CRISPR Screening Service

Three screening modes for diverse functional genomics applications

Perturb-seq (Single-Cell CRISPR Screening) visualization

Conventional single-cell sequencing reveals the 'state' (What) of cells but struggles to explain the underlying 'cause' (Why). Perturb-seq combines CRISPR-mediated genetic perturbation with single-cell transcriptomic sequencing, simultaneously achieving genetic perturbation (knockout/activation/inhibition, etc.) and whole-transcriptome readout within the same cell, thereby establishing causal links between 'genetic perturbation—molecular phenotype' at the whole-genome scale.

The core breakthrough of this technology lies in the fact that it does not observe correlations, but rather measures downstream effects by directly intervening in gene function — this is irreplaceable for functional genomics research, drug target discovery, and disease mechanism elucidation.

Applications

High-throughput gene function discovery, transcriptomic phenotype analysis, data production for predictive models

Workflow

① Project Design

Define experimental plan and technical route based on research goals, cell model, screening scale, and phenotype requirements

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② Pilot Experiment

Cell authentication, drug selection concentration testing, Cas9/dCas9 stable cell line construction, infection efficiency testing, etc.

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③ sgRNA Library Design

Design sgRNA library covering target gene regions based on genomic databases and algorithms, supporting whole-genome/sub-library/custom library

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④ Lentiviral Library Construction

Standardized library packaging, titer determination, and quality control

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⑤ Library Transduction

Optimize transduction conditions, control MOI, ensure uniform genomic integration

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⑥ Single-Cell Capture & Library Prep

Single-cell isolation and Perturb-seq library construction based on 10x Genomics / Miroculus platform

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⑦ NGS Sequencing

Standardized high-throughput sequencing

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⑧ Data Analysis & Visualization

From raw data QC, sgRNA counting & assignment, to differential expression analysis, perturbation effect evaluation & visualization

Key Capabilities

Deep dual-tech integration　 The core team is proficient in both CRISPR gene editing and single-cell sequencing, effectively bridging each step from molecular cloning to data interpretation, reducing cross-tech communication loss and experimental error.
Proprietary Tri-sgRNA library technology　 Using our proprietary Tri-sgRNA library design strategy, each gene is targeted by multiple independent sgRNAs, improving perturbation reliability and statistical robustness.
Deep data mining　 The bioinformatics team has multidisciplinary backgrounds in oncology, neuroscience, genetics, and developmental biology, capable of parsing causal relationships between genes and complex phenotypes from Perturb-seq data, delivering personalized in-depth mining beyond standard analysis reports.

Specific protocols require technical consultation to confirm.

Pooled CRISPR screening delivers a genome-wide or custom sgRNA library as a single "pool" into a Cas9-expressing cell population, where each sgRNA directs an independent gene perturbation in individual cells. After selective pressure (drug treatment, immune killing, nutrient deprivation, etc.), next-generation sequencing reads out sgRNA abundance changes — perturbations that confer a growth advantage lead to sgRNA enrichment, while deleterious ones cause depletion — thereby systematically identifying key candidate genes that drive the phenotype. This "population-level parallel screening" strategy answers the core question of "which genes drive the phenotype" with the most direct readout: changes in sgRNA abundance.

Applications

Drug Target Discovery & Validation　 Screen essential genes for tumor cell proliferation and survival at whole-genome scale, providing candidate targets for drug development
Synthetic Lethality Screening　 Large-scale screening of synthetic lethal interactions under specific genetic backgrounds (e.g., tumor driver mutations, tumor suppressor gene loss), identifying targets selectively lethal to mutant cells
Tumor Immunology Mechanism　 Screen key genes regulating tumor cell sensitivity to immune killing (e.g., T cells, CAR-T, NK cells), and functional modules controlling immune checkpoint expression
Drug Resistance Mechanism　 Screen gene perturbations conferring drug resistance under treatment conditions, dissect molecular pathways of acquired resistance, and inform combination therapy strategies
Viral & Infection Research　 Screen key host factors required for viral entry, replication, and host cell defense, identifying potential targets for antiviral therapy
Cell State & Lineage Regulation　 Screen key transcription factors and signaling pathway components regulating stem cell self-renewal, differentiation direction, and cellular reprogramming efficiency

Workflow

① Project Design

Define experimental plan based on research goals (whole-genome/custom library), cell model, screening mode (CRISPR KO / CRISPRa / CRISPRi, etc.), and phenotype endpoints

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② Pilot Experiment

Cas9 functional validation, drug selection concentration testing, infection efficiency testing, screening time window optimization, etc.

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③ sgRNA Library Design

Design sgRNA library based on genomic databases and algorithms, covering whole-genome, sub-library, or custom gene sets

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④ Lentiviral Library Construction

Standardized library packaging, titer determination, and quality control, ensuring library coverage and uniformity

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⑤ Library Transduction & Selection

Optimize transduction conditions, control MOI to ensure single sgRNA per cell; apply selection pressure (drug / immune killing / nutrient deprivation, etc.) while maintaining library representation

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⑥ Genomic DNA Extraction & Enrichment

Extract genomic DNA from selection and control groups, PCR-amplify integrated sgRNA sequences

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⑦ NGS Sequencing

Standardized high-throughput sequencing, ensuring sufficient sequencing depth to cover library complexity

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⑧ Data Analysis & Visualization

sgRNA counting, enrichment/depletion analysis, gene-level ranking based on MAGeCK and other algorithms, output candidate gene list and visualization report

Specific protocols require technical consultation to confirm.

Pooled CRISPR screening efficiently identifies candidate genes through a "population-level parallel" approach, yet it relies on next-generation sequencing to read sgRNA abundance as an indirect readout, making it difficult to directly observe complex cellular phenotypes caused by individual gene perturbations — especially functional changes that do not directly affect cell proliferation or survival. Arrayed CRISPR screening adopts a complementary strategy: sgRNAs or sgRNA combinations targeting each gene are distributed in a "one-gene-per-well" format into individual wells of multi-well plates (96-well or 384-well plates), enabling gene perturbation and phenotype detection to be performed one by one under physically separated conditions.

The core advantage of this well-by-well approach is that the gene perturbation in each well is known and unique, so the phenotype readout can be directly attributed to the target gene in that well without the need for sequencing-based "deconvolution." This allows Arrayed screening to be compatible with richer, higher-information phenotype detection methods — including high-content imaging, flow cytometry, real-time live-cell monitoring, and multi-parameter fluorescence analysis — thereby simultaneously acquiring multi-dimensional functional data in a single experiment.

Applications

Target Validation & Deep Functional Analysis　 Independently validate Pooled screening candidate targets well-by-well, confirm causal relationships between gene perturbation and phenotype through multi-parameter detection, and rule out off-target effects and false positives
Post-Translational Modification & Signaling Pathway Analysis　 Collect cell lysates well-by-well, detect changes in protein phosphorylation, acetylation, ubiquitination and other post-translational modifications via immunoblotting or mass spectrometry, and dissect the regulatory role of gene perturbation on intracellular signaling cascades
Cell Morphology & Subcellular Structure Analysis　 Perform fine morphological analysis of gene-perturbed cells in individual wells using high-content imaging, including neurite outgrowth and branching, synapse formation, cytoskeletal arrangement, organelle distribution, and protein subcellular localization — suitable for neuroscience, developmental biology, and other research areas requiring high-resolution morphological readouts
Secretome & Immune Microenvironment Analysis　 Collect cell culture supernatants well-by-well, quantitatively analyze changes in cytokines, chemokines, growth factors, and other secreted proteins via ELISA, Luminex, or multiplex detection platforms, and dissect the impact of gene perturbation on cell secretory function and microenvironment interactions
Drug Mechanism of Action & Resistance Research　 Apply candidate drugs to gene-perturbed cells in individual wells, compare changes in drug response across perturbation states, and dissect drug action targets and resistance mechanisms
Virus-Host Interaction Validation　 Validate functional conservation of virus host dependency factors and restriction factors identified from genome-wide screening across different viral strains and cell types in the Arrayed system
iPSC Differentiation & Disease Model Research　 Perform iPSC differentiation towards target cell types in individual wells, analyze differentiation efficiency, cell morphology, and functional marker expression well-by-well using high-content imaging, and dissect key genes regulating cell fate decisions and disease phenotypes

Workflow

① Project Design

Define array scale and experimental plan based on research goals, cell model, perturbation mode, and endpoint phenotypes

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② sgRNA Design & Synthesis

Design sgRNA sequences targeting genes of interest based on genomic databases, provided as synthetic or arrayed library format

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③ Arrayed Library Preparation

Distribute sgRNAs in a one-gene-per-well format into multi-well plates, verify accuracy of each well through quality control

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④ Cell Seeding & Perturbation Delivery

Seed target cells onto arrayed plates, deliver sgRNAs via lentiviral transduction

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⑤ Phenotype Detection

Configure detection systems: high-content imaging, flow cytometry, cell viability assays, live-cell dynamic monitoring, etc.

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⑥ Data Acquisition & Analysis

Acquire multi-parameter phenotype data, perform QC, normalization, clustering analysis, and functional annotation, output perturbation-phenotype association report

Key Capabilities

Arrayed-Pooled Integrated Strategy　 Seamlessly connect the genome-wide discovery power of Pooled screening with the multi-parameter validation capability of Arrayed screening. After the Pooled phase identifies candidate genes, they are directly transferred into the Arrayed system for independent validation and deep phenotypic analysis, forming a complete "discovery — validation — mechanism" closed loop.
Multi-Modal Phenotype Detection Platform　 Integrate high-content imaging, flow cytometry, real-time live-cell monitoring, and other detection modalities, enabling simultaneous acquisition of morphological, functional, and molecular phenotype data across multiple dimensions for the same set of gene perturbations in a single experiment — reducing batch effects and improving data consistency.
Custom Arrayed Library Capability　 Support flexible configuration of sub-libraries and custom gene sets, allowing selection of targeting scale (from a few to hundreds of genes) based on research needs, balancing experimental throughput and data depth.

Specific protocols require technical consultation to confirm.