Fig. 1
Schematic illustration of the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) in Aspergillus niger. a Protoplasts used for nuclei isolation and schematic procedure of ATAC-seq technique. Protoplasts were prepared under the cultivation condition by adding lywallzyme. After filtration via miracloth membrane, the concentration of extracted protoplasts reached 105/μL. b Fragment sizes for amplified ATAC-seq libraries by 15 cycles of PCR reaction. 5 × 104 protoplasts of A. niger CBS513.88 were used for Tn5 transposase reaction, respectively. Lane 1: replicate 1, WT1; Lane 2: replicate 2, WT2. c Insert sizes determined by high-throughput sequencing. Peaks with different fragment length indicate that the fragments contain one or more nucleosomes. d Heatmaps showing the distribution of accessible regions around TSSs in A. niger CBS513.88: The meaning of “ < 100” is that the fragment sizes of pair-end reads were less than 100 bp of fragment size. And the meaning of “ > 180” is that the fragment sizes of pair-end reads were more than 180 bp. Regions of < 100 bp were assigned as nucleosome free and those of > 180 bp were assigned as oligonucleosomal [27]. The signals are derived from two technical replicates. e Read coverage of the 1-kb region flanking TSSs in A. niger CBS513.88. f Heatmap clustering of Spearman correlation coefficients for 16 A. niger ATAC-seq datasets