# RNA Sequencing Solutions - CD Genomics
> Comprehensive RNA sequencing services focusing on transcriptomics, epitranscriptomics, non-coding RNA analysis, and RNA-protein interactions.

CD Genomics utilizes advanced Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) platforms (Illumina, PacBio, Nanopore) to provide full-spectrum RNA analysis. The portfolio specializes in detecting complex RNA modifications, characterizing non-coding RNAs, mapping RNA interactions, and performing single-cell/spatial analysis for biomedical and agricultural research.

## Epitranscriptomics (RNA Modifications)
- [m6A Sequencing (MeRIP-seq)](https://rna.cd-genomics.com/m6a-sequencing.html): Antibody-based immunoprecipitation for mapping N6-methyladenosine landscapes in mRNA and lncRNA to study post-transcriptional regulation.
- [m6Am Sequencing](https://rna.cd-genomics.com/m6am-seq.html): Specific detection of N6,2'-O-dimethyladenosine modifications at the 5' cap of mRNA affecting stability and translation.
- [m5C Sequencing](https://rna.cd-genomics.com/m5c-seq.html): Bisulfite conversion or antibody-based profiling methods to map 5-methylcytosine distribution in RNA.
- [m1A Sequencing](https://rna.cd-genomics.com/m1a-sequencing.html): Detection of N1-methyladenosine modifications critical for RNA structural stability and protein translation.
- [m7G/m3C Sequencing](https://rna.cd-genomics.com/m7gm3c-sequencing.html): Profiling of N7-methylguanosine and 3-methylcytosine modifications using TRAC-seq or specific chemical treatments.
- [acRIP Sequencing](https://rna.cd-genomics.com/acrip-sequencing.html): Acetyl-RNA immunoprecipitation for mapping N4-acetylcytidine (ac4C) sites associated with mRNA stability.
- [hMeRIP Sequencing](https://rna.cd-genomics.com/hmerip-sequencing.html): Genome-wide profiling of 5-hydroxymethylcytosine (5hmC) in RNA via antibody enrichment.
- [2'-O-Methylation Sequencing](https://rna.cd-genomics.com/2-o-methylation-sequencing.html): Detection of ribose methylation sites (Nm) utilizing specific reverse transcription pausing signatures.
- [Pseudo-seq](https://rna.cd-genomics.com/pseudo-sequencing.html): CMC-based chemical labeling for genome-wide mapping of Pseudouridine (Ψ) sites.
- [RNA Methylation Analysis](https://rna.cd-genomics.com/rna-methylation-analysis.html): Integrative analysis services covering diverse RNA chemical modifications and their biological functions.
- [O8G-seq](https://rna.cd-genomics.com/o8g-seq.html): Mapping of 8-oxo-7,8-dihydroguanosine to identify oxidative RNA damage sites.
- [Long-Read Epitranscriptomics](https://rna.cd-genomics.com/long-read-epitranscriptomics-sequencing.html): Direct detection of modifications on native RNA strands using Nanopore sensing technology without PCR amplification.

## RNA Interactomics (RBP & Chromatin)
- [CLIP-Sequencing](https://rna.cd-genomics.com/clip-sequencing.html): UV crosslinking and immunoprecipitation (HITS-CLIP, PAR-CLIP, iCLIP) to map precise RNA Binding Protein (RBP) sites.
- [lncRNA/circRNA RIP-Sequencing](https://rna.cd-genomics.com/lncrna-and-circrna-rip-sequencing.html): RNA Immunoprecipitation to identify native interactions between long non-coding/circular RNAs and specific proteins.
- [ChIRP-seq](https://rna.cd-genomics.com/chlrp-seq.html): Chromatin Isolation by RNA Purification to map genomic binding sites of lncRNAs.
- [ChIRP-MS](https://rna.cd-genomics.com/chirp-ms.html): Mass spectrometry analysis of protein complexes associated with specific RNA molecules via biotinylated probes.
- [RAP-MS](https://rna.cd-genomics.com/rap-ms.html): RNA Antisense Purification coupled with quantitative mass spectrometry for defining RNA interactomes.
- [RADICL-seq](https://rna.cd-genomics.com/radicl-seq.html): RNA And DNA Interacting Complexes Ligated and sequenced to map genome-wide RNA-chromatin interactions.
- [mRNA Interactome Capture](https://rna.cd-genomics.com/mrna-interactome-capture.html): Capture of polyadenylated RNA-bound proteomes utilizing UV crosslinking and oligo(dT) selection.
- [Protein-RNA Interactions](https://rna.cd-genomics.com/protein-rna-interactions.html): Comprehensive services for characterizing the dynamic interplay between transcriptomes and proteomes.
- [RNA-RNA Interaction Analysis](https://rna.cd-genomics.com/rna-interaction.html): Profiling direct hybridization and interaction networks between different RNA molecules (e.g., miRNA-lncRNA).

## Single-Cell & Spatial Transcriptomics
- [Single Cell RNA-seq](https://rna.cd-genomics.com/single-cell-rna-seq.html): Transcriptome profiling of individual cells to uncover heterogeneity, cell types, and lineage trajectories.
- [Drop-seq](https://rna.cd-genomics.com/drop-seq.html): High-throughput microfluidic droplet technology for parallel analysis of thousands of single cells.
- [Microwell-seq](https://rna.cd-genomics.com/microwell-seq.html): High-throughput, low-cost single-cell sequencing utilizing agarose microwell arrays.
- [Spatial Transcriptome Sequencing](https://rna.cd-genomics.com/spatial-transcriptome-sequencing.html): Spatially resolved gene expression mapping modifying histology with positional RNA sequencing.

## Non-Coding RNA Sequencing
- [Integrative miRNA Solutions](https://rna.cd-genomics.com/integrative-microrna-solutions.html): Small RNA sequencing for miRNA discovery, differential expression, and regulatory analysis.
- [Integrative lncRNA Solutions](https://rna.cd-genomics.com/integrative-lncrna-solutions.html): Strand-specific sequencing to characterize long non-coding RNAs and their cis/trans regulatory roles.
- [Integrative circRNA Solutions](https://rna.cd-genomics.com/integrative-circrna-solutions.html): Enrichment and sequencing of circular RNAs resistant to exonuclease R for functional biomarker discovery.
- [Integrative rRNA Solutions](https://rna.cd-genomics.com/integrative-rrna-solutions.html): Targeted analysis of ribosomal RNA, particularly suitable for microbial community or structural studies.
- [Integrative tRNA Solutions](https://rna.cd-genomics.com/integrative-trna-solutions.html): Specialized protocols (e.g., demethylation pretreatment) to overcome tRNA secondary structures for accurate quantification.
- [siRNA Sequencing](https://rna.cd-genomics.com/sirna-sequencing.html): Validation and quantification of small interfering RNAs in knockdown experiments.
- [sdRNA Sequencing](https://rna.cd-genomics.com/sdrna-sequencing.html): Profiling of small nucleolar RNA-derived RNAs to understand their regulatory functions.
- [Pandora-seq](https://rna.cd-genomics.com/pandora-seq.html): Enzymatic treatment to remove modifications blocking reverse transcription, enabling comprehensive small RNA discovery.
- [TagRNA-seq](https://rna.cd-genomics.com/tagrna-seq.html): Sequencing methods utilizing specific tagging strategies for rare or modified RNA species.
- [m5C lncRNA/circRNA Sequencing](https://rna.cd-genomics.com/m5c-lncrna-and-circrna-sequencing.html): Specialized bisulfite sequencing targeting methylated cytosines specifically in non-coding RNAs.

## Transcriptome Structure & Dynamics
- [CAPP-able-seq](https://rna.cd-genomics.com/cappable-seq-service.html): Capture and sequencing of 5' ends of primary transcripts to identify Transcription Start Sites (TSS).
- [Poly(A)-seq](https://rna.cd-genomics.com/polya-seq.html): 3'-end sequencing to map polyadenylation sites and quantify isoform-specific expression.
- [PAS-seq](https://rna.cd-genomics.com/pas-sequencing.html): Polyadenylation Site Sequencing for quantitative assessment of alternative polyadenylation (APA) events.
- [TAIL-LSO-seq](https://rna.cd-genomics.com/tail-lso-seq.html): Measurement of poly(A) tail length and sequence composition including non-A residues (uridylation/guanylation).
- [Degradome Profiling](https://rna.cd-genomics.com/degradome-profiling.html): Sequencing of uncapped 5' ends to identify miRNA cleavage targets and RNA decay intermediates.
- [NMD Analysis](https://rna.cd-genomics.com/nonsense-mediated-mrna-decay-nmd-analysis.html): Identification of targets regulated by the Nonsense-Mediated Decay surveillance pathway.
- [Transient Transcriptome Sequencing](https://rna.cd-genomics.com/transient-transcriptome-sequencing.html): Metabolic labeling (e.g., 4sU) to analyze nascent RNA turnover and synthesis rates.
- [Dynamic Transcriptome Analysis](https://rna.cd-genomics.com/dynamic-transcriptome-analysis.html): Kinetic modeling of RNA synthesis and degradation rates to understand temporal gene regulation.
- [dsRNA Sequencing](https://rna.cd-genomics.com/double-stranded-rna-sequencing-dsrna-seq.html): Enrichment and sequencing of double-stranded RNA structures (viral or endogenous).
- [Digital RNA Sequencing](https://rna.cd-genomics.com/digital-rna-sequencing.html): UMI-based counting for absolute quantification of transcript numbers, removing PCR bias.

## Exosomal & Biofluid Services
- [Exosomal mRNA Sequencing](https://rna.cd-genomics.com/exosomal-mrna-sequencing.html): Low-input protocols for profiling messenger RNA contents within exosomes.
- [Exosomal Long RNA-seq](https://rna.cd-genomics.com/exosomal-long-rna-seq.html): Comprehensive analysis including lncRNAs and circRNAs from exosomal isolates.
- [Exosomal Small RNA Sequencing](https://rna.cd-genomics.com/exosomal-small-rna-sequencing.html): Profiling of miRNA, piRNA, and other small RNAs in extracellular vesicles.
- [Biofluid miRNA Sequencing](https://rna.cd-genomics.com/biofluid-microrna-sequencing.html): Optimized extraction and library prep for miRNAs in serum, plasma, and urine samples.
- [Biofluid Small RNA-seq](https://rna.cd-genomics.com/biofluid-small-rna-seq.html): Detection of diverse small RNA species in complex biological fluids for biomarker discovery.
- [Circulating miRNA Sequencing](https://rna.cd-genomics.com/circulating-mirnas-sequencing-cell-free-mirna-seq.html): Analysis of cell-free biomarkers for liquid biopsy applications.

## General & Specialized Transcriptomics
- [Reference-based Transcriptome](https://rna.cd-genomics.com/reference-based-transcriptome-sequencing.html): Standard mRNA-seq aligning reads to known genomes for expression profiling and variant calling.
- [Eukaryotic mRNA Sequencing](https://rna.cd-genomics.com/eukaryotic-mrna-sequencing-with-reference.html): Poly(A) enrichment-based sequencing for standard eukaryotic gene expression studies.
- [Comparative Transcriptome Analysis](https://rna.cd-genomics.com/comparative-transcriptome-analysis.html): Differential expression studies across varying conditions, tissues, or species.
- [FFPE RNA-seq](https://rna.cd-genomics.com/ffpe-rna-seq.html): Specialized protocols for recovering and sequencing fragmented RNA from archival formalin-fixed paraffin-embedded tissues.
- [Comparative Tumor/Long RNA-seq](https://rna.cd-genomics.com/tumor-long-rna-seq.html): Deep sequencing of long RNA species in tumor tissues for oncology profiling.
- [Metatranscriptomics](https://rna.cd-genomics.com/metatranscriptomics-service.html): Analysis of community-wide gene expression in complex microbial environments.

## Long-Read Sequencing Platforms
- [SMRT Full-Length RNA Sequencing](https://rna.cd-genomics.com/smrt-full-length-rna-sequencing.html): PacBio Iso-Seq for detecting full-length isoforms without assembly.
- [Nanopore Full-Length cDNA Sequencing](https://rna.cd-genomics.com/nanopore-full-length-cdna-sequencing.html): Oxford Nanopore technology for long-read cDNA analysis and structural variant detection.

## Bioinformatics & Computational Analysis
- [miRNA Target Prediction](https://rna.cd-genomics.com/microrna-target-prediction.html): Computational algorithms to identify potential mRNA targets of miRNAs.
- [miRNA Expression Analysis](https://rna.cd-genomics.com/microrna-expression-analysis.html): Statistical quantification and normalization of miRNA count data.
- [circRNA-miRNA Interaction](https://rna.cd-genomics.com/circrna-mirna-interaction-analysis.html): Network analysis for "miRNA sponge" functions of circular RNAs.
- [circRNA-Protein Prediction](https://rna.cd-genomics.com/circrna-protein-interaction-prediction.html): In silico modeling of binding probabilities between circRNAs and RBPs.
- [circRNA Modification Analysis](https://rna.cd-genomics.com/circrna-modification-analysis.html): Identification of internal chemical modifications within circular RNA sequences.
- [lncRNA Target Prediction](https://rna.cd-genomics.com/lncrna-target-prediction.html): Cis- and trans-regulatory target identification for lncRNAs.
- [lncRNA-Protein Interaction Prediction](https://rna.cd-genomics.com/lncrna-protein-interaction-prediction.html): Computational docking and sequence motif analysis for lncRNA complexes.
- [lncRNA-RNA Interaction Prediction](https://rna.cd-genomics.com/lncrna-rna-interaction-prediction.html): Modeling base-pairing potentials between lncRNAs and other transcripts.
- [lncRNA Modification Analysis](https://rna.cd-genomics.com/lncrna-modification-analysis.html): Mapping of epitranscriptomic marks on long non-coding RNAs.
- [lncRNA/circRNA Encoding Analysis](https://rna.cd-genomics.com/encoding-activity-analysis-of-lncrnacircrna.html): Assessment of small peptide coding potential (sORF) in non-coding RNAs.

## Research Applications
- [Oncology Research](https://rna.cd-genomics.com/research-areas/health-research/rna-sequencing-oncology-research.html): Transcriptomic profiling for cancer typification and mechanism study.
- [Biomarker Discovery](https://rna.cd-genomics.com/research-areas/health-research/rna-sequencing-biomarker-discovery.html): Identification of diagnostic and prognostic RNA markers for clinical applications.
- [Drug Research](https://rna.cd-genomics.com/research-areas/rna-sequencing-drug-research-and-development.html): Gene expression analysis for drug target validation and toxicology screening.
- [Inherited Disease](https://rna.cd-genomics.com/research-areas/health-research/rna-sequencing-inherited-disease.html): Transcriptome analysis for elucidating mechanisms of rare and genetic disorders.
- [Microbiota Research](https://rna.cd-genomics.com/research-areas/rna-sequencing-microbiota-research.html): Host-microbe interaction studies via dual RNA-seq strategies.
- [Microbiology](https://rna.cd-genomics.com/research-areas/rna-sequencing-microbiology.html): Bacterial and fungal transcriptomics for pathogenesis and industrial applications.
- [Food & Agriculture](https://rna.cd-genomics.com/research-areas/rna-sequencing-food-agriculture.html): Crop improvement and livestock health studies using RNA-seq.

## Company Information
- [About Us](https://rna.cd-genomics.com/about-us.html): Overview of CD Genomics' mission and laboratory capabilities.
- [Solutions Overview](https://rna.cd-genomics.com/solutions.html): Comprehensive list of RNA sequencing strategies.
- [Platform Overview](https://rna.cd-genomics.com/rna-sequencing-platforms.html): Details on Illumina, PacBio, and Oxford Nanopore sequencing infrastructure.
- [Other Services](https://rna.cd-genomics.com/other-services.html): Supplementary molecular biology and sequencing services.