GSM5448669: LNCAP sgGAL4 rep1; Homo sapiens; ATAC-seq
ATAC-Seq on LNCaP cells were performed following knockdown of PTGES3 or control (GAL4). The experiment was carried out as described in the published method papers by Buenrostro, et al. and Corces, et al. with the following modifications. Cells were resuspended in buffer, incubated on ice for 10 minutes, and lysed using a dounce homogenizer. 50,000 nuclei were incubated with 25uL 2X TD Buffer and 1.25uL Transposase shaking at 300rpm at 37C for 30 minutes. Zymo DNA Clean and Concentrator 5 kit was then used to purify DNA. Transposed DNA was amplified using PCR master mix and indexes from Nextera DNA Library Prep kit for 5 cycles and then assessed using qPCR. Final cleanup was performed using 1.8X AMPure XP beads and libraries quantified using the DNA High Sensitivity Agilent 2100 Bioanalyzer System. Samples were sequenced at the UCSF Core Facility on the HiSeq4000 paired end 100. The entire experimental setup was performed in two technical replicates.