High-throughput illumina strand-specific RNA sequencing library preparation. Conventional Illumina RNA-Seq does not have the resolution to decode the complex eukaryote transcriptome due to the lack of RNA polarity information. Strand-specific RNA sequencing (ssRNA-Seq) can overcome these limitations and ...
Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012; 3:9. [PubMed: 23273270]Z. Zhang, W.E. Theurkauf, Z. Weng, P.D. Zamore, Strand-specific libraries for high throughput...
对于strand-specific的RNA-seq而言,我们必须得知道它是哪一种建库方式,才能进行后续的定量分析。 stringtie: 代码语言:javascript 代码运行次数: --rf Assumes a stranded library fr-firststrand.--fr Assumes a stranded library fr kallisto: 代码语言:javascript 代码运行次数:0 复制 代码运行 --fr-stranded runs...
现在这种特异性的library相对较少,而下面这种更为常见: 主要是“1+-,1-+,2++,2--”这种,也就是read1在+链,相对的gene其实是在-链(reverse)。这种就是“fr-firststrand”,也就是参数中的--rf。 同样两种在0.5附近的是non-specific: infer_experiment.py -r hg19.refseq.bed12 -i Pairend_nonStrandSpe...
All three RNA-seq methods used in this study are strand-specific. While Illumina TruSeq library kit uses dUTP labeling to degrade the second strand, Swift and Swift Rapid RNA kits maintain strand-specificity by making only one functional strand which is immediately ligated with a 3’ truncated ...
Several library preparation methods for strand-specific sequencing of RNA (ssRNA-seq) have been developed in the recent past3–8. However, a majority of these methods involve the synthesis of second-strand cDNA after reverse transcription (RT) that can entail multiple artefacts, including the loss...
Strand-specific ChIP-seq was carried out using formaldehyde crosslinking, mechanical cell lysis, chromatin shearing by sonication and immunoprecipitation (IP) with antibodies against the protein/tag of interest. DNA library preparation involved the purification of sample DNA, denaturation, and adaptase-...
Of or relating to a nucleotide sequence that is complementary to a sequence of messenger RNA. When antisense DNA or RNA is added to a cell, it binds to a specific messenger RNA molecule and inactivates it. American Heritage® Dictionary of the English Language, Fifth Edition. Copyright ©...
This constraint also influenced our sequencing strategy, sequencing mode (paired-end sequencing), library-type (strand-specific cDNA library) and choice of the read length (125 bp). The paired-end strand-specific RNA-Seq with a read length of 125 bp allows for higher levels of specific alignme...
The distribution of γH2AX within domains is influenced by gene transcription, as parallel mappings of RNA Polymerase II and strand-specific expression showed that γH2AX does not propagate on active genes. In addition, we showed that transcription is accurately maintained within γH2AX domains, ...