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Sample GSM3775829 Query DataSets for GSM3775829
Status Public on Jun 16, 2019
Title pT3N3: Ulcerative Adenocarcinoma
Sample type SRA
 
Source name lesser gastric curvature
Organism Homo sapiens
Characteristics tissue: stomach
cell_type: Ulcerative Adenocarcinoma
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with TRIzol® Reagent (Life technologies)
RNA sequencing libraries were prepared from 2μg of total RNA using the TruSeq Kit (Illumina, Inc.) with modifications. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, Inc). Poly-T oligo-attached magnetic beads (Illumina, Inc.) were used to remove residual poly-A RNA. All other steps were performed according to the manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing For circRNA expression analysis, the reads were to mapped genome using 1.the STAR (58) and DCC (59) was used to identify the cirRNA and to estimate the circRNA expression
TMM (trimmed mean of M-values) was used to normalize the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: txt TMM normalized junction read counts
 
Submission date May 17, 2019
Last update date Jun 16, 2019
Contact name Shan Kong
E-mail(s) 1816310060@yjs.ntu.edu.cn
Phone +8618860976895
Organization name Affiliated Hospital of Nantong University
Department Department of Laboratory Medicine
Lab Research Center of Clinical Medicine
Street address NO.20, Xisi Road
City Nantong
State/province Jiangsu
ZIP/Postal code 226001
Country China
 
Platform ID GPL24676
Series (1)
GSE131414 High-throughput sequencing identifies 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, in gastric cancer tissues
Relations
BioSample SAMN11671015
SRA SRX5855870

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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