4D Nucleome Network Wiki

Determine Experimental Protocol

• Create Protocol link to be public in the 4DN portal
• Make a recommendation working group about decision and present in the steering committee
• Variation in the protocol are expected And additional meetings to decide variations in the protocol
• Variations are minimal and it’s unclear if these variations are critical, may need further verification once more data are available
• Variations in the protocol need to be documented
• MicroC and HiC data analysis protocols need to be confirmed from members of corresponding labs
• A draft of finalized experimental protocol can be seen here:
• https://docs.google.com/document/d/1aF4Zq3CgXkcOZRXuzsXFCMjU-7-jvXK7sjNQ7KoPc3k/edit

Meta-data

• Fragmentation methods may have the same importance of antibody selection for Chipseq
• Gel pictures after fragmentation needed in the meta-data? Which gel pictures should be include? Gel pictures for linked products may be more useful than those of final library.
• Use “whether passed QC” instead? Some information may not be as useful past internal QC.
• In ENCODE some data are labeled with warning with sequencing depth, antibody annotation, etc when they are submitted to DCC. This provides DCC info to let them approve individual datasets. Also independent analysis can be carried out with controls for the data with those additional labels and information.
• Go through the meta-data table next time, considering the requirements of OMICS and DCIC. The meta-data table can be viewed and edited here:
• https://docs.google.com/document/d/1P3Nu23_xycyg7ACckMRFUABpljZ-cwzdTSi-Csn7Ydg/edit
• Set up pipelines with all data that has been submitted .Koray will generate a document of meta data to be included.
• Time frame to release data needs to be finalized

Data Format

• Has been proposed for HiC in Erez lab. Bring speakers for each available format during or after next meeting to adopt one of those formats or create a new one.
• There appears to be two formats going around: HiC format (based on hdf5) from Dekker’s group; the other format (similar to bigWig) from Feng’s lab for 3D browser. Feng will prepare a couple of slides for next meeting