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| Status |
Public on Jun 07, 2019 |
| Title |
H081048T |
| Sample type |
SRA |
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| Source name |
liver cancer
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| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
age: 66
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| Treatment protocol |
fresh frozen tissue
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| Growth protocol |
freezing liquid nitrogen
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
C-HCC
gene expression
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| Data processing |
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normaliztion for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.
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| Submission date |
Jan 07, 2019 |
| Last update date |
Jun 07, 2019 |
| Contact name |
Chang Ohk Sung |
| Organization name |
Asan Medical Center
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| Department |
Pathology
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| Street address |
Song-Pa gu,Pung-nap dong
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| City |
Seoul |
| ZIP/Postal code |
05505 |
| Country |
South Korea |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE124751 |
Gene expression profile of hepatocellular carcinoma with marked immune cell infiltration I |
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| Relations |
| BioSample |
SAMN10701941 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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