Get a Quote
quote
Get a Quote
×
Quote Request

pA-DamID Sequencing Service (RUO)

Map nuclear lamina–associated DNA using antibody-tethered Dam marking to generate analysis-ready LAD profiles, QC artifacts, and figure-ready track visualizations for research use only.

  • Antibody-guided mapping of lamina-associated domains (LADs).
  • Control-aware normalization for interpretable LAD profiles.
  • Audit-ready QC summaries and reusable track deliverables.
Request a Method-Fit Review

What you get (at a glance)

  • Genome browser tracks and LAD/domain annotations.
  • Mapping summaries, normalization notes, and QC report.
  • Figure-ready placeholders for stakeholder alignment (RUO).
  • Designed for perturbation and cell-state comparisons (RUO).

What this service is and when it’s the right fit

pA-DamID sequencing service (RUO) maps nuclear lamina–associated DNA via antibody-tethered Dam marking to generate analysis-ready LAD profiles and audit-friendly QC artifacts. Deliverables include reusable genome browser tracks, domain annotations, and figure-ready visualizations for mechanistic studies and perturbation comparisons—strictly for research use only.

Definition (RUO): pA-DamID is a chromatin profiling approach that uses an antibody-targeted, protein A–Dam fusion to deposit localized adenine methylation (Gm6ATC) near a chosen nuclear protein (often at the nuclear lamina). Sequencing-based readout yields genome-wide profiles of nuclear lamina association, commonly summarized as lamina-associated domains (LADs) and genome browser tracks.

What pA-DamID measures: genome-wide nuclear lamina association patterns (LADs and LAD boundary behavior), condition-dependent shifts in lamina association, and track-style evidence suitable for interpretation in genome browsers.

What it does not directly measure: 3D contact frequencies between loci. If your program also requires 3D contact evidence, consider Hi-C sequencing for 3D contact context or Micro-C for higher-resolution contact maps in a complementary design (RUO). Protein-anchored interaction evidence can be supported by HiChIP for protein-anchored interaction evidence or PLAC-seq for promoter-anchored contacts (RUO).

RUO boundary: This service is provided for Research Use Only (RUO). We do not provide clinical diagnosis, prognostic claims, or treatment recommendations.

When it’s the right fit

  • You need LAD maps to support a periphery-association mechanism hypothesis.
  • You are comparing perturbations and want a consistent LAD readout.
  • You want an auditable package of tracks, domains, and QC artifacts.
  • You need a lamina-association layer to complement other assays (RUO).

Use cases mapped to decisions

Below are common pA-DamID study intents translated into reviewable outputs (tracks, domains, and QC evidence) to help you decide method fit.

Perturbation studies: “Did lamina association shift after intervention?”

Decision supported: whether a perturbation is linked to nuclear periphery re-organization.

Outputs: per-condition genome browser tracks, LAD calls, and a comparative summary highlighting regions with consistent shifts (reported as domain/track differences without invented performance numbers).

Cell-state comparisons: “Are LAD patterns stable across states or transitions?”

Decision supported: whether state transitions show reproducible LAD remodeling consistent with your model.

Outputs: state-wise LAD profiles, replicate concordance evidence, and a domain-calling summary suitable for cross-state review.

Targeted nuclear protein context

Decision supported: feasibility of a protein-defined lamina association hypothesis.

Outputs: an antibody-defined pA-DamID profile (where feasible) with explicit documentation of antibody and control strategy, plus mapping summary and background correction notes.

Planning orthogonal follow-ups

Decision supported: selecting follow-up assays that test mechanism with higher spatial or interaction specificity.

Examples: Pore-C for multi-contact long-read 3D signals, ChIA-PET, or RNA–chromatin context via RADICL-seq for RNA–chromatin interaction context and ChAR-seq for RNA–chromatin association mapping (RUO).

Multi-layer interpretation programs (RUO)

Decision supported: whether lamina association is concordant with expression/accessibility changes (from your existing assays).

Outputs: LAD tracks/domains delivered in reusable formats so your team can layer them with other evidence in downstream analysis.

End-to-end pA-DamID workflow (RUO)

Workflow overview: Study design (antibody + controls) → experimental marking via antibody-tethered Dam → library preparation and sequencing → mapping and filtering → control-aware normalization → LAD/domain calling → track generation and visualization → QC report + deliverables packaging.

1) Study design and feasibility review (RUO)

Define biological question, grouping, and comparison logic. Confirm antibody target strategy and required controls (including Dam-only control where appropriate). Document required metadata: organism/genome build, sample grouping, and target protein.

2) Experimental marking and library generation

Antibody-guided tethering of Dam to deposit localized Gm6ATC marking near the targeted nuclear context, followed by library preparation for sequencing readout.

3) Read mapping and primary processing

Map reads to the agreed genome build and generate mapping summaries. Produce intermediate files suitable for downstream normalization and visualization.

4) Control-aware normalization and background correction

Apply a documented background correction approach aligned with your control design and record normalization decisions in an audit-friendly manner.

5) Domain calling and track generation

Generate genome browser tracks and LAD/domain annotations using a documented domain calling approach. Prepare visualization-ready snapshots for internal review (RUO).

6) QC packaging and delivery

Deliver an explicit QC report plus analysis-ready deliverables (tracks + domain calls + supporting summaries).

QC evidence types you can audit: mapping summary and filtering summary; replicate concordance evidence; notes on control strategy and normalization rationale; deliverables manifest (what files are included and how they map to workflow steps).

Workflow diagram for pA-DamID including experimental steps and QC checkpoints leading to analysis-ready deliverables.

Standardized end-to-end pA-DamID workflow with defined QC checkpoints (RUO).

Demo results you can expect (figure-ready, RUO)

This section shows the formats and visual patterns you can expect for stakeholder alignment. Images are placeholders intended for design; they do not imply performance metrics.

Demo Image 1: LAD profile tracks in a genome browser

What you see: a genome browser view with LAD profile tracks across a locus, LAD boundaries highlighted, and an overlay of two conditions for qualitative comparison.

What decision it supports: whether lamina association changes are directionally consistent with your hypothesis and which intervals warrant deeper review.

Demo Image 2: QC + deliverables snapshot panel

What you see: a report-style panel summarizing QC sections (mapping summary, normalization notes, replicate concordance) and the deliverable file types (tracks, domain calls, manifest).

What decision it supports: whether your team will receive an auditable package that is straightforward to reuse in downstream analysis.

If your program needs RNA–chromatin context extensions, you may integrate with iMARGI for RNA–genome proximity or RADICL-seq for RNA–chromatin interaction context. For R-loop hypotheses, consider R-loop sequencing to support R-loop hypotheses or DRIP-seq for R-loop signal profiling (RUO).

Placeholder genome browser tracks showing lamina-associated domain profiles and condition-specific shifts for pA-DamID.Demo 1: LAD profile tracks

Placeholder report mock showing QC sections and deliverable file types for pA-DamID sequencing service.Demo 2: QC + deliverables snapshot

Sample requirements (RUO)

The most important “sample requirement” for pA-DamID is feasibility for your biological system and antibody/control strategy. Inputs can vary by organism, tissue complexity, and study design, so requirements are confirmed during method-fit review.

Sample type Minimum input Recommended input Shipping
Cells / nuclei Project-dependent (discuss in method-fit review) Project-dependent (replicates recommended) Cold chain per sample type (RUO)
Fresh tissue Project-dependent (feasibility assessment needed) Project-dependent (replicates recommended) Cold chain per sample type (RUO)
Frozen tissue Project-dependent (quality-dependent feasibility) Project-dependent (replicates recommended) Cold chain per sample type (RUO)

Metadata checklist (required for evaluation): organism and genome build; sample grouping and comparisons; target protein and antibody details (if antibody-defined targeting is requested); replicate plan to support replicate concordance evidence.

Data analysis & deliverables (audit-ready)

Deliverables (RUO): analysis-ready genome browser tracks (per sample/condition), LAD/domain annotations, a QC report documenting mapping summaries, normalization/control rationale, and a deliverables manifest that maps each output to the workflow step that produced it.

Primary Outputs
Genome browser tracks and LAD/domain annotations produced by a documented domain calling approach.

Comparative Summaries (Design-Dependent)
Condition-to-condition summaries describing LAD profile shifts, supported by replicate concordance evidence where applicable.

QC and Audit Trail
QC report with mapping summary, filtering summary, and normalization/control notes, plus a deliverables manifest mapping files to workflow steps.

Integration-Friendly Packaging
Reusable file outputs intended for layering with other evidence in downstream analysis (RUO).

Case study: pA-DamID maps lamina-associated DNA dynamics (literature example)

Source (peer-reviewed): van Schaik T. et al. Cell cycle dynamics of lamina-associated DNA. EMBO Reports (2020).

Article | PDF

Lamina-associated domains (LADs) are a key organizing layer of nuclear architecture, often linked to gene regulation and chromatin state. A central question in nuclear biology is whether lamina association is static or dynamic across biological processes such as the cell cycle.

The study applied pA-DamID to generate genome-wide lamina association profiles across cell cycle contexts, leveraging an antibody-defined strategy to localize Dam marking and produce sequencing-based readouts suitable for LAD interpretation.

From a service evaluation perspective, this paper illustrates that pA-DamID can support genome-wide lamina association profiling as track-like evidence, domain-level summaries consistent with LAD interpretation, and comparative analysis framing across biological states when study design and controls are appropriately planned.

If your research question is about nuclear periphery association—and you need a genome-wide, sequencing-based LAD readout that can be compared across conditions—pA-DamID is often method-fit. Feasibility review should focus on antibody/control strategy, sample context, and how you plan to interpret LAD changes alongside orthogonal assays (RUO).

Decision-blocking FAQs

References

References

  1. Cell cycle dynamics of lamina-associated DNA.
  2. Cell cycle dynamics of lamina-associated DNA (PDF).
  3. Cell cycle dynamics of lamina-associated DNA (Europe PMC record).
  4. van Schaik T et al. (2020) PMID:32893442 – 4DN Data Portal.

For Research Use Only. Not for use in diagnostic procedures. CD Genomics does not provide clinical diagnosis or treatment recommendations.

Leading Your Research Forward

Enhancing your vision research capabilities.

High-confidence 3D genomics services for chromatin interaction analysis and regulatory insight.

Quick Links
Contact Us
Copyright © CD Genomics. All Rights Reserved.
Top