Agenda

1. Updates on the sub-working groups.
2. Potential feedbacks on the SPRITE protocol.
3. Scheduling of additional OMICS protocols for future discussion.

Updates on the sub-working groups

Two of the subgroups are discussing some of the protocols, such as PLAC-Seq, Hi-Chip, Single cell Hi-C data standards and SPRITE (by Mitch Guttman).

Miao Yu (from Bin Ren’s Lab) is leading one of the sub-working groups. The group has been discussing PLAC-Seq and Hi-ChiP protocols and have been testing them. There is also a related protocol called ‘In situ ChiP-PLAC’ and is very similar to PLAC-seq or Hi-ChiP with differences in how the in situ Hi-C in proximity ligation is carried out. The protocol will be presented in one of the sub-working groups and the discussion is ongoing.

In the second sub-working group lead by Burak, the group is working in collecting single cell data from different labs and will be discussing individually how the existing bioarchive pipeline may fit to single cell data and how need to be modified. The group is working currently with two labs (Frase and Bill Noble Labs) and over next week will start working with Leonid Mirny and Bing Ren Labs. Four labs total.

Daniel and John Carlo have some discussion about the allelic specific sub-working group and the agenda will be finalized between the participants.

Feedback of the SPRITE protocol

The protocol is shared at the following Google Doc address: https://drive.google.com/file/d/17hkhfodJ-XnRME38hWfPGWXHAP69IcyR/view

About the question about sharing the barcode of DNA involved in the protocol, The OH will serve a central repository to share the barcoded oligos.

A vote is planned on the next call in two weeks to determine whether this protocol will become a production protocol for 4DN groups to generate the data.

Administrative note: As long as the protocol is approved by the SC, it becomes a production data protocol and all data with the protocol become production data (instead of technology development) and will be subject to production data release policies.

Scheduling of additional OMICS protocols for future discussion

Candidate OMICS protocol table is available at the following address: https://docs.google.com/document/d/1xaPsuobGvyWc7T7Gq3nZwFnDK2jlGMZ-U94pBDKwAKU/edit

We have a list of techniques that are need to be schedule for presentation

Schedule a presentation for single cell Hi-C and other techniques that are production data.

Data sets received in the join analysis project, is there protocols that are not currently in the OMICS table?

Some of the datatype like micro-C, GAM are not mature yet and would be not ready to be classified as production protocols, and being subjected to production data release policies. The decision will be made together with the group submitting the protocol about whether the status of the protocol is production-ready.

TrAC-loop (Keji Zhao Lab) and NAD-seq (Paul Kaufman Lab, similar to damID) have data submitted but were not included in the OMICS table yet. These datasets may not be in production grade but are still worth discussing during OMICS meeting.

Criteria for technology considered available to production.

In most cases, the investigators holds the key to their protocol (as is the case with micro-C and GAM). When investigators approves and present to OMICS, are there additional criteria? Currently we rely on the investigators and the group will provide input and guidelines towards a production ready protocol.

However, we would like to complete the release of the protocols before the last year of the project so that DCIC will have enough time to prepare the data and release them. As this is in line with NIH’s goal, NIH may help in facilitating the timely release of those protocols.

Separation from ENCODE and 4DN. Some of the protocols may have ENCODE standards (currently there doesn’t appear to be any) and if that is the case, we may adapt the ENCODE standards to prevent duplicated effort.