title: GSM6762001: E12.5; Mus musculus; ATAC-seq
library_construction_protocol: Embryos were collected from pregnant female C57BL/6J mice at E11.5, E12.5, E13.5 and E14.5, which the day with the presence of vaginal plugs was defined as E0.5. For the embryos at E11.5, whole genital ridges (including gonad and mesonephros) were dissected. For the embryos at E12.5, E13.5 and E14.5, gonads were dissected free of the mesonephros. The sexing step was omitted to reduce the sample processing time, and the gonads from both sexes were pooled in equal numbers for subsequent steps. The XX and XY gonads at the same time points were pooled together. Each time point contains at least 6 embryos. Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ATAC-Seq Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed with PCR amplification as follows: 37 °C for 30 min, 85 °C for 10 min, 72 °C for 5 min, 98 °C for 30 s, eight cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. Emulsions were broken and products were cleaned up using Ampure XP beads. Barcoded amplicons were further amplified for 8 cycles. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were sequenced on HiSeq 2000 with 150 bp paired-end reads.