|
| Status |
Public on Nov 13, 2021 |
| Title |
1559-2 |
| Sample type |
SRA |
| |
|
| Source name |
HCC peritumor tissues
|
| Organism |
Homo sapiens |
| Characteristics |
patient diagnosis: hepatocellular carcinoma (HCC)
subject id: 1559
gender: Male
age: 56
tissue: liver
tissue region: peritumor
|
| 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 |
SAMN10415395 |
| SRA |
SRX5002786 |
