|
| Status |
Public on Feb 22, 2018 |
| Title |
HCC10 |
| Sample type |
SRA |
| |
|
| Source name |
Blood exosome
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: hepatocellular carcinoma
tissue: Blood
tissue compartment: exosome
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4 ml plasma were used to extract exosomal RNAs by exoRNeasy Serum/Plasma Maxi kit (Qiagen). The exosomal RNAs were further treated with DNAse I and subjected to ribosome minus low-input RNAseq library preparation.
RNA libraries were prepared for sequencing using ribosome minus RNAseq protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat
mRNA and lncRNA annotated in GENCODEv25 were quantified using featureCounts, and circular RNA were identified and quantified by ACFS (https://github.com/arthuryxt/acfs).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPM or FPKM values for each sample
|
| |
|
| Submission date |
Jun 19, 2017 |
| Last update date |
Oct 12, 2023 |
| Contact name |
Shengli Li |
| E-mail(s) |
lishenglibio@outlook.com
|
| Phone |
86-21-34777580
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
650 Xinsongjiang Road
|
| City |
Shanghai |
| ZIP/Postal code |
201620 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE100207 |
RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with hepatocellular carcinoma |
|
| Relations |
| BioSample |
SAMN07256000 |
| SRA |
SRX2932959 |
