GSM6043255: ME11_20um; Mus musculus; ATAC-seq
The fresh frozen tissue section on a standard aminated glass slide was first fixed with formaldehyde. Tn5 transposition was then performed, and adapters containing a ligation linker were inserted to transposase accessible genomic DNA. Afterwards, a set of DNA barcode A solutions were loaded via an array of microchannels 8 to the tissue section for in situ ligation of a distinct spatial barcode Ai (i = 1-50). Then, a second set of barcodes Bj (j = 1-50) were introduced on the tissue surface in microchannels perpendicularly to those in the first flow barcoding step. These barcodes were then ligated at the intersections, resulting in a mosaic of tissue pixels, each of which contains a distinct combination of barcodes Ai and Bj (i = 1-50, j = 1-50). During each flow or afterward, the tissue slides were imaged under the microscope such that spatially barcoded accessible chromatin can be correlated with the tissue morphology. After forming a spatially barcoded tissue mosaic (n = 2500), reverse crosslinking was performed to release barcoded DNA fragments and library construction was completed during the PCR. NGS sequencing was then performed using a HiSeq sequencer with pair-end 150 bp mode with custom read 1 primer.