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...
We begin by highlighting the fidelity and reproducibility of direct RNA-seq, while also leveraging short-read Illumina sequencing data to enable a new approach to error correction that significantly increases the proportion of error-free transcript sequences from which internal ORFs can be accurately t...
RNA sequence refers to the specific arrangement of nucleotides in a RNA molecule, which plays a crucial role in determining its structure and function within biological condensates. AI generated definition based on: Methods in Enzymology, 2018 ...
RNA sequence data may come from many sources (public databases, sequencing data, etc.) and have different file formats (Table 1.1). Before submission to the structure prediction program, this data must be prepared and formatted to an RNAstructure compatible input file. Databases and sequencing dat...
Therefore, we present Sequoia, a visual analytics application that allows users to interactively analyze signals originating from nanopore sequencers and can readily be extended to both RNA and DNA sequencing datasets. Sequoia combines a Python-based backend with a multi-view graphical interface that ...
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...
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。...
Gene and protein sequences for the Vibrio cholerae RNA-guided DNA integration machinery used in this study. ∗ The V. cholerae HE-45 genome contains another Tn7-like transposon (GenBank accession ALED01000025.1), which lacks an encoded CRISPR–Cas system and exhibits low sequence similarity to...