|
| Status |
Public on Jun 30, 2014 |
| Title |
Hepatocellular carcinoma (HCC),subclone1 |
| Sample type |
SRA |
| |
|
| Source name |
Human Hepatocellular Carcinomar cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hepatocellular Carcinomar
cell line: HCCLM3
organ-tropism: higher metastasis ability specific to lung
|
| Growth protocol |
The three HCC cell strains were cultured in DMEM medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Medium was removed, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags
Align small RNA tags to the human miRNA precursor/mature miRNA of corresponding species in miRBase17 using BLAST 2.2.25 ,with the following configurations:blastall -p blastn -F F -e 0.01
Normalize the expression of miRNA in two samples (control and treatment) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000
Calculate fold-change and P-value from the normalized expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Jun 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei zhong Wu |
| E-mail(s) |
wu.weizhong@zs-hospital.sh.cn
|
| Fax |
+86-21-5423 7181
|
| Organization name |
Fudan University
|
| Department |
Zhongshan Hospital
|
| Lab |
Liver cancer institute
|
| Street address |
Fenglin Rd 180, Xuhui district
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE39003 |
Small RNAs expression of three hepatocellular carcinoma cell lines with different organ-tropism. |
| GSE39053 |
Expression of three hepatocellular carcinoma cell lines with different organ-tropism |
|
| Relations |
| SRA |
SRX157300 |
| BioSample |
SAMN01085207 |
