GSM8163249: ERHoxa9_sgNTC_r2; Mus musculus; ATAC-seq
To generate ATAC-seq libraries for 63.3 cells, 50,000 cells were used and libraries were constructed as previously described (Buenrostro et al., 2013; Cheloufi et al., 2015). Briefly, cells were washed in PBS twice, counted and nuclei were isolated from 100,000 cells using 100 μl hypotonic buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) to generate two independent transposition reactions. Nuclei were split in half and treated with 2.5 μl Tn5 Transposase (Illumina) for 30 mins. at 37°C. DNA from transposed nuclei was then isolated and PCR-amplified using barcoded Nextera primers (illumina). Library QC was carried out using high sensitivity DNA bioanalyzer assay and Qubit measurement and sequenced using paired-end sequencing (PE50) on the Illumina HiSeq 2500 platform.