characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-11-17T20:25:52Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-04-01T00:21:39Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110271597
characteristics.characteristic: External Id
characteristics.text: Latvian Biomedical Research and Study Centre
characteristics.characteristic: INSDC center name
characteristics.text: 2022-11-17T20:25:52Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-04-01T00:21:39Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12369213
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-11910:217postP-v1
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: All patients had elevated levels of PSA (2.5 -50 ng/ml) at the time of diagnosis. Patient exclusion criteria included: blood transfusion in the last six months, another oncological disease, urinary tract infection and use of long-term urinary catheter. Sixty ml of the first morning urine were collected, centrifuged at 2000g for 15 min at room temperature, aliquoted and stored at -80ºC. Blood samples were collected in EDTA-coated tubes and processed at room temperature within 2 hours. Plasma samples were centrifuged twice at 3000g for 10 min, aliquoted and stored at -80°C. Samples were collected at two different time points: before radical prostatectomy (Pre) and 3 months after the surgery (Post). Tumor and normal prostate tissue samples were macroscopically dissected immediately after the surgery by experienced uropathologist. One slice of the tissue specimens was subjected to histological evaluation in order to verify the presence or absence of tumor cells in the tissue specimens and to assess the Gleason score in the given specimen, whereas the other part of the specimen was immediately placed into the RNALater solution (Thermo Fisher Scientific, USA) and stored at -20°C until processing. EVs were isolated from the plasma and urine samples using size exclusion chromatography (SEC) as described before (Endzeliņš et al., 2017) with some modifications. Briefly, the urine samples (20 ml) were thawed at +37˚C in a water bath and centrifuged at 10 000g for 15 min at + 4˚C to remove uromodulin and concentrated up to 500 µl using 100 kDa centrifugal filters (Merck Millipore, USA). The concentrated urine samples and 1 ml of plasma were loaded on Sepharose CL2B 10 ml columns. The eluate was collected in 12 sequential 0.5 ml fractions and each fraction was measured with Zetasizer Nano ZS (Malvern, UK). Fractions containing particles larger than 30 nm were combined and concentrated up to 100 μl using 3 kDa centrifugal filters (Merck Millipore, USA). EV samples were treated with Proteinase K (1mg/ml) (Thermo Fisher Scientific) for 60 min at 37°C followed by RNAse A (100 ng/μl) (Thermo Fisher Scientific) treatment for 15 min at 37°C. The purity, size distribution profile and concentration of EVs were assessed by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) using NanoSight NS500 instrument (Malvern, UK) as described before (Endzeliņš et al., 2017). Approximately 20 mg of tissues were homogenized using QIAzol Lysis Reagent (Qiagen, USA) and Lysing Matrix A tubes in a FastPrep-24 homogenizer (MP Biomedicals, USA). RNA was isolated using miRNeasy Micro Kit (Qiagen) following the small RNA enrichment protocol provided by the manufacturer, thus obtaining both, the long and small RNA fraction of each sample. From EVs, RNA was extracted using miRNeasy Micro Kit. On column DNAse treatment was performed according to the manufacturer’s instructions. RNA quantity and quality was assessed using Agilent pico RNA kit and Agilent 2100 Bioanalyzer (Agilent technologies, USA). EV-RNA libraries were constructed from half of the entire yield of extracted EV RNA without any size separation steps, whereas tissue small RNA libraries were constructed from 10 ng of tissue small RNA fraction using CleanTag® Small RNA Library Prep Kit (Trilink Biotechnologies, USA). The libraries were cleaned using Blue Pippin DNA Size Selection with 3% gel Blue Pippin Cassette (Sage Science, USA) setting target length to 130 - 250 bp. All libraries were constructed in duplicates. Transcriptome libraries were built in duplicates from 100 ng of long tissue RNA fraction using TruSeq Stranded mRNA library Prep (Illumina, USA) following manufacturer's instructions. Libraries were size-selected using Blue Pippin system with 2% gel Blue Pippin Cassette (Sage Science, USA) with a range of 200 - 600 bp and their quality and quantity was assessed using Agilent DNA kit (Agilent technologies, USA).
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: prostate cancer
characteristics.characteristic: disease
characteristics.text: not available
characteristics.characteristic: fraction
characteristics.text: 217
characteristics.characteristic: individual
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: blood plasma
characteristics.characteristic: organism part
characteristics.text: blood
characteristics.characteristic: sampling site
characteristics.text: not available
characteristics.characteristic: sampling time point
characteristics.text: Homo sapiens
characteristics.characteristic: scientific name
characteristics.text: male
characteristics.characteristic: sex
characteristics.text: 217postP-v1
characteristics.characteristic: title