title: GSM9222105: ATAC_seq_leaf_rep5; Solanum lycopersicum; ATAC-seq
library_construction_protocol: ATAC-seq: Six biological replicates of 1g of freshly collected terminal leaflet of young M82 leaves were ground in ice-cold isolation buffer  (300 mM sucrose, 20 mM Tris pH 8.0, 5 mM MgCl2, 5 mM KCl, 5 mM beta-mercaptoethanol, 35% glycerol, 0.2% Triton X-100). After grinding, the suspension was filtered through a series of cell strainers (the smallest being 70 mm). Samples were further disrupted using a Dounce homogenizer, and then washed four times with ice-cold isolation buffer. The enriched nuclei samples were resuspended in Resuspension Buffer (50 mM Tris pH 8.0, 5 mM MgCl2, 5 mM beta-mercaptoethanol, 20% glycerol). Hi-C: The cauliflower-like tissue from young an inflorescences was harvested 10 weeks after sowing, with tissue collected from two different plants to obtain two biological replicates (3.3 g and 3.1 g, respectively). Hi-C data was generated using the Arima Hi-C 2.0 Kit (PN A410110) according to the manufacturer's user guide for plant tissues (PN A160163 v00). Nuclei extraction was done using the CelLytic Plant Nuclei Isolation/Extraction Kit according to the manufacturer's recommendations for cell lysis and semi-pure preparation of nuclei, with the addition of a Dounce homogenizer to increase nuclei yield (Sigma, CELLYTPN1). DNA fragmentation was performed with the Bioruptor Pico (Diagenode) using 4 cycles of 15 s sonication followed by 90 s rest. ATAC-seq: For the transposase reaction 100,000 nuclei were resuspended  in 22.5 ml freezing buffer (5 mM MgCl2, 0.1 mM EDTA, 50 mM TRIS pH 8.0, 40% glycerol), and were mixed with  2X DMF Buffer (66 mM Tris-acetate (pH 7.8), 132 K-Acetate, 20 mM Mg-Acetate, 32% DMF) and 2.5ul Transposase enzyme from Illumina Nextera Kit (Catalog No. FC-121-1031), and incubated at 37°C for 30 min. Tagmented DNA was isolated using NEB Monarch PCR Purification kit (Catalog No. NEB #T1030). Next-generation sequencing (NGS) libraries were amplified in two steps (Buenrostro et al. 2015) using KAPA HiFi HotStart ReadyMix PCR kit (Catalog No. KK2601). NGS libraries were PE50 sequenced on an Illumina MiSeq SY-410-1003 instrument. Hi-C: Library preparation was performed using the Swift Biosciences Accel-NGS 2S Plus DNA Library Kit, Swift Biosciences Indexing Kit, KAPA Library Quantification Kit for Illumina Platforms, and KAPA Library Amplification Kit according to the Arima Hi-C 2.0 library preparation guide (PN A160164 v00). Each library was sequenced in paired-end mode (2 × 250 bp) on an Illumina NovaSeq 6000 SP flowcell, yielding 463,915,437 reads for replicate 1 and 461,940,842 reads for replicate 2.