One-stop Cross-Linking and Immunoprecipitation(CLIP) Services

What is CLIP Services?

CLIP is a class of molecular biology methods that are applied to identify RNA binding protein (RBP) targets across the transcriptome of cells. A brief description of the procedure is as follows: the cells are treated with UV light, which crosslinks the RBPs to RNA. The RBP of interest is then precipitated using antibodies and the RNA is extracted. The RNA is fragmented and the resulting ends are converted into cDNA libraries. CLIP cDNA libraries are then subject to high-throughput sequencing. CLIP methods provide a transcriptome-wide and nucleotide-resolution view of RBP binding and function. CLIP services are used to study post-transcriptional regulation, RNA stability, splicing, localization, and other gene expression regulation at the RNA level in neurobiology, cancer, RNA therapeutics and more.

Applications of CLIP Services

Mapping RNA–protein interaction sites at nucleotide resolution

Studying post-transcriptional gene regulation

Identifying RNA targets of RNA-binding proteins (RBPs)

Investigating alternative splicing and RNA stability

Exploring regulatory networks in disease models (e.g., cancer, neurodegeneration)

Supporting RNA therapeutics and biomarker discovery

Why Choose Creative Diagnostics' CLIP Services?

Qiagen TissueLyser II

Qiagen QIAcube®

Illumina NovaSeq 6000

Creative Diagnostics provides comprehensive Cross Linking and Immunoprecipitation (CLIP) Services to support the investigation of RNA protein interactions essential for understanding post transcriptional gene regulation. With extensive expertise in RNA biology, we offer customized CLIP assay strategies tailored to various research needs, including RNA binding protein target identification, mapping of interaction sites, and transcriptomic regulation analysis. Our advanced platform integrates optimized crosslinking conditions, high affinity antibody selection, and sensitive RNA detection methods to ensure high quality, reproducible results. We provide:

Optimized cross-linking conditions ensure RNA-protein complex stability and efficient capture.

High-affinity antibody screening solutions enable specific enrichment of target RNA-binding proteins.

A rigorously controlled immunoprecipitation protocol ensures high experimental reproducibility and low background signal.

Precise RNA fragment recovery and purification steps effectively preserve key sequence information.

High-throughput sequencing-compatible library construction solutions enable transcriptome-wide RNA binding site analysis.

Bioinformatics analysis support facilitates the elucidation of regulatory networks and functional pathways of RNA-binding proteins.

Customized experimental protocols meet the individual needs of different sample types and research objectives.

Our Services

To address the demand for fast and precise interrogation of RNA–protein interactions, we offer Cross Linking and Immunoprecipitation (CLIP) Services. With our well-established RNA–protein crosslinking, cell lysis, and immunoprecipitation methods, we can readily purify target RNA binding proteins (RBPs) and identify their binding sites on target transcripts. CLIP services address challenges associated with non specific interactions, background noise, and sample complexity. Our CLIP Services cover optimized sample preparation, high specificity antibody screening, stringent immunoprecipitation steps, and highly sensitive downstream detection and sequencing methods for improved data quality and analytical resolution. This approach has been broadly applied to study RNA metabolism, transcript stability, post transcriptional regulation, and RBP in diseases. Relying on robust quality control systems and extensive technical expertise, we ensure each experimental result is highly specific, reproducible, and stable. Our core services include:

Sample Preparation and Cross-linking

Optimize conditions to maximize preservation of native binding states using ultraviolet (UV) cross-linking for RNA and RNA-binding protein complexes.
Tailor cross-linking optimization to various cell types (adherent cells, suspension cells and tissue samples).

Cell Lysis and RNA-Protein Complex Extraction

Use lysis buffers that have been optimized to maintain protein function and RNA integrity.
Shear the RNA to the desired fragment length for downstream library construction.

Specific Antibody Screening and Co-immunoprecipitation (IP)

Recommend high-affinity and high-specificity antibodies for screening or provide customized antibody processing.
Control the co-immunoprecipitation process rigorously to selectively purify binding proteins and their target RNAs.

RNA Extraction and Linker Ligation

Extract co-precipitated RNA efficiently and enzymatically treat RNA (e.g. dephosphorylation, adapter ligation).
We can perform various CLIP variants (PAR-CLIP, iCLIP, and eCLIP) based on research needs.

Reverse Transcription and Library Construction

RNA is reverse-transcribed into cDNA, amplified by PCR, and a sequencing library is constructed for Illumina or other platforms.
Multiple quality control steps ensure library quality, complexity, and specificity.

High-Throughput Sequencing

We provide high-quality single-end or paired-end sequencing services for the Illumina platform.
Sequencing depth can be adjusted to meet your needs for qualitative or quantitative analysis.

Data Analysis and Reporting

Professional bioinformatics analysis, including peak identification, annotation, and visualization
Provide detailed experimental reports covering experimental design, data quality, and result interpretation

Bioinformatics Analysis (Optional)

Provide one-stop data processing services, from raw data quality control, shearing, alignment, to peak identification.
Analyze target RNA profiles, binding site distribution, and enrichment motifs of RNA-binding proteins.
Generate visualization maps, such as aggregation maps, metagene maps, and heat maps.

CLIP Services Process

Use UV light to fix RNA-protein binding.

Lyse cells and shear RNA.

Enrich RNA-protein complexes using antibodies.

Purify RNA, ligate adapters, perform reverse transcription, and construct libraries.

Sequencing and data analysis and technical support are provided.

Case Study

The figure shows a histogram of GO functional enrichment analysis of CLIP targets

The figure shows a histogram of GO functional enrichment analysis of CLIP targets. The X-axis represents different functional categories, including RNA binding, mRNA splicing, translation regulation, RNA stability, and cell cycle; the Y-axis represents the enrichment score, reflecting the degree of enrichment of each functional category in the target. The number above each bar corresponds to the enrichment score. The most enriched function was "RNA binding", suggesting that CLIP targets are highly related to biological processes that involve binding to RNA. The next most enriched functions were mRNA splicing, translation regulation, RNA stability, and cell cycle, suggesting that these biological processes play an important role in regulating CLIP targets.

FAQs About CLIP Services

How does CLIP help me find the "intimate relationship" between RNA and protein?

Simply put, CLIP uses ultraviolet light to "glue" RNA and protein together, then uses antibodies to capture the target protein and the RNA it's bound to. Finally, sequencing reveals where they interact.

Can I use CLIP to study all RNA-binding proteins? Are there any limitations?

Theoretically, most RNA-binding proteins can be studied, but high-quality antibodies are crucial, and the protein's abundance and binding stability in the cell also affect the results.

What sample size is sufficient for CLIP? What if I have very little material?

CLIP has high sample requirements, generally requiring millions of cells. If you have limited material, you can try optimizing the protocol or using specialized low-input methods.

Can CLIP tell me the specific binding sites of RNA-binding proteins?

Yes, CLIP can accurately locate protein binding sites on RNA down to the nucleotide level, making it ideal for analyzing regulatory mechanisms.

Is the data analysis complex? Do I need to know programming to understand the results?

CLIP data is indeed professional, and the analysis steps are complex. We typically provide a one-stop bioinformatics analysis report to help you interpret key results without having to worry about writing code yourself.

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