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RNA-seq data analysis generally includes reads alignment, gene expression quantification, differentially expressed genes/isoforms or alternative splicing detection and novel transcripts discovery (Table 4).
Gene copy numbers were expressed with the comparative CT method for relative gene expression quantification against GAPDH.
In particular real-time PCR techniques using SYBR Green and melting curve analysis allowing verification of specific product amplification have become a well accepted laboratory technique for rapid and high throughput gene expression quantification.
The gene expression quantification reactions were performed in an ABI Prism 7900HT system.
Tissue extraction and relative gene expression quantification were conducted as described previously.
For gene expression quantification, cDNA samples prepared from 48 fibroblast cell lines were examined.
Prior to gene expression quantification, the primers were optimized to ensure close to 100% amplification efficiency.
For gene expression quantification by qPCR, the Grubb's test for outliers was calculated for each three triplicate measurement.
The resulting data were analyzed with the comparative CT method for relative gene expression quantification against house keeping gene GAPDH.
The gene expression quantification reactions were performed according to the manufacturers' instructions on an ABI Prism 7900HT system.
Since gene expression quantification using RT-qPCR requires a steady reference gene, we selected three genes frequently used for normalization of the data, ABL1, RPLP0, and HPRT1.
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