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Sample GSM3467142 Query DataSets for GSM3467142
Status Public on Nov 13, 2021
Title 1497-1
Sample type SRA
 
Source name HCC tumor tissue
Organism Homo sapiens
Characteristics patient diagnosis: hepatocellular carcinoma (HCC)
subject id: 1497
gender: Male
age: 61
tissue: liver
tissue region: tumor
Extracted molecule total RNA
Extraction protocol Total RNA from HCC tumor and peritumor tissue samples were extracted using TransZol reagents. rRNAs were removed by a Ribo-Zero Magnetic kit, and linear RNA was digested by RNase R before construction of the RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing The sequencing reads that meet any of the following criteria were removed: (1) containing adaptor sequence; (2) with >10% ambiguous bases (N) of total read length; (3) containing >20% low quality bases (base quality ≤ 20) of total read length
Qualified reads were aligned to ribosomal rRNA sequences download from RNAcentral database to remove possible rRNA inference.
The unmapped reads were aligned to UCSC human genome reference (GRCh37/hg) using TopHat2
All the reads that could not align to the genome were extracted to identify the potential back-spliced junction reads by TopHat-Fusion. The identified potential candidate reads that could be mapped to the same chromosome but in reverse order were further considered as the candidate back-spliced junction reads
After removing any circular RNA with less than two unique back-spliced reads in one tissue sample, the expression levels for each circular RNA were calculated, according to reads Per Million mapped reads (RPM) using all the junction reads within the circular RNA region
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.
 
Submission date Nov 13, 2018
Last update date Nov 13, 2021
Contact name Liman Qiu
E-mail(s) liman0280@163.com
Organization name Mengchao Hepatobiliary Hospital of Fujian Medical University
Street address Xihong Road 312, Fuzhou 350025, Fujian, P. R. China.
City Fuzhou
ZIP/Postal code 350025
Country China
 
Platform ID GPL21290
Series (1)
GSE122482 The circular RNA profiling of 10 paired HCC and matched peritumor tissues
Relations
BioSample SAMN10415385
SRA SRX5002773

Supplementary file Size Download File type/resource
GSM3467142_1497-1_circ_RPM.txt.gz 784.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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