Mammalian testis development is a complex and highly sophisticated process. To study the dynamic change of normal testis development at the transcriptional level, we investigated mouse testes at three postnatal ages: 6 days postnatal, 4 weeks old, and 10 weeks old, representing infant (PN1), juvenile (PN2), and adult (PN3) stages, respectively. Using ultra high-throughput RNA sequencing (RNA-seq) technology, we obtained 211 million reads with a length of 35 bp. We identified 18837 genes that were expressed in mouse testes, and found that genes expressed at the highest level were involved in spermatogenesis. The gene expression pattern in PN1 was distinct from that in PN2 and PN3, which indicates that spermatogenesis has commenced in PN2. We analyzed a large number of genes related to spermatogenesis and somatic development of the testis, which play important roles at different developmental stages. We also found that the MAPK, Hedgehog, and Wnt signaling pathways were significantly involved at different developmental stages. These findings further our understanding of the molecular mechanisms that regulate testis development. Our study also demonstrates significant advantages of RNA-seq technology for studying transcriptome during development.
GONG WeiPAN LinLinLIN QiangZHOU YuanYuanXIN ChengQiYU XiaoMinCUI PengHU SongNianYU Jun
利用SUPPA(a super-fast pipeline for alternative splicing)软件分析癌症基因组数据库癌基因组图谱中肺腺癌和肺鳞癌样本的RNA-Seq数据,发现在鉴定的7种主要可变剪接转录本中外显子跳跃转录本发生频率最高.通过癌组织与癌旁组织的比较,系统地鉴定了肺腺癌和肺鳞癌中差异表达的可变剪接转录本,发现约60%的差异可变剪接转录本是两种肺癌亚型所共有的.功能富集分析表明,癌组织特异的可变剪接转录本主要富集在细胞周期调控、脱氧核糖核酸代谢和核糖核酸代谢等生物过程中,而癌旁组织特异的可变剪接转录本则主要富集在囊泡介导转运、多肽转运和脂质转运等生物过程中.通过肺癌驱动基因可变剪接转录本的比较分析,鉴定了两种肺癌亚型共有或特有的可能具有癌驱动功能的可变剪接转录本.
Biocuration involves adding value to biomedical data by the processes of standardization, quality control and information transferring(also known as data annotation). It enhances data interoperability and consistency, and is critical in translating biomedical data into scientific discovery. Although China is becoming a leading scientific data producer, biocuration is still very new to the Chinese biomedical data community. In fact, there currently lacks an equivalent acknowledged word in Chinese for the word ‘‘curation". Here we propose its Chinese translation as ‘‘审编"(Pinyin: sheˇn bi"an), based on its implied meanings taken by biomedical data community.The 8th International Biocuration Conference to be held in China(http://biocuration2015.tilsi.org)next year bears the potential to raise the general awareness in China of the significant role of biocuration in scientific discovery. However, challenges are ahead in its implementation.
