Update on the sub-working group focusing on PLAC-seq standard (Miao Yu)

PLAC-Seq experimental protocols have been finalized and tested by several groups.

Antibody selection protocols have been discussed. It is very crucial to demonstrate the specificity of antibody. Since ENCODE has an extensive protocol for antibody already, the sub working group decided to adapt the protocol. Antibodies should be tested and recorded by batches in this case.

The pre-processing protocol is still under development together with DCIC.

The lab can choose different library prep protocols (TN5 digestion on beads or not) depending on their capacities. There may be some resource-sharing activities among groups to facilitate that.

There are three protocols: HiChip, ChIA-PET and PLAC-Seq

In ChIA-PET, TN5 is also used in the protocol. There is a new protocol called in situ ChIA-PET now, doing the digestion, ligation, etc. similar to in situ HiC protocol to reduce non-specific ligation on beads, so that the resolution is improved.

There may need to be some reconciliation among the three protocols to prevent repeat work among those similar protocols.

The original ChIA-PET includes sonication to get chromatin fragment, then IP, then approximate ligation.

In situ Chia-PET, PLAC-seq and Hi-Chip are similar to one another and these are based protocol variants. The critical part is the digestion part in the protocol. An unified standard should be implemented. The long-read version of ChIA-PET is the protocol Yijun’s group has discussed previously but the in situ Chia-PET, is not published yet or approved by 4DN.

We can have PLAC-Seq sub working group have a presentation with two presentations from the other groups so that we can find the consensus among the three.

Update on the sub-working group focusing on single cell Hi-C discussion (Burak Alver)

In parallel DCIC are working with other labs to include other experiments. Keep processing the QC

A multiplexing approach vs a one cell per experiment approach. Currently DCIC is working with each group to get the data into their system and convert them to 4DN format.

The original paper by Noble and Shendure lab uses HeLa cell. However, Encode is not using or accepting HeLa Cells data because of the restrictions and difficulty to standardize the data.

Currently these groups are working with the joint analysis working group and will post data about HFF, GM12878 and other cell lines to the Data Portal.

DCIC would need to take metadata from raw experiment results and start processing from there.

Update on the sub-working group focusing on allelic analysis of HiC and other OMICS data (Burak Alver)

Both of the allele specific sub-working group call focused on hybrid mice analysis, including QC steps and concerns about mouse haplotype. Yunjiang from Ren lab also talked about phasing and distinguishing H1 from H9 cell lines. Mouse and human should probably been treated differently since in human phasing quality tends to be poorer. So in human we may look at the SNPs while in mouse we may take a more extensive approach.

Another topic is “region blacklist”, i.e. repeat elements of regions. Currently DCIC is using Juicer and Cooler to filter out genomic regions that are quiet or noisy and those filers have different resolutions and we are trying to compare.

When comparing different data, one unified blacklist may be helpful.. For the allele specific data has not been implemented yet.

This will be brought up in the next joint analysis call.

Data submission deadline for raw files and metadata is still Jan 15th because otherwise DCIC will not be able to process them for Jan 23 release (first freeze). Resequencing data with previously submitted metadata may be possible to submitted later but DCIC will be very busy processing them so it is not recommended.

Data freezing date is equal to data releasing data for production data types. For technology development data types, the data will be released after the next joint analysis call and will probably be negotiated with NIH.

In the first stage, raw data, metadata and processed files will be accepted since DCIC is not possible to complete the pipeline. The groups submitting the processed data should conform to established 4DN standards (GRCh38 reference, Juicer/Cooler format, etc).

It might be helpful for DCIC to remind everyone about the data submission deadlines. DCIC is currently cleaning up their repos on Github and will send out the link to the repos to the consortium. The documentation will also need be updated and will be provided by the end of January.

Vote to recommend the approval of the Dnase-HiC protocol (attached). \__This protocol was presented by Vijay Ramani from Jay Shendure lab on November 13.

DNase-HiC protocol has not been changed. The data has been uploaded to DCIC.

The protocol has been unanimously approved during the meeting and the protocol should be published to the entire consortium.