Agenda For PU1

  • ☐ Matt needs to send me PBM data
  • ☐ Need to rerun reli datasets

TODO Find threshold to remove weird samples (pairwise reli)

  • ☐ Try threshold based on average overlap within cell type.

TODO Alzheimer's disease examination

  • ☐ sort vertically by significance

TODO Finish first draft of manuscript [0/2]

  • ☐ Finish methods section
  • ☐ Finish supplemental stuff (lower priority)

DONE Extra Analysis

  • Note taken on [2025-12-18 Thu 09:18]
    Not planned
  • Histogram of peak widths
  • De-novo HOMER

DONE Unify genesets [1/1]

  • Note taken on [2025-07-31 Thu 10:21]
    shared​7​8
  • [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

DONE Percent ChIP peaks (Part C) [1/1]

  • [X] Integrate phil's script into nextflow pipeline

DONE GREAT analysis (Part D) [6/7]

  • In the Figures folder
  • Where did bed files come from?
  • [X] Emailed Lee about code
  • [X] Use fold enrichment instead of odds ratio
  • [X] 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)
  • [X] Add to Nextflow implmentation

Figure 3

DONE Part A [1/1]

  • [X] 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) [1/1]

  • ☐ 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

DONE Heatmap (Part A) [1/1]

  • [X] disease only
  • [X] cell counts only
  • [X] all

  • DONE RELI summary table [0/0]

DONE Mario Analysis

  • Identifies allele dependant behavior
  • Talk to Xioting

DONE 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?

DONE Browser sessions

  • Note taken on [2025-08-20 Wed 10:41]
    Lee said we could contact her about it
  • Look for SNPs that show up as differentially regulated
  • Reaquaint myself with Trackgen

Papers to Read

DONE Harley et al

DONE Figure 5

  • Make square
  • Put R score (Spearman) in top left
  • GM12878 only

Figure 6

  • Table for is this variant significant in each method?

Supplemental datasets