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| Status |
Public on Feb 18, 2014 |
| Title |
LM3 mRNA |
| Sample type |
SRA |
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| Source name |
HCCLM3
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| Organism |
Homo sapiens |
| Characteristics |
cell type: hepatocellular carcinoma cell line
cell line: HCCLM3
strategy: mRNA
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| Growth protocol |
Human liver carcinoma cell lines, including Hep3B, HCC-LM3 (LM3) and MHCC-97H (97H) cells, cells were obtained from American Type Culture Collections (ATCC, Rockville, MD, USA). LM3 and 97H cells were maintained in complete DMEM media (Invitrogen, Carlsbad, CA, USA), supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (Invitrogen) and 10 μg/mL ciprofloxacin. Hep3B cells were cultured in complete MEM media (Invitrogen), supplemented with 15% FBS, 1 mM sodium pyruvate, 1% penicillin/streptomycin (Invitrogen) and 10 μg/mL ciprofloxacin
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| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA and RNC-mRNA was extracted according to the literature "Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific" Nucleic Acids Res. 2013
The library was constructed by using NEBNext mRNA Sample Prep Master Mix Set for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
total polyA+ mRNA
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| Data processing |
The sequencing reads were mapped to the Ensembl-v72 RNA reference sequences using FANSe2 algorithm (http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters of –L55 –E3 –S14. Alternative splice variants were merged.
The genes with at least 10 mapped reads were deemed confident gene identification and quantification
Gene expression levels within a single cell line were calculated using the rpkM method
The differential expression level across cell lines were performed using edgeR software package
Genome_build: hg19 (Ensembl-v72 RNA reference sequence)
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| Submission date |
Aug 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Gong Zhang |
| E-mail(s) |
zhanggong@jnu.edu.cn
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| Organization name |
Jinan University
|
| Department |
Institute of Life and Health Engineering
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| Lab |
Translatomics Lab
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| Street address |
Huang-Pu Avenue West 601
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| City |
Guangzhou |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE49994 |
mRNA and RNC-mRNA deep sequencing of three hepatocellular carcinoma cell lines |
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| Relations |
| BioSample |
SAMN02318977 |
| SRA |
SRX336429 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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