GSM4455552: HAP1 SMARCA4KO_SMARCA2dTAG_C8 dTAG 47 6h_2; Homo sapiens; ATAC-seq
ATAC-seq was performed according to Buenrostro et al. with small adaptations(Buenrostro et al., 2015). In brief, 50,000 cells (1:2 drosophila S2 cells : HAP1 cells) were resuspended in 25 µl transposase reaction mix (0.02% digitonin (Promega G9441), 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880). The libraries were checked on a Bioanalyzer instrument using High Sensitivity DNA Chips (Agilent), quantified using Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Q32854) and pooled. Libraries were sequenced using the Illumina HiSeq3000/4000 platform with the 75 bp paired-end configuration. ATAC-seq was performed according to Buenrostro et al. with small adaptations(Buenrostro et al., 2015). In brief, 50,000 cells (1:2 drosophila S2 cells : HAP1 cells) were resuspended in 25 µl transposase reaction mix (0.02% digitonin (Promega G9441), 1x TD
GEO Accession
GSM4455552