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Series GSE131414 Query DataSets for GSE131414
Status Public on Jun 16, 2019
Title High-throughput sequencing identifies 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, in gastric cancer tissues
Organism Homo sapiens
Experiment type Other
Summary Purpose: With the advent of human genome sequencing project, circRNAs attracted widespread attention in cancer research due to its stable ring structure. Our aim was to identify differentially expressed circRNAs in GC and explore their potential roles in GC diagnosis and treatment.
Methods: Total RNA from tissues was isolated by Hipure Total RNA Mini Kit (Magen, Germany). Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, California) was used for RNA concentration measurement while Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA) for RNA integrity estimation. A RIN value over 7.0 was considered eligible. RNA-seq library was prepared with approximately 2μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA). Briefly, total RNA was incubated at 37 °C for 30 min with 10 units RNase R (Epicentre Technologies, Madison, USA) after removing ribosomal RNA. Next, the ribominus RNase R (+) RNAs was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. Each library was diluted to 10 nM and pooled equimolar prior to clustering. Paired-End (PE150) sequencing was performed on all samples.
Results: A total of 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, were detected and defined. Among them, there were 2,007 circRNAs with statistically significant differences in expression in GC tissues, in which fold changes>2.0 and P<0.05 were identified.
Overall design Three pairs of gastric cancer tissues and their corresponding adjacent non-cancerous tissues were detected by circRNA-sequencing.
Contributor(s) Ju S, Shen X
Citation(s) 31616472
Submission date May 17, 2019
Last update date Aug 10, 2021
Contact name Shan Kong
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
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (3)
GSM3775829 pT3N3: Ulcerative Adenocarcinoma
GSM3775830 pT2N1: Ulcerative Adenocarcinoma
GSM3775831 pT3N2: Ulcerative Adenocarcinoma
BioProject PRJNA543502
SRA SRP198778

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Supplementary file Size Download File type/resource
GSE131414_CancervsNormal_all_detectable_circRNA.txt.gz 1.5 Mb (ftp)(http) TXT
GSE131414_TMM_normalized_reads_count_per_million.txt.gz 1.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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