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| Status |
Public on Sep 04, 2010 |
| Title |
YanHuang1_methy_rep19 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human peripheral blood mononuclear cells
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| Treatment protocol |
bisulphite treated
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| Growth protocol |
using fresh blood cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
standard Illumina Genome Analyzer protocol
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
sample for paired-end library with insert size of 200 bp
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| Data processing |
There are three parts in the methylation pipeline: pretreatment, alignment and caculation. Here are the steps: First, we pretreat both the solexa reads and the reference, transforming C to T or G to A. Then, we use SOAP to do the alignment and choose the best reads if appearing in several alignment results. After that, we filter duplicate reads and get the infomation of former reads to judge the methylation profile.Finally, in order to caculate methylation rate and convertion rate, we gather the information of each site on each chromosome.
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| Submission date |
Sep 04, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong zhi Cao |
| E-mail(s) |
caohongzhi@genomics.cn
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| Phone |
8675525274032
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| Organization name |
BGI-SHENZHEN
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| Department |
Bioinformatics
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| Street address |
F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE17972 |
The DNA methylome of human peripheral blood mononuclear cells |
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| Relations |
| SRA |
SRX019423 |
| BioSample |
SAMN00011793 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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