GSM3861284: DZC ATAC Seq  Replicate2; Bos taurus; ATAC-seq
Newly isolated bovine superficial zone articular chondrocytes and deep zone articular chondrocytes were cultured (in DMEM/F12 plus 10% FBS) for three days prior to performing ATAC-Seq analysis. ATAC-Seq (Buenrostro et al., 2013; Buenrostro et al., 2015) was performed on replicate samples of 8,000 to 35, 000 superficial zone chondrocytes or deep zone chondrocytes. Nuclear pellets were isolated and treated with Nextera Tn5 Transposase.Transposed DNA was immediately isolated using a Qiagen MinElute PCR Purification Kit, and then PCR amplified in a 50 μl reaction using a common forward primer and different reverse primers with unique barcodes for each sample as per (Buenrostro et al., 2015). ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.