|
Status |
Public on Jun 30, 2014 |
Title |
Hepatocellular carcinoma (HCC), subclone1 |
Sample type |
SRA |
|
|
Source name |
Human Hepatocellular Carcinoma cell line
|
Organism |
Homo sapiens |
Characteristics |
cell type: Hepatocellular Carcinoma 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 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 |
SRX156170 |
BioSample |
SAMN01057825 |