Chromatin accessibility · Research internship

Bulk ATAC-seq analysis of mature and memory NK cells

Do mature and memory human NK cells show reproducible differences in chromatin accessibility across public bulk ATAC-seq samples?

View GitHub repository
Editorial illustration of DNA transitioning between compact and accessible chromatin around nucleosomes
Illustrative editorial visual of chromatin accessibility; complete analytical results and interpretation are documented in the repository.

I designed and implemented the full reproducible analysis workflow for 10 public samples, from quality control and alignment through donor-aware differential testing, motif exploration, genome-browser review, documentation, and a synthetic demonstration.

Completed during a bioinformatics internship at University Medical Center Göttingen using public data.

  1. 01FastQC quality review and Bowtie2 alignment
  2. 02SAMtools processing and MACS3 peak calling
  3. 03Consensus-region counting with featureCounts
  4. 04Donor-aware differential accessibility with DESeq2
  5. 05HOMER motif exploration and IGV review
  • 59,186 consensus regions passed the analysis filter.
  • The workflow connects quality review, alignment, consensus-region counting, donor-aware differential testing, motif exploration, and genome-browser review.
  • The repository preserves the complete workflow, statistical results, tutorial material, and a synthetic demo for reproducibility.
  • The public cohort was small, limiting statistical power.
  • Exploratory motif and browser observations are not causal or mechanistic evidence.
  • Public-data analyses remain sensitive to cohort composition, preprocessing choices, and available metadata.
BashRPythonFastQCBowtie2SAMtoolsMACS3featureCountsDESeq2HOMERIGV
Next case studyBerlin Airbnb price prediction