4D Nucleome Network Wiki

Document for ChIA-PET standards

Protocol

• Relation to current technologies such as Hi-ChIP and PLAC-seq
  • ChIA-PET is a more mature stand-alone method that deserves its position in the documentation
  • Do we need to compare ChIA-PET and other protocols, mentioning those so that people can expect what their data may look like
  • Standard can be defined in a way to allow future improvements to the protocol, together with a basic standard for the technology
• Library quality controls
  • At the end of the documents, QC for various steps of library are listed
  • Basic numbers, key steps for QC
    • Number of cells: 1e8 (100M) would be comfortable, less is doable but may result in complexity problems and may be affected by PCR redundancies
    • Antibody robustness: follow the current parameter from ENCODE regarding to ChIP-seq, antibodies able to generate qualified ChIP-seq data should be good enough for ChIA-PET
    • Sequencing can be done in two levels: 1) sequencing on known binding sites to verify; 2) should pass miSeq QC first, then the number of reads should be ~100M to ~150M
• Proximity ligation would affect ChIA-PET library quality (without ligation the results become ChIP-seq). Chromatin contact can be used to verify.
• Collision rate to assess QC
• Gold standard loops or features for ChIA-PET
  • For example, MALAT1-NEAT1 interaction in Hi-C