📋 Workflow
Full workflow, products add-to-cart directly1
Crosslinking
30 minFormaldehyde crosslinks chromatin to fix spatial proximity, quench and collect
💡 Tip Optimize crosslink time per cell type
⚠️ Caution Quench fully to stop reaction
🧪 Materials for this step (click to shop by spec/brand)
2
Restriction digest and end-label
OvernightDigest with a rare-cutter restriction enzyme, biotinylate ends
💡 Tip Biotin enables pull-down of contact fragments
⚠️ Caution Digest completely
🧪 Materials for this step (click to shop by spec/brand)
3
Blunt-end ligation and purification
4 hLigate fragments blunt-end under proximity conditions, reverse crosslinks and purify DNA
💡 Tip Proximity ligation is the core principle
⚠️ Caution Avoid random ligation artifacts
🧪 Materials for this step (click to shop by spec/brand)
4
Library, sequencing and analysis
2–3 daysBuild library enriching biotinylated fragments, sequence and analyze contact matrix and TADs
💡 Tip Use dedicated software for contact maps
⚠️ Caution Enough depth for resolution
🧪 Materials for this step (click to shop by spec/brand)
⚠️ 5 Common Beginner Mistakes
- ① Poor/over crosslinking loses architecture info
- ② Random ligation creates artifact contacts
- ③ Low depth gives poor resolution
- ④ Missing biotin loses fragments
- ⑤ Improper analysis misreads structures
❓ FAQ
+What structures can Hi-C reveal?
TADs, loops, A/B compartments and long-range enhancer-promoter interactions.
+How deep to sequence?
Depends on resolution; TAD-level needs hundreds of millions of reads, enhancer-resolution more.
+Hi-C vs other C-methods?
Hi-C is genome-wide unbiased; 4C/3C/ChIA-PET focus on loci or protein-mediated interactions.