Analysis of H3K4me1, Mesp1 ChIP-seq in 2i and in Zic2/3 double KO cells

FastQ files were cleaned and trimmed using Trimmomatic⁷³. Paired-end reads were aligned using Bowtie2⁷⁷. Picard tools were used to remove PCR duplicates (Broad Institute), samtools to remove mitochondrial reads and low-quality alignments⁷⁸. Peaks were called using MACS2⁷⁹ with a threshold p-value of 10^-10. Where duplicates available (all the Mesp1 ChIP-seq samples), the intersection peaks of both replicates were kept for further analysis. For Mesp1 ChIP-seq samples, peaks were then compared to those obtained in Mesp1 ChIp-seq during differentiation using BEDtools⁸².