title: GSM8800317: CB_NUP98-NSD1/WT1ko_edited CD34+HSPC scATAC; Homo sapiens; ATAC-seq
library_construction_protocol: Nuclei isolation procedure is the same as scATAC-seq, and the isolated nuclei were processed according to the Chromium Next GEM Single Cell ATAC Solution User Guide (version CG000209 Rev F, 10x Genomics) with some modifications: During the GEM generation and barcoding reaction, GoT-Cha primer mix was added to the barcoding mixture. During the post-GEM incubation clean-up, 45.5 µl of Elution Solution I was used to elute material from SPRIselect beads. A total of 5 µl was used for GoT-ChA library construction, and the remaining 40 µl was used for ATAC library construction as per the standard protocol. Two additional PCR reactions were performed for GoT-Cha library construction. The first PCR amplifies genotyping fragments before sample indexing. After a 1.2 x SPRIselect cleanup, biotinylated PCR products were bound using Dynabeads M-280 Streptavidin magnetic beads (Thermo Fisher) at room temperature for 15 minutes. The beads were washed twice with 1x SSPE buffer and once with 10 mM Tris-HCl (pH 8.0) before resuspending in water. The bead-bound fragments were amplified and indexed using P5 and P7 primers. The final libraries were quantified using a High-Sensitivity DNA Chip (Agilent Technologies) run on a Bioanalyzer 2100 system.