Agenda For PU1

  • Note taken on [2025-07-31 Thu 10:21]
    shared78
  • [X] Combine long-name cell intersections (bedtools merge)

Figure 1

DONE Create UMAP and PCA (Part B) [3/3]

  • Molly made the samplesheets manually so need to regenerate with code to add more metadata columns
  • [X] Matt wants supplemental figures for antibody and experiment
  • Antibody already has label, but need experiment annotations
  • [X] Antibody supplement
  • [X] Set colors to match cell type diagram

Figure 2

TODO Percent ChIP peaks (Part C) [0/1]

  • ☐ Integrate phil's script into nextflow pipeline

TODO GREAT analysis (Part D) [4/6]

  • In the Figures folder
  • Where did bed files come from?
  • [X] Emailed Lee about code
  • [X] Use fold enrichment instead of odds ratio
  • ☐ Generate Tables
  • [X] Integrate great script with makefile?
  • [X] Combine long-name cell intersections (bedtools merge)
  • ☐ Update to set consistent radius (don't need the fold change)

Figure 3

TODO Part A-B [0/1]

  • ☐ Move SPI1/ets/PU.1 to bottom of bar plot, and make coloring consistent by setting a specific order to the motifs in the bar plot

DONE SPAMO analysis (Part C)

  • Note taken on [2025-07-31 Thu 10:23]
    not doing this anymore?
  • Identifies likely partners for PU.1
  • May or may not be working on it?

DONE Contact Diego

  • For motifs

Figure 4

Phenotype RELI (Part A) [0/1]

  • ☐ Need to rerun phenotype RELI using top 10 (page two of excel sheet)
  • ☐ Need to add Union set categoreis + EBV+ + EBV- to phenotype reli results

TODO Heatmap (Part A) [0/3]

  • ☐ disease only
  • ☐ cell counts only
  • ☐ all

TODO Mario Analysis

  • Identifies allele dependant behavior
  • Talk to Xioting

TODO Download EGA datasets (vcf files)

  • Required for MARIO analysis
  • Need Permission still (shreeja will know)

Nextflow Pipeline

DONE Dockerize/Nixify R dependencies

  • Note taken on [2025-08-07 Thu 16:11]
    Pipeline exists here: https://github.com/cchmc/PU1-Nextflow

  • Note taken on [2025-07-31 Thu 10:30]
    Trying to implement a nextflow pipeline.

    Already implemented dockerization/nixification of depenedencies, so just need to write the pipelines themselves.

  • Are we publishing code?

DONE Draft Methods

-Note taken on [2025-06-03 Tue 13:06]
Added to wiki at https://tfwiki.cchmc.org/wiki/PU.1_Project/Methods

  • Put in Docs folder
  • Maybe put on wiki instead?

TODO Browser sessions

  • Look for SNPs that show up as differentially regulated
  • Reaquaint myself with Trackgen

Papers to Read

TODO Harley et al