Overview

NGS-based RNA sequencing (RNA-seq) converts RNA into cDNA fragments through reverse transcription, followed by high-throughput short-read sequencing. Without relying on predefined microarray probes, RNA-seq provides unbiased digital quantification, enabling accurate measurement of gene expression abundance across an ultra-wide dynamic range.

Gene Expression Profiling

Quantify differential gene expression across tissues, developmental stages, and drug-induced conditions.

Transcript Characterization

Identify novel transcripts, alternative splicing events, and gene fusions.

Disease Mechanisms & Biomarker Discovery

Characterize disease-associated regulatory networks and non-coding RNA biomarkers in cancer and complex diseases.

X1 Bioinformatics Workstation

X1 Bioinformatics Workstation is an integrated bioinformatics solution, designed to streamline sequencing data analysis from raw data to application-ready reports. Featuring flexible hardware configurations and pre-built bioinformatics pipelines, it delivers plug-and-run, end-to-end data analysis for diverse laboratory throughput needs.

X1 requires no complicated deployment or professional bioinformatics setup, allowing one-click standardized analysis to cut hands-on work, shorten turnaround time, boost data security and deliver actionable sequencing results faster.

X1 Bioinformatics Workstation

Highlights

Versatile Bioinformatics

Supports multiple bioinformatics plugins for a wide range of analysis applications.

Secure Offline Operation

Runs reliably offline to help keep sensitive data secure and private.

Easy to Use

No complex command-line operations required, enabling streamlined analysis with minimal training.

Intelligent System Management

Real-time memory and storage monitoring with early warnings to help prevent capacity issues.

01

Total RNA & mRNA Sequencing

Bulk RNA-seq enables transcriptome-wide profiling through mRNA enrichment or rRNA depletion. mRNA sequencing targets protein-coding transcripts, while Total RNA sequencing retains both mRNA and long non-coding RNA (lncRNA) following rRNA depletion.

Workflow

  • 1. RNA Extraction & Quality Control

    Extract total RNA and perform stringent RNA integrity assessment, including RIN evaluation.

  • 2. Enrichment / Depletion

    Use magnetic beads to capture poly(A)-tailed mRNA, or enzymatic methods or hybridization probes to directly remove ribosomal RNA.

  • 3. Fragmentation & Reverse Transcription

    Randomly fragment RNA and use random primers for reverse transcription to synthesize double-stranded cDNA.

  • 4. NGS Library Preparation & Sequencing

    Perform end repair, A-tailing, paired-end adapter ligation, and PCR amplification, followed by paired-end sequencing.

Key Advantages

Sensitive Digital Quantification

Detect gene expression changes with high sensitivity, including low-abundance transcripts.

High-Throughput Profiling

Automated library preparation supports efficient expression profiling across large clinical and research cohorts.

02

Small RNA Sequencing

Small RNA sequencing enriches and quantifies short non-coding RNAs of approximately 18–30 nt, including miRNAs, siRNAs, and piRNAs. These small RNAs play key roles in post-transcriptional regulation.

Workflow

  • 1. Small RNA Size Selection

    Use polyacrylamide gel electrophoresis (PAGE) or specialized magnetic beads to selectively isolate short RNA fragments of approximately 18–30 nt.

  • 2. Specialized Adapter Ligation

    Directly ligate single-stranded RNA adapters to the 3′ and 5′ ends of small RNA molecules without fragmentation.

  • 3. Reverse Transcription & Amplification

    Reverse-transcribe the RNA into cDNA followed by PCR amplification.

  • 4. NGS Single-End Sequencing

    Due to the short fragment length, single-end sequencing, such as SE50 or SE75, is typically used for efficient sequencing.

Key Advantages

Full-Length Small RNA Profiling

Preserves native full-length sequences and terminal information without fragmentation, enabling high-resolution analysis.

Novel Small RNA Discovery

Enables de novo identification of novel small RNAs and their precursor structures without prior sequence information.

03

Single-Cell RNA Sequencing (scRNA-seq)

Single-cell RNA sequencing resolves cellular heterogeneity beyond bulk RNA-seq. Microfluidic or microwell technologies enable transcriptome profiling of thousands of individual cells at single-cell resolution.

Workflow

  • 1. Single-Cell Suspension Preparation

    Dissociate tissues into a high-viability single-cell suspension.

  • 2. Droplet-Based Partitioning

    Use a microfluidic system, such as the 10x Genomics platform, to encapsulate individual cells together with gel beads carrying cell barcodes and unique molecular identifiers (UMIs) within droplets.

  • 3. Cell Lysis & Barcoding

    Lyse cells within droplets. Released mRNA molecules are labeled with cell-specific barcodes to identify their cell of origin and UMIs to distinguish individual transcript molecules.

  • 4. Library Preparation & Sequencing

    Break the droplets, pool cDNA from all cells, and perform high-depth paired-end NGS.

Key Advantages

High-Resolution Cell Atlasing

Identify rare cell types and define novel cell subpopulations.

Lineage & Trajectory Tracing

Use bioinformatics algorithms to infer pseudotime trajectories of cellular differentiation and development, providing insights into dynamic cellular changes.

04

Spatial Transcriptomics

Spatial transcriptomics maps gene expression within the native tissue context. Spatially barcoded arrays enable high-throughput transcriptome profiling while preserving the spatial organization of cells.

Workflow

  • 1. Tissue Sectioning & Fixation

    Place fresh-frozen or FFPE tissue sections onto specialized chips containing spatial barcode arrays.

  • 2. Staining & Imaging

    Perform H&E or immunofluorescence staining followed by microscopic imaging to record tissue morphology.

  • 3. Permeabilization & In Situ Capture

    Permeabilize the tissue to release mRNA, which is captured in situ by spatially barcoded primers on the chip surface.

  • 4. Elution, Library Preparation & NGS

    Recover spatially barcoded cDNA, construct sequencing libraries, and perform NGS. Integrate sequencing data with microscopy images based on spatial coordinates.

Key Advantages

Spatial Context Preservation

Preserving complex tissue architecture without tissue dissociation, including the tumor microenvironment (TME), neuroanatomical structures, and neighboring cell-cell interactions.

Morphology & Transcriptomics Integration

Integrating conventional histopathological visualization with high-throughput quantitative transcriptomic profiling.