyses using R.

Repositories


GEO

GSE75539

ArrayExpress

E-GEOD-75539

BioProject

PRJNA304504

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Contact


binay panda