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[mRNA-seq] 这篇转录组文章用到了BGI数据?

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发表于 2016-11-22 11:55:23 | 显示全部楼层 |阅读模式
昨晚被朋友圈BGI的数据刷屏了,我简单了看了一下该文章。http://www.sciencedirect.com/sci ... i/S096517481630162X
文章只上传了Illumina HiSeq 2500 platform的测序数据,(Pyrrhalta aenescens: SRX2253604; P. macolicollis: SRX2253605).而且是做 De novo assembly and annotation,走得的标准化流程,没什么好说的,只是会比较耗时。

文章里面提到了BGI测序仪及测序数据的地方是:Based on the de novo transcriptomic data, we quantified the expression levels of chemosensory genes using the BGIseq500 platform (BGI, Wuhan, China, http://www.seq500.com/en/) with 4 P. aenescens and 3 P. maculicollis biological replicates. The antennal tissue was collected, pooled, and treated using the same methods as described in section 2.1. To rule out the uncertainty in assignment of isoforms to orthologs, the expression profiles were only compared between the pairwise orthologs confirmed by the above ML analyses. Gene expression levels were estimated by RSEM。大家可以点进去仔细看看。

然后走得是标准的差异分析流程。

rsem定量然后DESeq2找差异,标准是 log2foldchange >1 and a Padj-value <0.05,比较是 4 P. aenescens and 3 P. maculicollis biological replicates,看起来是很正常的转录组分析流程,最后实验验证,用的qRT-PCR,看了OBP4, OBP10, OBP22, CSP2, CSP4, SNMP1a, OR11, OR15, OR16, GR4, GR5, IR2这些基因

没有上传BGI数据,也没讲清楚用了BGI数据干嘛了。我很好奇,他们这难道说就是纯粹的友情推荐?




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