Genome-wide 3D mapping
| Workflow | Details | Best | Services | Genomics | Trustworthy |
|---|---|---|---|---|---|
| Question → assay fit | Define discovery vs comparison, expected resolution, depth constraints, and sample limits. | First-pass discovery; architecture changes across conditions; genome-wide hypothesis generation. | Hi-C Core, Hi-C Sequencing, Micro-C | Compartments, TADs, loops, stripes; comparative maps | Clear expectations for resolution and interpretability before you spend more. |
| Library & sequencing QC | Complexity/duplication, mapping, contact yield; flag low-input and tissue risks early. | Budget-sensitive projects that need “go/no-go” clarity. | Hi-C Sequencing, Micro-C | Depth-to-resolution expectation | Early risk flags to avoid costly dead-ends (low yield, low complexity, sample limits). |
| Analysis & interpretation | Loop/TAD/compartment calling, reproducibility, differential architecture, figure-ready outputs. | Manuscript/grant deadlines; internal milestone reviews. | Hi-C Sequencing, Hi-C Core | Decision-ready conclusions for follow-up assays | Results packaged for follow-up design and publication-ready figures. |
Targeted 3D for V2G & enhancer assignment
| Workflow | Details | Best | Services | Genomics | Trustworthy |
|---|---|---|---|---|---|
| Target design & enrichment plan | Define promoter/region panels, ROI strategy, on-target expectations, and control design. | V2G, enhancer–promoter linking, regulatory region deep interrogation. | Capture Targeted, Capture-C, Capture Hi-C, Promoter Capture Panel | High-signal contacts at regulatory regions | Panel/ROI design aligned to V2G decision logic and controls. |
| QC (capture-specific) | On-target rate, enrichment, duplicate/complexity, reproducibility across replicates. | Teams that must justify vendor outputs to PM/procurement. | Capture-C, Capture Hi-C | Promoter–enhancer link confidence | Capture performance summarized for procurement-friendly review. |
| Link calling → validation path | Report prioritized links, candidate genes, and a suggested validation route (3C-qPCR/ddPCR or FISH). | Go/No-Go target nomination; functional follow-up planning. | 3C-qPCR, 3C-ddPCR, 3D DNA-FISH | Actionable V2G evidence package | Validation path included (3C-qPCR/ddPCR or imaging) to strengthen conclusions. |
Protein-anchored 3D for mechanism
| Workflow | Details | Best | Services | Genomics | Trustworthy |
|---|---|---|---|---|---|
| Factor strategy (biology → assay) | Choose HiChIP vs PLAC-seq vs ChIA-PET based on factor type, enrichment need, and interpretation goals. | Mechanism studies linking binding to looping; pathway-centric hypotheses. | HiChIP, PLAC-seq, ChIA-PET, ChIP-loop | Factor-centric loops, anchored interactions | Factor choice mapped to biological interpretation and enrichment expectations. |
| Library QC & enrichment | Assess enrichment, complexity, duplication, anchored contact quality and signal-to-noise. | Projects where “interpretability” matters more than breadth. | HiChIP, PLAC-seq | Anchored loop maps | Signal-to-noise assessed so anchored loops remain interpretable. |
| Mechanistic interpretation | Integrate peaks + contacts; prioritize loops for perturbation/validation experiments. | Cross-functional reviews (biology + translational + PM). | HiChIP, ChIP-loop | Evidence linking factor binding to regulation | Prioritized loops ready for perturbation and mechanistic follow-up. |
Long-read multi-contact & SV context
| Workflow | Details | Best | Services | Genomics | Trustworthy |
|---|---|---|---|---|---|
| Feasibility & design | Define SV/assembly goal, repeat complexity, required multi-way information, and long-read constraints. | SV interpretation, de novo scaffolding, complex loci and repeats. | Pore-C, HiPore-C, T2C, Tri-C | Multi-way contacts, long-range scaffolding evidence | Feasibility framed around your SV/assembly question and genome complexity. |
| QC (long-read aware) | Read length distribution, mapping strategy, contact yield, multi-contact characteristics. | Teams that need confidence before expanding spend. | Pore-C, HiPore-C | Depth vs interpretability trade-off | Long-read characteristics summarized for “expand or stop” decisions. |
| SV/assembly interpretation & reporting | Deliver contact evidence supporting rearrangements/scaffolds; highlight regions needing orthogonal validation. | Non-model organisms; complex genomes; SV-heavy disease models. | Pore-C, HiPore-C, 3D DNA-FISH | SV/assembly decision-ready package | Evidence organized for orthogonal confirmation at complex loci. |
