GSM9228169: Mouse Brain R6; Mus musculus; OTHER
brains of C57BL/6 mice are sectioned in coronal (cross) oreintation. Brains are snapped frozen in OCT without any fixative, sectioned in coronal orientation at a thickness of 7-10 microns. Sections are mounted on microarray grade slides and crosslinked with 2% (final concentration) formaldehyde to preserve native chromatin structure. After nuclei permeabilization with 0.55% SDS solution, enzyme digestion and proximity ligation of chromatin DNA fragments was performed on the tissue slide. Next, Tn5 transposition is performed directly on tissue sections using in-house assembled Tn5 transposome complex to fragment proximity-ligated chromatin DNA. Horizonal barcodes A (A1–A50) and vertical barcodes B (B1–B50) are sequentially delivered across tissue surface, using microchannels and ligated to the universal ligation linker. This creates a two-dimensional grid of spatially barcoded tissue pixels (n = 2,500). After reverse crosslinking and purification, the biotin-ligated chromatin fragments are enriched for sequencing library preparation. Finally, based on the barcode information, we can build the chromatin interaction maps for each pixel from the original tissue slides.