|
| Status |
Public on Feb 17, 2017 |
| Title |
T25 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
primary tumor
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: hepatocellular carcinoma (HCC) patient
patient id: #25
gender: male
age: 48
tumor size (cm): 6.7
hbv infection: Yes
cirrhosis: No
tissue: primary tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were treated with 1mL TRIzol reagent (Life Technologies Cat.#15596-026) according to manufacturer's instructions. Nanodrop ND-1000 was used for RNA density/purity detection. Agilent BioAnalyzer 2100 was used for RNA quality control.
rRNA depletion was conducted before RNA-seq library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina Cat.#RS-122-2302).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Real Time Analysis (RTA) and CASAVA v1.8 for base-calling
Bowtie2 and Tophat2 for pair-end read mapping
Subread for raw read counts according to gene annotations
Use size factor to normalize raw counts
Genome_build: hg19
Supplementary_files_format_and_content: tab-limited text file for size-factor normalized read counts
|
| |
|
| Submission date |
Feb 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jin Gu |
| E-mail(s) |
wellgoo@gmail.com
|
| Organization name |
Tsinghua University
|
| Department |
Automation
|
| Street address |
FIT Building 1-112C
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE77276 |
The molecular landscape of hepatocellular carcinoma with portal vein tumor thrombosis |
| GSE77509 |
RNA-seq analysis of hepatocellular carcinoma with portal vein tumor thrombosis |
|
| Relations |
| BioSample |
SAMN04453160 |
| SRA |
SRX1558064 |
