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Sample GSM450017 Query DataSets for GSM450017
Status Public on Sep 04, 2010
Title YanHuang1_methy_rep2
Sample type SRA
 
Source name PBMC
Organism Homo sapiens
Characteristics cell type: human peripheral blood mononuclear cells
Treatment protocol bisulphite treated
Growth protocol using fresh blood cells
Extracted molecule genomic DNA
Extraction protocol standard Illumina Genome Analyzer protocol
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer
 
Description sample for paired-end library with insert size of 200 bp
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.
 
Submission date Sep 04, 2009
Last update date May 15, 2019
Contact name Hong zhi Cao
E-mail caohongzhi@genomics.cn
Phone 8675525274032
Organization name BGI-SHENZHEN
Department Bioinformatics
Street address F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
City Shenzhen
State/province Guangdong
ZIP/Postal code 518083
Country China
 
Platform ID GPL9052
Series (1)
GSE17972 The DNA methylome of human peripheral blood mononuclear cells
Relations
SRA SRX019406
BioSample SAMN00011776

Supplementary data files not provided
SRA Run SelectorHelp
Processed data is available on Series record
Raw data are available in SRA

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