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
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