Open AccessApplication of unique sequence index (USI) barcode to gene expression profiling in gastric adenocarcinoma
Author(s) -
Fattahi Sadegh,
Pilehchian Langroudi Maryam,
Samadani Ali Akbar,
Nikbakhsh Novin,
Asouri Mohsen,
AkhavanNiaki Haleh
Publication year - 2017
Publication title -
journal of cell communication and signaling
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.329
H-Index - 44
eISSN - 1873-961X
pISSN - 1873-9601
DOI - 10.1007/s12079-017-0376-8
Subject(s) - barcode , oligonucleotide , gene expression profiling , gene knockdown , computational biology , rna , gene expression , microbiology and biotechnology , biology , dna microarray , real time polymerase chain reaction , gene , computer science , genetics , operating system
Accurate expression profiling is imperative for understanding the biological roles of mRNAs. Real‐time PCR have been at the forefront of biological innovation in detection and monitoring of gene expression, however, fluorophore‐labeled oligonucleotides and double‐stranded DNA binding dyes, the two most frequently used dyes in RNA detection, are not very cost effective and have poor specificity, respectively. We have developed a cost effective and specific approach for mRNA expression profiling via added unique sequence index (USI) to cDNAs before amplification. USI is a barcode which enable the detection of each target RNA. Using this method, caudal type homeobox 1 ( CDX1 ) and FAT atypical cadherin 4 ( FAT4 ) expressions were investigated in tumoral and non‐tumoral tissues of gastric cancer patients and compared with commercial ABI kit. Both methods indicated that FAT4 and CDX1 expression were significantly reduced in gastric cancer tissues compared with adjacent noncancerous tissues. Moreover, we have shown that this assay is highly sensitive, linear and reproducible. USI barcode not only provides a powerful tool for mRNA detection due to its sensitivity, specificity and cost‐effectiveness, but also allows comfortable design for real‐time qPCR assays within the least time and empowers the analysis of many transcripts of virtually any organism. Furthermore, USI barcode is highly affordable for large numbers of different samples or small sample sizes without microarray and expensive commercial platforms.