Figure 3:

Quality Control steps for Basic Protocol 1. Critical quality controls for each step are evaluated via Bioanalyzer. A. QC #1. DNA size distribution profiles of the chromatin DNA after In situ AluI digestions. The distribution usually peaks at around 5–8 kbps, as determined by Bioanalyzer profiling. B. QC #2. DNA size distribution profiles after proximity ligation of the AluI-digested chromatin sample. It is expected that after ligation, the size of chromatin DNA fragments would increase accordingly. Indeed, as shown in this sample data, the DNA size observed in QC #2 is approximately 2–5 kb larger than the DNA fragments in QC #1, indicating the proximity ligation was successful. C. QC #3. DNA size distribution profiles of sonication-sheared chromatin DNA fragments, showing obvious shift of peak from >10 kb to short chromatin fragments in the range of 2–3 kb. D. QC #4. After ChIP-enrichment, the enriched chromatin DNA is analyzed by Bioanalyzer for quality and quantity. The profile looks the same as in QC 3#, as expected. E. QC #5. DNA size distribution profiles of tagged-DNA fragments after tagmentation by Tn5 transposase step, showing the desired shifting of DNA fragments to the size range of 200–700 bp. F. QC #6. DNA size distribution profiles of PCR-amplified DNA fragments, showing that the majority of amplicons are in the 300–700 bp range. G. QC #7. DNA size distribution profiles of the final In situ ChIA-PET library after size selection for the 350–600 bp range, which is the ideal size range for Illumina paired-end-tag sequencing analysis.