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Sample GSM5585346 Query DataSets for GSM5585346
Status Public on Dec 07, 2021
Title Rv1_Des2
Sample type SRA
 
Source name prostate cancer
Organism Homo sapiens
Characteristics cell type: prostate cancer cells
treatment: treated with deslanoside for 48 hours
Extracted molecule total RNA
Extraction protocol Remove the supernatant and wash with PBS, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model MGISEQ-2000RS
 
Data processing Illumina Casava1.7 software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI, which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Genome_build: GCF_000001405.39_GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and gene countsfor each Sample ...
 
Submission date Sep 17, 2021
Last update date Dec 07, 2021
Contact name Jin-Tang and Dong
E-mail(s) dongjt@sustech.edu.cn
Phone 86-755-88018032
Organization name Southern University of Science and Technology
Street address 1088 Xueyuan Blvd., Research Building 2B
City Shenzhen
State/province Guangdong
ZIP/Postal code 518055
Country China
 
Platform ID GPL30209
Series (1)
GSE184380 The cardiac glycoside deslanoside imposes an anticancer effect on prostate cancer involving multiple signaling pathways
Relations
BioSample SAMN21490557
SRA SRX12237598

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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