title: GSM4290977: HS_Rep2 93-11 ATAC-seq; Oryza sativa; ATAC-seq
library_construction_protocol: Freshly purified nuclei to be used for ATAC-seq were kept on ice prior to the transposase integration reaction. Transposase integration reactions and sequencing library preparations were then performed as previously described (Bajic et al., 2018). In brief, 50 ng of genomic DNA was used in each 50 μl Tn5 transposase integration reaction for 30 min at 37°C using Nextera reagents. DNA fragments were purified using the Minelute PCR purification kit (Qiagen), eluted in 11 μl elution buffer, and the entirety of each sample was then amplified using High Fidelity PCR Mix (NEB) and barcode primers for 9-12 PCR cycles. These amplified ATAC-seq libraries were purified using AMPure XP beads (Beckman Coulter), quantified by qPCR with the NEBNext Library Quantification Kit (NEB), and analyzed on a Bioanalyzer High Sensitivity DNA Chip (Agilent) prior to pooling and sequencing. A Qubit fluorometer and Aglient Bioanalyzer were used to check library quality and concentration. DNA libraries were constructed using NEBNext DNA Library Prep Kit (Neb) and sequenced on an Illumina HiSeq X-ten platform with 150-bp paired-end reads.
attributes.tag: GEO Accession
attributes.value: GSM4290977