GSM8705047: Empty Vector Day1 (snATAC-seq); Mus musculus; ATAC-seq
For scATAC-seq, mouse prostates were freshly dissociated (described above), and flow sorted for live single cells using DAPI. Fresh nuclei were isolated before processing for 10X Genomics Chromium single cell multiome ATAC + gene expression sequencing following manufacture's instructions. [scATAC-seq]  Mouse prostates were harvested and subsequently digested with collagenase type II (Gibco) for 2 hrs at 37 °C, followed by TrypLE (Gibco) digestion at 37 °C until a single-cell suspension was obtained. Digestions were supplemented with Y-27632 (10 μM) to inhibit anoikis and filtered to obtain single cell suspension. [scATAC-seq]  Murine prostate organoid culture was established and maintained under standard conditions. Briefly, dissociated prostatic epithelial cells were embedded in 20-µl drops of Matrigel (Corning) and overlaid with mouse prostate organoid medium. [scRNA-seq]  Mouse prostate organoids cultured in medium and single cell were sorted for 10X multiome sequencing [scRNA-seq]  Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.