CD8+ splenic T cells from wild-type and cTKO mice were isolated by flow cytometry. ChIP against H3K27me3 (1 μg; Millipore, 07–449) and H3K36me2 (1 μg; Millipore, 07–274) and sequencing library preparation was performed exactly as previously described26 (link). Adapters were trimmed using BBTools28 (link). Alignment to mm10 was performed using Bowtie221 (link) and duplicate reads were marked using Picard and removed using SAMtools. Signal normalization between samples was performed using THOR30 (link). ChIP-seq signal intensity was calculated for chromatin states using GRanges and custom R scripts (Supplementary File 1 ).
Protocol detail
ChIP-seq Analysis of H3K27me3 and H3K36me2
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Corresponding Organization :
Other organizations : Albert Einstein College of Medicine, Columbia University Irving Medical Center, New York Hospital Queens, NewYork–Presbyterian Hospital, New York University, Cornell University, Memorial Sloan Kettering Cancer Center, University of Pennsylvania
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Variable analysis
independent variables
- Wild-type and cTKO mice
- H3K27me3 chromatin states
- H3K36me2 chromatin states
- CD8+ splenic T cells
- ChIP against H3K27me3 (1 μg; Millipore, 07–449) and H3K36me2 (1 μg; Millipore, 07–274)
- Alignment to mm10 using Bowtie2
- Duplicate reads marked using Picard and removed using SAMtools
- Signal normalization between samples using THOR
- None specified
- None specified
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