最近刷到了一个2023的文章《DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens》,家禽蛋壳的质量与蛋品生产的盈利能力密切相关。蛋壳斑点是影响鸡蛋外观和顾客偏好的一个重要品质性状。然而,斑点的形成机制仍然知之甚少。有斑点蛋和正常蛋的主要区别包括:
所以研究者就针对有斑点蛋和正常蛋的whole-genome bisulfite sequencing (WGBS) and RNA-seq 数据,然后发现几乎没有差异,并且完全没有交集。。。
转录组测序后的差异分析
从质量控制可以看到, 有斑点蛋和正常蛋应该是在表达量的全局水平是没有分组差异的,如下所示:
全局水平是没有分组差异
很明显就:
RNA-seq analysis identified seven DEGs between the speckle and normal groups, includ- ing IQSEC3, BFSP2, TMOD4, LOC112530987, GABRA2, TRIQK, and a pseudogene. IQSEC3,
Three DEGs (BFSP2, IQSEC, TMOD4) identified by RNA-seq were verified using quantitative real-time PCR
同样的,从质量控制可以看到, 两个分组的wgbs数据其实是有系统性的分组差异,所以有A total of 2788 differentially methylated regions (DMRs) were identified between the normal and speckle groups.