GSM9230309: 24132-02-06V1; Homo sapiens; ATAC-seq
ATAC-seq was performed as described previously (Corces et al., 2007). In brief, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience, Massachusetts, USA). 50K to 100K nuclei were then centrifugesd at 500g in a pre-chilled centrifuge for 10 min. Supernatant was removed and the nuclei were resuspended in 50 uL tagmentation by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 300 r.p.m., and then cleaned up by MiniElute reaction clean up kit (Qiagen, Hilden, Germany). Tagmentated DNA was amplified with barcode primers . Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 200M PE reads (100M in each direction) per sample. ATAC-seq was performed as described previously (Corces et al., 2007). In brief, frozen cells were thawed and washed once with PBS and then resuspended in 500 uL of cold ATAC lysis buffer. The cell number was assessed by Cellometer Auto 2000 (Nexcelom Bioscience, Massachusetts, USA). 50K to 100K nuclei were then centrifugesd at 500g in a pre-chilled centrifuge for 10 min. Supernatant was removed and the nuclei were resuspended in 50 uL tagmentation by pipetting up and down six times. The reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 300 r.p.m., and then cleaned up by MiniElute reaction clean up kit (Qiagen, Hilden, Germany). Tagmentated DNA was amplified with barcode primers . Library quality and quantity were assessed with Qubit 2.0 DNA HS Assay (ThermoFisher, Massachusetts, USA), Tapestation High Sensitivity D1000 Assay (Agilent Technologies, California, USA), and QuantStudio ® 5 System (Applied Biosystems, California, USA). Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 200M PE reads (100M in each direction) per sample.