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Review of the Phase 1 PsychENCODE capstone resource: �Layers of distributed information

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Material in the 3 capstones:

AC - Wang et al. ('18)

DC - Li et al. ('18)

NC - Gandal et al. ('18)

Resource.psychencode.org

Development.psychencode.org

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Base Data Layer

Organizing Metaphors

Future considerations

  • New "Axes" ?
  • New sets to merge (GTEx v8, HCA)?
  • Reference brain ?

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[AC,DC]

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Pipeline Results

  • ChIP-seq & Me
    • signal tracks & peaks
    • Differential H3K27ac & Me peaks
  • Bulk RNA-seq quantifications
  • Single-cell
    • Quantifications
    • Cell-type signatures & fractions
  • Imputed genotypes
  • Hi-C matrix & TADs

Future considerations

  • ATAC-seq pipeline? sc-ATAC?
  • More cell types
  • WGS vs. imputed genotypes

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[AC,DC]

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Derived Results

  • DEX genes & co-expr. modules
    • Across development, �regions & conditions
    • Differential splicing
  • PFC QTLs
    • cis-eQTLs - ~2M (sat’d)
    • fQTL, cQTLs
  • Enhancers (init. PFC & CBC)

Future considerations

  • Trans QTLs? More regions?
  • Starr-seq enhancers?

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[AC,NC]

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Integrative Models

  • Integ. Regulatory Networks
    • Activity+Hi-C+QTL
    • Double overlap high-conf. linkages (eg A+H)
  • Init. disease prediction model (DSPN)

Future considerations

  • Better networks? Single-cell?
  • How to distribute models ?

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[AC]