T cell ATAC-seq & ChIP-seq Tracks

Contact: mpipkin@scripps.edu
Supported by NIAID #1P01AI145815-01A1: Transcription factor regulation of CD4 and CD8 T cell effector and memory differentiation and function

>>Link to UCSC truck hub<<

• CD8+ T cells play a key role in anti-viral and anti-tumor immune responses. Upon stimulation, antigen inexperienced naïve CD8+ T cells undergo rapid expansion and extensive chromatin landscape remodeling & transcriptional profile reprogramming, leading to formation of different phenotypes.
  
• This is a repository of ATAC-seq genome tracks of murine CD8 T cells, together with ChIP-seq tracks of important transcription factors in CD8 T cells. It can be used as a reference for CD8 T cell chromatin landscape at different stages of development / phenotypes.
  
• Consider citing Immunity (2018) and original references
  

ATAC-seq of murine CD8 T cells

1. In vitro TCR stimulation time points:

• 0, 2, 6, 12, 24 hours
• WT and Runx3KO P14 cells
• GEO accession number: GSE111149

2. In vitro cultured CD8 T cells:

• High(100U) / low(10U) IL-2 levels
• Different combinations of PMA/Iono/CsA stimulation
• GEO accession number: GSE88987

3. In vivo sorted CD8 T cells phenotypes:

• Naive, MPEC, SLEC, Memory, Exhausted
• GEO accession number: GSE88987

Reference ChIP-seq of key transcription factors

Bach2 BATF cJun IRF4 JunB JunD Runx3 day6 (d6) Runx3 ex vivo Stat5a Stat5b Tbet Tcf7