ChIP-seq in Bl6xSpretus F1 hybrid mESCs

To confirm the loss of transcription factor (TF) occupancy at SNP-containing motifs, we performed ChIP-seq for three TFs in the Bl6xSpret hybrid mESC line. This dataset includes cross-link ChIP-seq data for CTCF, KLF4, and SOX2. Two biological replicates were generated for each TF. The protocol was adapted from Trovato et al. (2024), with minor modifications. Chromatin was sheared using a Bioruptor Pico (Diagenode) and incubated overnight at 4 °C with rotation with antibodies against KLF4 (AF3158, R&D Systems), CTCF (07-729, Merck Millipore), or SOX2 (AF2018, R&D Systems). Bead–immunocomplexes were reverse cross-linked after RNA and protein digestion, and DNA was purified using 1.4x SPRI-select beads. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit (New England Biolabs) and sequenced on an AVITI platform, using Cloudbreak Low 2x150 bp runs (250 M clusters/run) for H3K27Ac and Cloudbreak High 2x75 bp runs (1000 M clusters/run). AVITI and Illumina adapters were trimmed using TrimGalore! v0.6.7 (Krueger et al., 2023). Trimmed reads were competitively aligned to the Bl6 and Spret genomes and filtered to discard reads with allelic mapping bias using a version of WASP extended to include indels (van de Geijn et al., 2015; Sigalova et al., 2025). Finally, duplicate reads were identified and removed using the Picard tool MarkDuplicates v2.15.0. (https://github.com/Krebslabrep/TF-chromatin.git).