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多组学数据联合是趋势

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发表于 2017-2-15 15:38:32 | 显示全部楼层 |阅读模式
这已经是2014年的nature genetic文章了,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997489测了4种组学数据:
We integrated deep-sequencing analysis of 36 tumor–normal pairs (20 whole genome sequencing (WGS; Illumina Hiseq 2000) and 16 whole exome sequencing (WES; Applied Biosystems SOLiD 5500xl)), with comprehensive methylation (28 DIPGs; Illumina Infinium450K methylation array), copy number (45 DIPGs, Affymetrix SNP6.0) and expression data (35 DIPGs; Illumina HT-12 v4)
但是NGS的数据貌似下载会比较麻烦,但是3种芯片数据下载都很简单,因为都是在GEO数据库里面:
数据地址如下:
The whole genome sequencing data is accessible through The European Genome-phenome Archive (accession number: EGAS00001000575).
The methylation data is accessible through Gene Expression Omnibus archive (accession number: GSE50022).
The gene expression data is accessible through Gene Expression Omnibus archive (accession number: GSE50021).
The SNP6.0 copy number data is accessible through Gene Expression Omnibus archive (accession number: GSE50024).


这个 EGAS00001000575有点诡异,https://www.ebi.ac.uk/ega/dacs/EGAC00001000149 里面没有下载数据的链接!


联合分析可以把他们的癌症样本分成3个亚组,如下:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997489/table/T1/
we integrated whole-genome sequencing with methylation, expression and copy number profiling, discovering that DIPGs comprise three molecularly distinct subgroups (H3-K27M, silent and MYCN)


事实上我是找不到那些WGS和WES数据的,我可能要写信问作者了! pawel.buczkowicz@sickkids.ca



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发表于 2018-3-20 16:19:43 | 显示全部楼层
在EGA中下载数据只能发邮件询问吗?
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