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Sample GSM3567338

Query DataSets for GSM3567338

Status

Public on Apr 05, 2023

Title

castration-resistant prostate cancer6

Sample type

SRA

Source name

plasma exosome

Organism

Homo sapiens

Characteristics

subject id: B6A
tissue: plasma
tissue compartment: exosome
patient diagnosis: castration-resistant prostate cancer
Sex: male

Extracted molecule

total RNA

Extraction 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.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

HiSeq X Ten

Description

Ribosomal-depleted RNA
B6A
sample paired with:
B6

Data processing

Illumina Casava1.7 software used for basecalling.
The raw sequencing reads were subjected to trimming process with Trimmomatic (v.0.32)
High-quality reads were aligned to the Homo sapiens reference genome (GRCH37/hg19) by BWA (v.0.7.12). The resulted sequence alignment files (bam formatted file) were then sorted by reference position as required by SAMtools(v.2.6.2).
CircRNAs was identified and quantified by CIRI2
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: text file with abundance data, logFC, logCPM, Pvalue, FDR. circRNAs are identified by their chromosome coordinates (chromosome:position1|position2).

Submission date

Jan 17, 2019

Last update date

Apr 05, 2023

Contact name

wen tao

E-mail(s)

15627860761@163.com

Phone

15627860761

Organization name

The Third Affiliated Hospital, Sun Yat-sen University