siRNA Sequencing

Small interfering RNAs (siRNAs) are important RNA fragments involved in RNA interference (RNAi), targeting specific genes and regulating their expression. We offer siRNA sequencing services based on our next-generation sequencing platform to efficiently capture and sequence siRNAs accumulated in samples, to help you analyze their role in biological regulation, as well as to monitor the delivery and biodistribution of siRNA molecules and resolve the specificity and efficacy of siRNA therapies.

Overview

siRNA is a double-stranded RNA, usually 21-24 bp, containing 2 3'-overhang perfectly base-paired nucleotides. siRNA is widely found in fungi, invertebrates, plants and mammals, which is the intermediate utilized by the cytoplasmic surveillance system, RNAi. The siRNA generated by cleaving dsRNA or small hairpin RNA (shRNA) guides RNA-induced silencing complex (RISC) to cleave mRNA molecules. In addition, siRNA has been designed as a potential therapeutic agent as a targeted drug to downregulate specific gene expression for the treatment of autoimmune diseases, malignancies and neurodegenerative disorders. CD Genomics offers high-resolution and coverage small RNA sequencing services to help you detect known and unknown siRNAs on a large scale. In addition, we offer mRNA sequencing and whole transcriptome sequencing services, combined with siRNA expression detection, enabling you to study the role of siRNA in cell signaling and regulation mechanisms, and resolve the effect of siRNA molecules in regulating gene expression in diseases.

Features

Any Species High Sensitivity Bioinformatics Analysis One-Stop Solution
This method can be applied to any species, from microorganisms to humans. Theoretically detect siRNA at levels down to one copy in a single cell. Our integrated bioinformatics pipeline can be tailored to suit your project, data visualization. From sample QC, library construction, to deep sequencing and custom data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

Quality assessment and quantification

Library Preparation

2. Library Preparation

RNA Selection – Size Fractionation; 18~40 bp insert cDNA library; Optimized for biofluids with limited RNA content.

Sequencing

3. Sequencing

50 SE / 75 SE; 7-10 Million Reads.

Data Analysis

4. Data Analysis & Delivery

Visualize and preprocess results, and custom bioinformatics analysis.

Bioinformatics Analysis Pipeline

siRNA Sequencing

In-depth data analysis:

  • Biostatistical analysis –transcript copy number comparisons, expression analysis, multi-parameter data analysis, etc.
  • Differential expression analysis of siRNA
  • siRNA cluster analysis
  • GO and KEGG enrichment analysis
  • Detect novel and rare siRNAs
  • Target gene prediction and functional analysis of siRNAs
  • Interactive network analysis

Sample Requirements

RNA sample (concentration ≥ 1 ng/uL, amount ≥ 2 ug)

1.8 ≤ OD260/280 ≤ 2.2, OD260/230≥2.0, RIN ≥ 6.5, 28S/18S ≥1.0.

Please make sure that the RNA is not degraded.

Sample Storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

Shipping Method: When shipping RNA samples, the RNA sample is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis report.

Reference:

  1. Niu X, Sun Y, Chen Z, et al. Using small RNA-seq data to detect siRNA duplexes induced by plant viruses. Genes, 2017, 8(6): 163.
* For Research Use Only. Not for use in diagnostic procedures.


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