We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to ...
1、比较miRNA及其靶基因的表达模式,联合sRNA-seq和RNA-Seq数据进行分析。正如预期的那样,大多数靶基因的表达趋势与相应的miRNA相反。 2、dcl1-9突变体中,DEGs数量大幅降低,突出dcl1-9对抗TCV反应起负作用。此外,PPR基因可能在植物抗病毒防御中发挥重要作用。 参考文献: Analyses of ...
Subramanian D, Bhasuran B, Natarajan J. 7 October 2018. Genomic analysis of RNA-Seq and sRNA-Seq data identifies potential regulatory sRNAs and their functional roles in Staphylococcus aureus. Genomics https://doi.org/10.1016/j.ygeno.2018.09.016....
The ncPRO-seq pipeline supports input read sequences in fastq, fasta and color space format, as well as alignment results in BAM format, meaning that sRNA raw data from the three current major platforms (Roche-454, Illumina-Solexa and Life technologies-SOLiD) can be analyzed with this ...
viral defense in TCV-infected Arabidopsis thaliana Chao Wu1, Xinyue Li2, Song Guo3 & Sek-Man Wong1,3,4,5 In order to identify specific plant anti-viral genes related to the miRNA regulatory pathway, RNA-Seq and sRNA-Seq were performed using Arabidopsis WT and dcl1-9 mutant ...
利用PBOX-sRNA-seq,研究人员可以从严重降解的RNA样本(RIN=4.15)以及AGO-RIP样品中高效克隆出全长的miRNA和siRNA。对拟南芥hen1-2弱突变体进行分析发现,HEN1的部分缺失更容易引起miRNA甲基化水平的下降。与预期一致,大量截短和加尾的miRNA(被认为是非甲基化的miRNA)在PBOX-sRNA-seq中不能被克隆。然而,相较于长...
测序方案:对所取样本进行mRNA-seq,sRNA-seq及降解组。并通过RT-qPCR和Northernblot进行验证。 结果 1 营养组织和生殖组织对热胁迫的不同的转录反应 对常温下生长的玉米自交系B73在V3期和R1期分别进行了短(2h)或长(48h)的热胁迫(38°C)处理。热胁迫后,V3期玉米新生叶片比对照叶片卷曲,叶片中叶绿素含量下降。在...
seqpac的分析步骤主要为四步: Generate a PAC object from fastq-files Preprocess the PAC object Annotate the PAC object Analyze the PAC object. 示例数据 seqpac包中自带了一个示例数据,6 sRNA fastq文件。 image-20230823222638876.png 样本组织类型为果蝇胚胎,测序平台为Illumina NextSeq 500,测序读长为75个...
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinformatics. 2012;28(23):3147-9.Chen CJ, Servant N, Toedling J, Sarazin A, Marchais A, Duvernois-Berthet E, et al. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. ...
RNA-seq and sRNA-seq analysis in lateral buds and leaves of juvenile and adult rosesrosevegetative phase changetranscriptomemiRNAtranscription factorsThe timing of juvenile-to-adult phase changes are crucial for woody plants, but the molecular mechanisms involved in these changes are still unclear. In...