Lung D150-RML-BPS_snATAC-Seq: Sample D150-RML-BPS
"Lung tissue was homogenized using using mortar and pestle in liquid nitrogen and an aliquot was resuspended in premeabilization buffer. After permeabilization, 2000 nuclei were tagmented in each well of a 96-well pate with barcoded Tn5 transposomes. Tagmentation was qeunched, nuclei from all wells combined, and 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells). Tagemted DNA was released and PCR-amplified with well-specific barcoded primers. After PCR, all wells were combined, purified using columns, and size selected using SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were sequenced on a NextSeq500 or HiSeq 4000 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2). For each sequenced snATAC-Seq library, we obtained four FASTQ files, two for paired-end DNA reads as well as the combinatorial indexes for i5 (768 different PCR indices) and T7 (96 different tagmentation indices). We selected all reads with <= 2 mistakes per individual index (Hamming distance between each pair of indices is 4) and subsequently integrated the full barcode at the beginning of the read name in the demultiplexed FASTQ files."
D150-RML-BPS__snATAC-Seq