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SRX5258557: GSM3567319: metastasis castration-resistant prostate cancer2; Homo sapiens; RNA-Seq
1 ILLUMINA (HiSeq X Ten) run: 30.9M spots, 9.3G bases, 3.4Gb downloads

Submitted by: NCBI (GEO)
Study: A landscape of circular RNAs expression in the castration-resistant prostate cancer
show Abstracthide Abstract
Prostate cancer is one of the major cancers that seriously affect men's health. It has high morbidity and high mortality, but there is still no ideal molecular markers for the diagnosis and prognosis of prostate cancer. Castration-resistant prostate cancer is associated with wide variations in survival. To determine whether differentially expressed circRNAs in plasma exosomes can be used as a novel biomarker for castration-resistant prostate cancer prognosis, we performed high-throughput circRNA sequencing on 15 pairs of plasma exosomes from 30 metastatic castration-resistant prostate cancer patients, with or without early progression, to screen differentially expressed circRNAs. Overall design: We performed deep RNA-sequencing on ribosomal-depleted RNA isolated from 15 pairs of plasma exosomes from 30 independent patients with castration-resistant prostate cancer, with or without the presence of metastases, using Illumina X Ten. Patients were paired according to their age and clinical indicators.
Sample: metastasis castration-resistant prostate cancer2
SAMN10765015 • SRS4259649 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: HiSeq X Ten
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Isolation of exosomes using ExoQuick(SBI,Palo Alto,CA,US) according to the manufacturer's instructions.Exosomal RNA was isolated from samples using RNAiso Plus Total RNA extraction reagent (TAKARA, Dalian, China) according to the manufacturer's instructions and the RIN number was checked to detect RNA integrity by Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Further purification of qualified total RNA using RNAClean XP Kit (Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set(QIAGEN, GmBH, Germany). The total RNA were treated with the RiboZero rRNA Removal Kit (Epicentre, WI, USA) to delete rRNA and digested linear RNA using RNase-R (Epicentre, WI, USA) according to the manufacturer's instructions. Next, strand-specific libraries were constructed by using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme, Nanjing, CHN) following the manufacturer's instructions. In brief, The enriched circRNAs were fragmented using fragmentation buffer and then reverse transcribed into first-strand cDNA and second-strand cDNA in orderly. Then, the cDNA fragments were purified, subjected to end-repair, and modified to add poly (A) to the 3' end. The sequencing adapters were ligated to the cDNA fragments. The double strand cDNA are digested by uracil-DNA glycosylase (UDG) (Cwbio, Beijing, CHN) to remove the second-strand cDNA before sequencing. The purified ligation products were performed 13-15 cycles of PCR amplification. The PCR amplification products of cDNA were purified with Agencourt AMPure XP Beads(Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and then sequenced by Illumina Hiseq X Ten system (Illumina, San Diego, CA, USA) on paired-end(PE) mode with length 150 bases following the vendor's recommended protocol.
Experiment attributes:
GEO Accession: GSM3567319
Links:
Runs: 1 run, 30.9M spots, 9.3G bases, 3.4Gb
Run# of Spots# of BasesSizePublished
SRR845178430,925,1349.3G3.4Gb2023-04-05

ID:
7094863

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