在全长转录组基础之上,ONT-三代测序平台的直接RNA测序(Direct RNA-seq),相对于传统的反转录cDNA - PCR扩增(二代和三代RNA-seq测序都有相应的建库方案)流程,其能够保留并检测天然RNA碱基修饰信息,还原真实RNA特征,也省去了传统 RNA m6A甲基化修饰繁琐的实验检测步骤, 如 MeRIP-seq/m6A-seq和m6A-SEAL-seq等 。
在全长转录组基础之上,ONT - 三代测序平台的直接RNA测序(Direct RNA-seq),相对于传统的反转录cDNA - PCR扩增(二代和三代RNA-seq测序都有相应的建库方案)流程,其能够保留并检测天然RNA碱基修饰信息,还原真实RNA特征,也省去了传统 RNA m6A甲基化修饰繁琐的实验检测步骤, 如 MeRIP-seq/m6A-seq和m6A-SEAL-seq等...
FISH原位杂交结果显示转座子L1的RNA仅位于细胞核内,而缺失SAFB1时,细胞质中L1的RNA含量则会显著增加,表明SAFB蛋白可结合转座子L1,维持其定位在核内,并抑制逆转座发生(图2f)。 哺乳动物中转座子L1 RNA的编码区富含腺嘌呤(A),并且可以通过优化密码子序列来调节腺嘌呤含量,比如在高度活跃的L1突变RNA ORFeus中,...
这些产物并不局限于ONT数据,在Iso-Seq(Isoform sequence,PacBio)数据中也是如此。作者从人样本(阿尔茨海默脑、淋巴母细胞样细胞系COLO829BL、黑色素瘤细胞系COLO829T和人类通用参考RNA)的公共Iso-Seq数据中检测到57个新isoform 中有33个falsitrons。 图2 在cDNA-seq和dcDNA-seq中检测falsitrons 作者进一步分析了...
and gray—undefined). Multiple ORFs are grouped in polycistronic units and these are indicated by black hatched boxes. They-axis represents absolute read-depth counts. Inset windows (blue hatched boxes) exemplify the 3′ bias inherent to direct RNA-seq (due to sequence reads being generated 3′...
direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts inArabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands ofA. thalianagene loci, with TE sequences often being ...
RNA structure is hierarchical, from primary, to secondary, to tertiary, and to quaternary structure [9]. The primary structure is the covalent structure, i.e. the sequence of nucleotides. The secondary structure is the set of canonical base pairs, including A-U, G-C, and G-U pairs. Thes...
西湖大学近期在开放获取期刊Genome Biology上发表了一项研究成果Direct-seq,该研究开发了一种将CRISPR遗传筛选与单细胞RNA-seq结合的新技术,通过改造gRNA序列,在单细胞水平将细胞的“基因型-基因表达谱-表型”关联起来,从而克服了上述两点局限性。...
Figure 17.5.RNA-Seq workflow. There are three stages for an RNA-Seq experiment: (A) Library preparation; (B) Sequencing to generate short read sequences; (C) Data analysis, which includes mapping of short reads to the reference genome and gene annotations or through de novo assembly (not ...
EpiNano relies on the use of base-calling 'errors' to detect RNA modifications; however, direct RNA sequencing base-calling produces a significant amount of 'errors' in unmodified sequences. Therefore, to obtain higher confidence m6A-modified sites, we recommend to sequence both modified and unmod...