|
| Status |
Public on Jun 30, 2014 |
| Title |
Hepatocellular carcinoma (HCC), parent |
| Sample type |
SRA |
| |
|
| Source name |
Human Hepatocellular Carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hepatocellular Carcinoma
cell line: HCCLM3
organ-tropism: low metastasis ability
|
| 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 RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Remove reads with adaptors, remove reads in which unknown bases are more than 10%, Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 26, 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) |
| GSE38945 |
Gene 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 |
SRX156169 |
| BioSample |
SAMN01057824 |
