than another.\n"However, existing methods to discover them suffer from either low discovery rates or high rates of\nfalse positives.\n"We introduce Dawnn, a deep neural network able to find differential abundance with higher accuracy\nthan current tools, both on simulated and biological datasets...
As a proof of concept, we designed a ladder comprising eight different hash oligos, theoretical abundance ranging from 0.1–12.8 picomoles per one million nuclei, and introduced into a sci-RNA-seq library preparation of HEK293T cells during the cell lysis step (Fig.1a). As expected, we reco...
Single-cell RNA-seq (scRNA-seq) enables the quantification of RNA abundance at the resolution of individual cells4. The maturation of single-cell technologies now enables large-scale comparisons of cell states within complex tissues, thus providing the appropriate resolution to dissect cell-type-speci...
Many methods have been used to determine differential gene expression from single-cell RNA (scRNA)-seq data. We evaluated 36 approaches using experimental and synthetic data and found considerable differences in the number and characteristics of the genes that are called differentially expressed. Prefil...
Although it is possible that manipulation occurring during surgery contributed to the abundance of PanIN-like lesions proximal to ligation, these lesions also occur in mice that are not subjected to surgery23 (data not shown). When KrasG12D mutation was introduced into ductal cells of 6 mice, ...
Information about Transcript Size: Northern blot analysis is the easiest method for determining both transcript size and the presence of alternatively spliced or multiple transcripts generated from a single locus. Quantitation: Northern blot analysis allows a direct relative comparison of mes...
Differential gene expression, commonly abbreviated as DG or DGE analysis refers to the analysis and interpretation of differences in abundance of gene transcripts within a transcriptome (Conesa et al., 2016). From: Encyclopedia of Bioinformatics and Computational Biology, 2019 ...
hierarchy in cell type-specific differential analyses of bulk data. Extensive simulation and real data analyses demonstrate that this approach significantly improves the accuracy and power in detecting cell type-specific differential signals compared with existing methods, especially in low-abundance cell ...
The 18S, 28S, and mitochondrial sequences itemized above were then added to the reference, so that the number of reads that mapped to these high-abundance sequences could be quantified. This produced a reference of 26,514 transcripts. The modified reference, including single copies of the ...
As of now, prokaryotic scRNA-Seq approaches are lacking in that prokaryotes have extremely low RNA abundance, lack mRNA polyadenylation, and have thick cell walls [139]. While the recent development of techniques such as PETRI-seq [139] and microSPLiT [140] has enabled the capture of single-...