title: GSM9185481: siControl, Sample 3; Mus musculus; ATAC-seq
library_construction_protocol: The libraries were prepared using the ATAC-seq Kit (Active Motif) following the manufacturer's protocol. Briefly, cell viability was assessed by AO/PI staining with bright-field microscopy, and all samples had a viability of 80 percent or higher. Fresh cells were lysed, followed by tagmentation with Tn5 transposase to fragment accessible chromatin and to insert partial sequencing adapters. The resulting DNA fragments were purified, PCR-amplified to add unique dual barcodes to each library and cleaned up with magnetic beads to remove adapter dimers. Construction of the ATACSeq libraries and sequencing on the Illumina NovaSeq 6000 were performed at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign. The final libraries were quantitated with Qubit (ThermoFisher) and the average cDNA fragment sizes were determined on a Fragment Analyzer. The libraries were diluted to 5nM and further quantitated by qPCR on a CFX Connect Real-Time qPCR system (BioRad) for accurate pooling of barcoded libraries and maximization of number of clusters in the flowcell.  The pooled barcoded ATACseq libraries were loaded on one SP lane on a NovaSeq 6000 for cluster formation and sequencing. The libraries were sequenced from both ends of the fragments for 150 cycles per end. The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).
identifiers.namespace: GEO
identifiers.id: GSM9185481_r1