Sequencing data related to Gutekunst et al. "Nucleosome linker DNA methylation by DNMT3A/DNMT3B3 is controlled by nucleosome binding and multimerization of DNMT3 complexes on DNA"

In the second PCR reaction, 1 µL of PCR1 product was amplified using i5 and i7 indexing primers and Q5 polymerase (New England Biolabs). Successful amplification was verified by agarose gel electrophoresis. Samples were pooled in equimolar amounts, purified with NucleoSpin® Gel and PCR Clean-up kit and used for Illumina paired end 2×250 bp sequencing conducted at Novogene.

Bioinformatic analysis of NGS data was conducted using a local instance of a Galaxy server. Obtained sequence reads were trimmed with the Trim Galore! Tool, discarding tails with a quality score below 20.

Afterwards reads were paired using PEAR. Reads were filtered according to the expected DNA length using the Galaxy Filter FASTQ tool. The de-multiplexing was done by the selection of the reads with specific combinations of barcodes and Illumina adapters which were then then mapped against a corresponding reference sequence using bwameth (github.com/brentp/bwa-meth).

Finally, the DNA methylation of individual CpG sites was computed using MethylDackel (github.com/dpryan79/MethylDackel). Here, the final analysed sequences are provided. DNA sequencenes Dinucleosome Linker-70 CGAGGTCGACGGTATCGATAAGCTTCTGGAGAATCCCCCAGCCGAGGCCGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGTTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCAGGTGTCAGATATATACATCCTGTAACGCTATCCGCGCCACGTCTACGCTNNNTACGAGAACGCCGAGACGTGCGAGCAGCGAAAGCGGCCGaCCTGGAGAATCCAGGTGCTGAGGCAGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGTTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACCACTCAGATATATACATCCTGTAAGGGCGAATTCCACATTG Dinucleosome Linker-58(1) CGAGGTCGACGGTATCGATAAGCTTCTGGAGAATCCCCCAGCCGAGGCCGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGTTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCAGGTGTCAGATATATACATCCTGTGCCACGTCTACGCTNNNTACGAGAACGCCGAGACGTGCGAGCAGCGAAAGCGGCCGaCCTGGAGAATCCAGGTGCTGAGGCAGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGTTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACCACTCAGATATATACATCCTGTAAGGGCGAATTCCACATTG Dinucleosome Linker-58(2) CGAGGTCGACGGTATCGATAAGCTTCTGGAGAATCCCCCAGCCGAGGCCGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGTTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCAGGTGTCAGATATATACATCCTGTAACGCTATCCGCGCCACGTCTACGCTNNNGAGACGTGCGAGCAGCGAAAGCGGCCGaCCTGGAGAATCCAGGTGCTGAGGCAGCTCAATTGGTCGTAGCAAGCTCTAGCACCGCTTAAACGCACGTACGCGTTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACCACTCAGATATATACATCCTGTAAGGGCGAATTCCACATTG CpG rich DNA CTATGGAAACCCCTGTGGAGCTTCAGGGGCACGAGTGAGGCGGGCGCTGGCGGGCCAAGGTGACGAAGGCGCCTCCGGCTCTTGGGCCAGCGGACTGAGCGGTGGAGCAGAACTTGGGTGCCTCGGGGACCGCCAAAAAGTGGCCTTGTCCACTTCTCTGAG Further information The primers are provided in "NGS_Primers" A compilation of the sequencing reads provided here is given in "NGS_Table" References The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.

Nucleic acids research 2022, 50, W345-W351, doi: 10.1093/nar/gkac247 Albrecht, C., Bashtrykov, P., and Jeltsch, A. (2024) Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol.

Methods

Mol Biol 2842, 405-418, doi: 10.1007/978-1-0716-4051-7_21 For all details regarding furhter analysis and interpretation of the data, refer to the corresponding manuscript (Gutekunst et al., 2026), which is connected with this data entry.