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| Status |
Public on Sep 01, 2014 |
| Title |
N321_HpaII |
| Sample type |
SRA |
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| Source name |
Normal liver tissue
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Normal liver
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
All HCC tissue were obtained from patients who underwent surgical resection for their tumors and provided informed consent prior to liver surgery. The primary tumor specimens were immediately frozen at -80°C until DNA/RNA extraction. Genomic DNA was extracted from all patients and cells using the QIAamp DNA Blood Mini Kit (Qiagen).
HSMT-Seq library construction was performed following our previously reported protocol (Gao et al. 2013). The libraries were sequenced using single-end 50 bp sequencing strategy with an Illumina HiSeq2000 sequencing system.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
HpaII library (indicating unmodified cytosines) of the sample
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| Data processing |
Library strategy: HSMT-Seq
Illumina BclConverter-1.9.0 software used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean HMST-seq reads were mapped to hg19 virtual library with no more than one mismatch using open-source programming language Perl.
The data for three libraries were normalized according to a previous method (Global Rank-invariant Set Normalization, GRSN) (Pelz et al. 2008) based on the normalized tag counts, and the modification abundance of a specific CCGG site was determined as the ratio between the tag counts of two libraries. For instance, the hydroxymethylation level can be defined as the ratio between “C+mC+hmC” and “C+mC” tags. Furthermore, CCGG sites with significantly different tag counts (sequencing depth >10X, FDR <0.001) based on Poisson distribution with a ratio of tags between two libraries larger than 1 were determined to be significantly modified sites.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include tags abundance, p-value of Poisson test and FDR for each sample.
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| Submission date |
Jan 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Desheng Gong |
| E-mail(s) |
[email protected]
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| Organization name |
Agricultural Genomes Institute at Shenzhen
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| Street address |
No.7 PengFei road
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| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE54141 |
Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5 and EOMES in human hepatocellular carcinoma |
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| Relations |
| BioSample |
SAMN02585297 |
| SRA |
SRX434645 |
| 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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