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Introduction: Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs (ncRNAs) longer than 200 nucleotides, widely present in diverse organisms. They play crucial roles in numerous biological processes, including epigenetic regulation, cell-cycle control, and the regulation of cellular differentiation. LncRNAs are closely associated with the growth and development of animals and plants, as well as with the pathogenesis of human diseases, and can serve as biomarkers for disease diagnosis or as important therapeutic targets.
By employing high-throughput sequencing technologies for lncRNA profiling and bioinformatics analysis, it is possible to rapidly and accurately identify lncRNAs with critical regulatory functions, elucidate their relationships with specific biological processes, and gain deeper insights into their functional roles and the mechanisms governing their expression and regulation. These include ceRNA regulatory networks that competitively sequester miRNAs, as well as a range of chromatin‑modulating activities, such as the regulation of enhancers, promoters, insulators, and other genomic elements.
Initial Sample Amount and Submission Recommendations
| Sample Type | Initial amount |
| Animal and clinical organ tissues, such as brain tissue, etc. | >20mg |
| Animals and clinical skin/bone/vascular/fat tissues, etc. | >100mg |
| Plant leaf tissue/flower | >200mg |
| Plant roots/stems/fruits/seeds | >500mg |
| Primary cells/cell lines | >5×10 6 one |
| Neutrophils/Eosinophils/Basophils | >5×10 7 one |
| Exosome sample | >1×10 8 one |
| Serum/plasma/cerebrospinal fluid/joint effusion/follicular fluid | >2mL |
| Cell culture supernatant | >20mL |
| Urine | >30mL |
| Total RNA | >1 μg and RIN > 7.0 |
Precautions:
① Tissue samples are recommended to be stored in RNAlater, RNAHold, RNAProtect, or other suitable tissue preservation solutions, and then either frozen at −80°C or shipped on dry ice.
② After thoroughly lysing the cell samples with a lysis buffer such as TRIzol, store them at −80°C or ship them on dry ice.
③ For more detailed sample preparation guidelines, please contact online customer service.
Bioinformatics Analysis Workflow and Analytical Content
| lncRNA | Analysis Content | Remarks |
| Sequencing data quality control | Statistics on the raw sequencing data volume and the clean data volume | |
| Sequencing quality metrics (Q20, Q30) and GC content analysis; removal of adapter sequences, low-quality reads, and contaminant sequences from the raw output data. | ||
| Genome alignment | Reference genome alignment / region-based alignment | |
| Chromosome density distribution | ||
| Expression analysis | Global expression profile of genes/transcripts | |
| Statistical Analysis of the Distribution of Sample Gene Expression Values | ||
| Statistical distribution of expression value ranges for different genes in the sample | ||
| Statistical analysis of sample transcript coverage depth | ||
| Density plot of gene expression values | ||
| Box plot of gene expression levels | ||
| Sample Correlation Analysis | Pearson/Spearman correlation analysis | |
| PCA cluster analysis | ||
| mRNA analysis | Genetic Variation Analysis | |
| Transcriptome Differential Analysis | ||
| Volcano plot of differentially expressed genes | ||
| Overall Statistical Plot of Differentially Expressed Genes | ||
| Heatmap of Differentially Expressed Genes | ||
| Differential Gene GO Enrichment Analysis | ||
| KEGG enrichment analysis of differentially expressed genes | ||
| GSEA analysis | ||
| lncRNA analysis | Transcript reconstruction and lncRNA prediction | |
| lncRNA expression analysis | ||
| Differential expression analysis of lncRNAs | ||
| Volcano plot of differential lncRNAs | ||
| Overall Statistics of Differentially Expressed lncRNAs | ||
| Differential lncRNA clustering heatmap | ||
| Comparison of Structural Features Between lncRNAs and mRNAs | Comparison of lncRNA and mRNA lengths | |
| ORF distribution of lncRNAs and mRNAs | ||
| Statistical analysis of the number of exons in lncRNAs and mRNAs | ||
| Statistical analysis of lncRNA and mRNA expression levels | ||
| lncRNA target gene prediction | ||
| GO enrichment analysis of lncRNA-targeted differentially expressed genes | ||
| KEGG enrichment analysis of lncRNA-targeted differentially expressed genes | ||
| SNP/INDEL analysis | SNP/INDEL Count Statistics | |
| Location of SNP/INDEL | ||
| SNP Mutation Pattern Statistics | ||
| SNP and INDEL annotation of genomic regions |
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