小RNA测序(sRNA-seq)是高通量表征和分析各类小RNA的重要手段。但常规sRNA-seq中大量的测序数据(很多时候超过40%)来自结构型RNA(包括rRNA、tRNA、snRNA、snoRNA)以及其它RNA的降解片段,不仅降低了目标sRNA的比例,还影响了实验的批次间可重复性,有时甚至导致文库构建失败。因此,常规sRNA-seq对于样品和建库技术的要求通常...
研究人员分析来自TE的24-nt sRNA的变化与其邻近基因表达变化之间的可能关系,对玉米基因组进行分析以识别邻近基因1kb范围内的TE。在R1-雄穗和V3-根的0、2和48HAH时期对在基因范围1kb内产生24-nt sRNA的TE进行了鉴定。分析表明,在产生24-nt sRNA的TE中有20%-30%的TE在1kb范围内有邻近基因,并且这个比例不受热胁...
Hinton A, Hunter SE, Afrikanova I et al (2014) sRNA-seq analysis of human embryonic stem cells and definitive en- doderm reveals differentially expressed microRNAs and novel IsomiRs with distinct targets. Stem Cells 32, 2360- 2372Hinton A, Hunter SE, Afrikanova I, Jones GA, Lopez AD, ...
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 ...
reads长度是150bp，是用磁珠把所有的有polyA的mRNA都调出来，一个miRNA测序，是切胶回收22-50bp的sRNA...
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots 来自 Semantic Scholar 喜欢 0 阅读量: 204 作者:EA Vidal,TC Moyano,G Krouk,MS Katari,M Tanurdzic,W Mccombie,GM Coruzzi,RA Gutiérrez ...
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 ...
The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-speci... This suggests a role of BORIS in SVA expression regulation. RNA-seq analysis indicates that BORIS largely serves as a repressor of SVA ...
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...