Moran Lab Meeting 3-12

John Cheney

500 Queer Scientists Project

Meet Maeve McLaughlin

International Day of Women and Girls in Science

  • Shari Dilley (6th Grade)
  • Sarah Dutcher (9th Grade)
  • Dr. Martin (12th Grade @ WOU)
  • Dr. Emma Coddington (Soph. Year Underg.)
  • Dr. Melissa Marks (Jr Year Undergrad)
  • Dr. Rosa Leon Zayas (Jr Year Undergrad)
  • Dr. Leslie Coonrod (Masters)
  • Dr. Stacey Wagner (Masters)
  • Dr. Duygu Altinok Dindar (CEDAR)
  • Dr. Theresa Lusardi (CEDAR)
  • Dr. Amy Moran

Today’s Plan – Jurkat ATAC

  • Profiling Accessible Chromatin with Updated JASPAR Putative ARE files
  • Functional Genomics on Chromatin Accessibility Data
  • Genomic Binning for Identification of Changes in Chromatin State

Profiling Accessible Chromatin – Putative ARE’s

Here I profile Differentially Accessible Peaks containing ARE’s in conditions of interest

  • I’ve done this previously, but this update is with a more enumerated version of JASPAR motifs
  • Thanks Amy, Rachel and Reed for spending mental energy on this with me

JASPAR Database – MA0007

ARS ARSR down || ARS ARSR up

ARS EVS down || ARS EVS down

Functional Genomics on Chromatin Accessibility Data

  • Methodology and visual walkthrough
  • Results so far

Differential Peak Accessibility DESeq2-style

Consider an experiment with 4 conditions with -up and -down regulated genes/peaks between conditions:

  • A
  • B
  • C
  • D

Differential Peak Accessibility DESeq2-style

The following sets of iterative comparions would be generated:

  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up
  • A-B-down
  • A-C-down
  • A-D-down
  • B-C-down
  • B-D-down
  • C-D-down

Sort Everyone into their groups

  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up
  • A-B-down
  • A-C-down
  • A-D-down
  • B-C-down
  • B-D-down
  • C-D-down

Sort Everyone into their groups

  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up
  • A-B-down
  • A-C-down
  • A-D-down
  • B-C-down
  • B-D-down
  • C-D-down

Sort Everyone into their groups

  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up
  • A-B-down
  • A-C-down
  • A-D-down
  • B-C-down
  • B-D-down
  • C-D-down

Regressing to colors and shapes

Kindergardners could never do this

Kindergardners could never do this

Kindergardners could never do this

Kindergardners could never do this

Kindergardners could never do this

Kindergardners could never do this

Kindergardners could never do this

Functional Plot Results – GO

Genomic Binning for Identification of Changes in Chromatin State

Alluvial Plot Techniqe and Interpretation

  • Takes in raw peak data
  • Genome is binned in 100bp bins
  • Chromatin constituentively closed is discarded
  • Frequency matrix is collapsed to a table
  • One condition serves as the focal condition
  • Blue is closed
  • Red is open
  • Hi-lights interesting chromatin

Alluvial Examples

  • EVSR -> ARSR
  • EVS -> EVSR -> ARS -> ARSR

Future Directions with Genomic Binning

  • Using isolated instances of peak behavior as an input for motif enrichment/TFBS searching
  • i.e. Which motifs/TF’s are enriched in peaks that only open with AR or Ligand?

Gag Reel

The End :)

Kindergardners could never do this 3

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  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up

  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up

  • A-B-up
  • A-C-up
  • A-D-up
  • B-C-up
  • B-D-up
  • C-D-up

Bell Curve Example

Bell Curve Example smaller