title: GSM8715428: Multiome, PDX, Neratinib Treatment, ATAC; Homo sapiens; ATAC-seq
library_construction_protocol: Nuclear dissociation was performed based on the 10X Genomics' Nuclei Isolation Guide (CG000366). HCI032 tumors were cut into <2 mm pieces, homogenized using a Dounce homogenizer in 1ml of ice-cold lysis buffer until the solution was uniform, and incubated on ice for 5 minutes with an additional 0.5 ml of lysis buffer. The suspension was filtered through a 70 μm Flowmi Cell Strainer, followed by a 40 μm strainer and centrifuged at 500 x g for 5 min at 4°C. The pellet was washed twice with 1 ml of cold wash buffer and twice with 1ml of cold dilution buffer, with a 5-minute incubation, and centrifugation at 500 x g for 5 min at 4°C after each wash. The pellet was then resuspended with 1ml of sort buffer (2.5% BSA in DPBS with DTT and RNAse inhibitor) and 5 μl 7-ADD stain solution and incubated at room temperature for 10 minutes, followed by a 20-minute incubation on ice. Following centrifugation, the nuclei were washed twice with 500 μl sort buffer and filtered through a 40 μm Flowmi Cell Strainer after each wash. Nuclei were then centrifuged at 500 x g for 5 min at 4°C and resuspend in diluted Nuclei Buffer (10× Genomics, PN-2000153, add 0.1% RNase inhibitor). FACS sorted, and counted using a Countess® II Automated Cell Counter. The multi-omics snRNA-seq and snATAC-seq libraries were constructed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle Kit (Cat# 1000283, 10x Genomics) according to the manufacturer's guidelines. Libraries were sequenced on Illumina NovaSeq 6000 instruments using 50 bp paired-end sequencing targeting 6000 cells per sample with a depth of 60000 reads per cell according to the manufacturer's recommendations (10x Genomics).