Shanghai Biochip Co., Ltd.
Shanghai Biochip Co., Ltd.
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Long-chain non-coding RNA (lncRNA) is a type of non-coding RNA longer than 200 nt. It has important functions in transcriptional silencing, transcriptional activation, chromosome modification, and nuclear transport. LncRNA was once compared to the dark matter of the universe. In recent years, research has found that it is involved in a variety of biological processes, is an important basis for maintaining gene function, and is associated with a variety of complex diseases. However, the specific mechanism of action of a large number of lncRNAs is still unclear, which has also made lncRNAs a current research hotspot.
As a mature technology platform, gene chip has been widely used for the detection of gene expression profiles for more than two decades. For lncRNA gene expression profiling, gene chips have many important and irreplaceable advantages over RNA sequencing:
· The chip detects the expression abundance by using the fluorescent signal obtained by complementary hybridization and scanning of the oligonucleotide probe with the target gene base. Compared with RNA sequencing, the accuracy of microarray detection is less affected by low-abundance transcripts, making it more suitable for detecting lncRNA with low overall expression abundance. Increasing the sequencing depth will increase the detection probability of processed incomplete RNA, and increasing the sequencing depth may cause a decrease in reliability.
· LncRNA does not have the translation start and stop positions of proteins. RNA sequencing is less reliable in identifying lncRNA transcripts than mRNA. Shorter chip probes allow specific design and more specific detection.
Chip design strategy:
Human lncRNA chip design flow chart
Design and collect the latest version of database information and high-quality literature reports of lncRNA, remove redundancy, and remove lncRNA fragments and unreliable lncRNA by strict bioinformatics methods. CAGE-seq and RNA-seq data were used to identify lncRNA with high reliability 5'TSS and its expression in various tissues or cells. HGNC included and lncRNAdb collected experiments to verify functional lncRNA as high confidence lncRNA . The probe is designed based on the eArray software, and the probe is double-checked using the SBC's own analysis process to ensure that the probe distinguishes mRNA and lncRNA with high specificity.
lncRNA classification map
lncRNA regulation mechanism diagram
LncRNA detection technology is mature and sensitive, and the chip is more suitable for detecting low expression lncRNA than sequencing;
· The lncRNA is comprehensive, reliable, and updated in a timely manner; the lncRNA annotations are comprehensive and practical, and the lncRNA classification information;
· Short experiment period, mature and fast data analysis methods;
· Functional mechanism prediction, providing references for further research on the biological functions of lncRNA, including: highly conserved lncRNA; lncRNA binding protein prediction; lncRNA biological function prediction; lncRNA subcellular localization; disease-related lncRNA prediction; super enhancer lncRNA; enhancer lncRNA.
Chip technical parameters:
Super enhancer lncRNAs
SurePrint G3 Human lncRNA Microarray
NCBI, UCSC, Ensembl, Gencode, lncpedia, lncrnadb, dbSUPER, NONCODE
SurePrint G3 Mouse lncRNA Microarray
NCBI, UCSC, Ensembl, lncrnadb, dbSUPER, NONCODE, RNAcentral
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