title: 4f-SAMMY-seq (Sequential Analysis of MacroMolecules Accessibility) and total RNA-seq data from prostate biopsies of 25 chemo-naïve patients (7 healthy biopsies and 18 tumor biopsies)
design: 4f-SAMMY-seq (Sequential Analysis of MacroMolecules Accessibility) and total RNA-seq data from prostate biopsies of 25 chemo-naïve patients (7 healthy biopsies and 18 tumor biopsies)
library_construction_protocol: Our cohort includes chemo-naïve patients followed in the Urology Division of Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico (Milan) who underwent the transrectal ultrasound-guided systematic sampling of prostate tissue (TRUS biopsy). This diagnostic procedure was performed as part of routine clinical management following the detection of abnormal digital rectal examination or an elevated PSA blood level. According to the current standard for the detection of PCa, 14 ultrasound-guided biopsy cores (diagnostic biopsies), seven from each side of the prostate gland, were collected from each patient for the clinical diagnosis. During the same procedure, one additional biopsy core to be used for our research project (research biopsy), was taken from a site directly adjacent to one of the diagnostic biopsies. Samples selected for epigenome studies consist of 17 fresh biopsies divided on the bases of the histology and the spatial distribution of the positive cores in two different groups: 10 PCa biopsies with histologically confirmed prostate cancer and 7 who had no cancer in any biopsy core.  Ten thousand cells retrieved from the digestion step were stabilized in 200μl of 1Thioglycerol/Homogenization Solution of the Maxwell® RSC miRNA Tissue Kit (Promega, AS1460) and stored frozen at -80°C for total RNA automated purification using Maxwell® RSC 48 Instrument (Promega, AS8500). Total RNA was quantified by Qubit 4 fluorometer with Qubit RNA HS Assay Kit (Invitrogen, Q32852) and assessed by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) to inspect RNA integrity. For each sample, 1 ng of total RNA was used to construct strand specific RNA-seq libraries with SMARTer Stranded Total RNA-Seq Kit - Pico Input (Takara, 634487). The yield and quality of the libraries were evaluated on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent, 5067-4626).