In prokaryotes, the proportion of messenger RNA to total RNA is rather low. Therefore, the main strategy of library preparation for sequencing is mRNA enrichment. Ribosomal and transfer RNAs, both monophosphorylated at the 5′-ends, are the major fractions of total RNA, while the bulk of ...
As bulk RNA-seq library preparation methods are known to be sensitive to RNA input amount, in this study we tested the three different methods with varying input amounts of RNA. While RNA is typically abundant in in vivo experiments, many human stem cell model systems that are used to mimic...
Here, we report a single-cell method (scMspJI-seq) that enables strand-specific quantification of 5mC, allowing us to systematically probe the dynamics of global demethylation. When applied to mouse embryonic stem cells, we identified substantial cell-to-cell strand-specific 5mC heterogeneity, ...
Although a number of high-throughput methods have been developed, each fills a specific role. For example, the methods that rely on split-pool barcoding of cells or nuclei, such as sci-RNA-seq (Cao et al., 2017) or SPLiT-seq (Rosenberg et al., 2018), can examine tens to hundreds ...
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 is an RNA-guided DNA endonuclease system that targets specific genomic sequences [1]. Genome editing via the non-homologous end-joining (NHEJ) or homology-directed repair (HDR) after CRISPR-mediated double-stranded DNA (dsDNA) ...
MustSeq will greatly accelerate the application of bulk RNA-seq on different fields, and potentially applicable for single cell RNA-seq.doi:10.1080/15476286.2021.1974208L.MaiY.QiuZ.LianC.ChenL.WangY.YinS.WangX.YangY.LiW.PengRNA BiolRNA biology...
Here we designed a specialized bioinformatics pipeline cscMap for de novo identification of the cross-strand chimeric RNAs directly from the RNA-seq reads, in a context-specific manner. A series of measurements were carefully implemented by cscMap to obtain high accuracy for capturing the cross-...
‘H2’, respectively; Fig.1b). Using the female-derived NA12878 cell line, we compared haplotype-specific NO to haplotype-resolved gene expression measurements from bulk RNA-seq data34(Methods). We identified a significant increase of NO in gene bodies mapping to H1 compared with H2 across ...
However, the genome-wide distribution of these AP-sites was found to be stochastic and due to the cellular heterogeneity within a population, identification of specific hotspots of AP-sites remains challenging. In repair-assisted damage detection sequencing (RADD-Seq), the DNA was extracted and in...
To explore data from this initial Repair-seq screen, we considered two complementary perspectives. First, we examined the effects of many different gene knockdowns on specific repair outcomes, producing “parts lists” of genes involved in creating or preventing each outcome (Figure 1E). For examp...