4D Nucleome Network Wiki

Standard guidelines
Consist of experimental part and protocols, agreed on using the in situ Hi-C paper as a standard
MInor variations on the experimental protocols
This document may be updated on an annual basis and will be kept stable in the meantime.
Concerns:

1. Which other enzymes can be used? Hind III give very good quality data
2. and are more reproducible but may have lower resolution than 4-base cutters. The current wording allows individual PIs to choose their restriction enzyme based on their current situation.
3. Biotin removal step will affect yield and should be kept optional instead of mandatory. The SOP will be without biotin removal (all published in situ Hi-C data have no such step).
4. All variations from the base protocol (SOP) should be recorded in the meta data so that DCIC can work on those.
5. Cell density at the time of harvest: Is the cell density need to be standardized? \Suspension cells will be in per unit volume and adherent cells will be in per unit area. - Although this appears out of scope - it need to be included in experimental / cell-line WG SOP so that researchers will record it before actually generating data (and submitting them), it might still be OK to include in this data standard document. - Indicating whether there are other frozen aliquots and point to them in meta data so that people know which datasets are coming from the same biological replicate. - Crosslinking: standardized in SOP and have no dramatic differences among groups. - Sequencing Depth: required 500M raw paired-end sequence reads now in the final document. - Earlier experiments may use variations. - Format for pairs file
   Standardized file format for read pairs (developed by Burak), text-based file before chromosomal binning
   Planned to be approved during next meeting: . - ChIA-PET
   Defer to the next meeting - Other data types - Joint WG of OMICS and Images
   Maybe incorporate a larger group than the current OMICS WG to include some members from the imaging WG.
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