US Based · Epigenomic Sequencing Services
Epigenomic Sequencing Services
Services for chromatin accessibility, histone modifications, and DNA methylation. Bulk and single-cell services from cell prep to analysis in our SF Bay Area lab.
Epigenomic Services
Comprehensive Chromatin & Methylation Mapping Solutions
Bulk ATAC-Seq Service
High-quality chromatin accessibility mapping and nucleosome positioning for inputs ≥100k cells.
Single-Cell ATAC-Seq Service
Cell-level chromatin profiling to resolve epigenetic heterogeneity with inputs ≥100k cells using 10x genomics.
Single-Cell Multiome (ATAC + GEX)
Simultaneous profiling of open chromatin and gene expression using 10x Genomic or BD Rhapsody.
Hi-C Chromatin Service
High-resolution mapping of 3D genome architecture, looping, and long-range chromosomal interactions.
Methyl Profiling Service
Illumina 5 Base, Em-Seq Methyl or PacBio long read Methyl support genome-wide DNA methylation analysis.
CUT&RUN Seq (OCM or Hashing)
Ultra-low background, antibody-targeted mapping of transcription factors and active histone marks from Epicypher.
ChIP-Seq Service
Send in your IP and pull down DNA for our team to complete final library prep using NEB Ultra II workflow.
Not sure which service fits your project? Our team provides complimentary technical consultations to help you select the optimal workflow based on your sample quality and research objectives. > Or view our Technical Specifications & Sample Requirements or FAQ for more information.
The Signios Advantage
Superior Epigenomic Performance & Technical Excellence
From optimized nuclear extraction and sample handling expertise to integrated captures, our workflows maximize peak signal density delivering high-quality, reproducible datasets optimized for your unique discovery goals.
End-to-end Solutions
Integrated epigenomic workflows spanning nuclei isolation, library prep, deep Illumina sequencing, and peak-calling bioinformatics — all managed within a single laboratory.
Flexible Epigenetic Profiling
Map open chromatin, transcription factor footprints, 3D architecture, and base-resolution methylomes using bulk, single-cell, or custom targeted enrichment assays.
High Signal-to-Noise Ratio
Validated enzymatic and cleavage chemistries minimize background noise and mitochondrial contamination to enable ultra-sensitive peak detection from low-input clinical samples.
Stringent Quality Controls
Rigorous fluorometric quantification and fragment analyzer sizing flag compromised genomic DNA or low cell viability prior to sequencing to guarantee data reproducibility.
Local Expert Processing
All sample preparation, instrument cycles, and bioinformatic pipelines are performed in-house at our Foster City facility under a unified chain of custody.
Advanced Data Delivery
Receive comprehensive, pre-aligned dataset matrices, publication-ready genome browser tracks, and multiomic interactome analyses tailored directly to your research goals.
The Signios Partnership
Laboratory Workflow & Quality Assurance
A transparent, five-step quality loop engineered to maximize target fragment capture efficiency and structural regulatory alignment.
Step 1
Consultation on starting material and analysis goals are aligned to compatible service.
Step 2
Ship cryopreserved cells, tissues, or isolated DNA securely to our SF Bay Area lab.
Step 3
Experts isolate nuclei or extract DNA followed by appropriate QC before proceeding.
Step 4
Samples undergo controlled tagmentation or antibody-targeted cleavage, libraries are constructed with dual-index barcoding, and samples are deep-sequenced on Illumina NGS platforms.
Step 5
Receive complete, pre-aligned peak files, footprinting profiles, and differential methylation matrices ready for publication.
Consultation on starting material and analysis goals are aligned to compatible service.
Register samples via our streamlined customer portal. Schedule a local Bay Area pick-up or ship directly when ready.
Experts isolate nuclei or extract DNA followed by appropriate QC before proceeding.
Samples undergo controlled tagmentation or antibody-targeted cleavage, libraries are constructed with dual-index barcoding, and samples are deep-sequenced on Illumina NGS platforms.
Receive complete, pre-aligned peak files, footprinting profiles, and differential methylation matrices ready for publication.
Beyond the FASTQ
Comprehensive Bioinformatics for Our Epigenetic Services
Our specialized bioinformatics services automates delivery of structural matrices, peak calling, and functional motif maps.
- Primary Analysis: Quality control, alignment, peak calling, and methylation calling.
- Downstream Analysis: Differential peak/methylation analysis, motif enrichment, transcription factor binding prediction, and annotation to regulatory regions.
- Integrated Analysis: Cross-assay correlation of ATAC-Seq and RNA-Seq data for regulatory network inference.
- Visualization: Publication-ready figures including heatmaps, metagene profiles, methylation tracks, and peak intensity plots.
Deliverables Include
- FASTQ files
- Illumina Data QC report
- Alignment files (BAM)
- Processed results
- Publication-ready figures
- Secure delivery (SFTP, AWS, or Google Cloud)
Scoring Heat Map
Delta Distribution
Clonotype Expansion
Cell Type Annotation
Dimensionality Reduction (UMAP / t-SNE) Cluster Plots
Cell-Type Annotation & Subpopulation Distribution
TCR/BCR Clonal Frequency Repertoire Maps
Cell-to-Cell Interaction
Pathway Analysis
V-J Circos Plot
Applications of Sequencing-Based Epigenomic Mapping
Our epigenomic whole-genome services accelerate translational insights across principal biological disciplines:
Oncology
Uncover how aberrant chromatin remodeling drives tumor heterogeneity, track therapeutic resistance profiles, and identify novel epigenetic biomarkers.
Neuroscience
Map distinct transcriptional priming and chromatin state dynamics within precise brain subregions to explore neural plasticity and neurodegenerative diseases.
Immunology
Profile chromatin accessibility and histone mark shifts during T-cell exhaustion, immune differentiation, and acute inflammatory responses.
Developmental Biology
Visualize real-time gene regulation waves and cell fate choices driven by dynamic enhancer activation during embryogenesis.
Regenerative Medicine
Characterize stem cell pluripotency landscapes to optimize cellular reprogramming, scaffold engineering, and cell-based therapeutics.
Inflammatory Disease
Identify pathogenic regulatory niches and epigenetic variations that differentiate active versus quiescent zones in chronic fibrotic diseases.
Resources & Insights
SERVICE OVERVIEW TECH SHEET
Epigenentic Sequencing Services
Download the full technical sheet detailing our complete bulk and single cell configurations, platform specifications, and recommended sequencing depths.
Service Flyer
Epigenetic Analysis
End-to-end pipelines transforming raw sequencing data into actionable genomic insights, including QC, FASTQ/BAM/VCF generation, germline and somatic variant annotation, CNVs, SVs, joint genotyping, and gVCF outputs, with flexible analysis packages.
BLOG
RNA Sequencing Demystified: From Sample Prep to Insight
Take an in-depth look at our five-step laboratory workflow. Discover how we transition your project seamlessly from extraction to publication-ready bioinformatic analysis.
Frequently Asked Questions
Streamlined Epigenetic Services FAQ
What is epigenomic sequencing?
Epigenomic sequencing analyzes chromatin states, histone modifications, and DNA methylation to understand how genes are regulated and turned on or off without altering the underlying DNA sequence.
What types of epigenomic services does Signios Bio offer?
We provide a comprehensive suite of advanced epigenomic assays:
- Chromatin & Binding: ATAC-Seq (bulk and single-cell), CUT&RUN, ChIP-Seq, and HiC.
- Methylation: Methylome Profiling, Whole Genome Bisulfite Sequencing (WGBS), and Long-Read Methylation.
How much sample input is required for each assay?
Typical input requirements vary by assay type and sample material:
- Bulk ATAC-Seq: ≥ 100k cells or 20–50 mg tissue
- Single-Cell ATAC-Seq: 500k–1M cells with >85% viability
- CUT&RUN: ~250k cells per antibody
- ChIP-Seq: ≥ 1 ng immunoprecipitated DNA
Methylome Profiling / WGBS / Long-Read: 100–1000 ng high-quality DNA
💡 Detailed sample prep guidelines are available in our Epigenomics Whitepaper or upon request.
What are the sequencing depth requirements?
Sequencing depth scales with genome size, assay type, and structural targets. General recommendations include:
- Bulk ATAC-Seq: 30–50M paired-end reads for open chromatin mapping.
- Transcription Factor CUT&RUN: 10–20M paired-end reads to confidently map narrow binding footprints.
- Histone Modification Mapping & ChIP-Seq: 40–50M paired-end reads to fully capture broad structural chromatin marks.
- Genome-Wide Methylation (WGBS): 30–50X coverage is recommended.
Can I integrate epigenomics with other multiomic workflows?
Yes. Signios Bio specializes in cross-assay correlation. You can seamlessly combine your epigenomic data with RNA-Seq, single-cell sequencing, spatial transcriptomics, and proteomics to unlock deep, multiomic insights.
What bioinformatics support and data deliverables do you provide?
We offer end-to-end bioinformatics via a secure online portal. Your delivery includes:
- Primary & Downstream Analysis: QC, alignment, peak/methylation calling, differential peak analysis, and motif discovery.
- Multiomic Integration: Cross-assay correlation (e.g., ATAC-Seq + RNA-Seq).
- Publication-Ready Assets: High-resolution figures (heatmaps, metagene plots, methylation tracks) and comprehensive summary tables.
What makes Signios Bio’s services unique?
- Low-Input Workflows: Validated protocols for scarce or challenging sample types.
- True Multiomic Integration: Seamless blending of chromatin data with transcriptomic and spatial datasets.
- End-to-End Consultations: Expert guidance spanning experimental design, stringent QC, and publication-ready bioinformatics.
What is the expected timeline from shipment to results?
- Turnaround Time: Standard bulk assays typically take 4–6 weeks. Multiomic or complex single-cell projects may require additional time. Expedited options are available.
- Shipment Requirements: Cells and tissues must be snap-frozen in liquid nitrogen and shipped on dry ice. Purified gDNA can be shipped at 4°C.
- Logistics: We offer local courier pickup or overnight shipping to our Foster City, CA
How do I get started?
Simply fill out our Request a Quote form or contact our team. We will assist you with study design, assay selection, and logistics to ensure your project aligns with your biological question and publication goals.
Explore Related Sequencing Solutions
High-resolution transcriptomics to resolve individual cellular heterogeneity.
Resolving complex structural variations and full-length RNA isoforms.
High-plex protein profiling for functional multi-omic integration.
Get started with your project
Ready to uncover the regulatory mechanisms driving your
biology? Contact our team for a technical consultation. We’ll help you select the right epigenomic assay, optimize sample requirements, and design a sequencing strategy tailored to your research goals.
- End-to-end epigenomic sequencing solutions
- DNA Methylation, ATAC-seq, ChIP-seq, CUT&Tag & CUT&RUN
- Expert library preparation, sequencing & bioinformatics
- Publication-ready data and comprehensive analysis support
Request a quote