Cells were grown to a confluence of ~70% and treated with TrypLE Express with Phenol red (Thermo Fisher, 12605010) for 3 min, quenched with an equal volume of growth medium and centrifuged for 5 min at 200g. The supernatant was removed, and the cells were resuspended in 1× DPBS ...
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the...
(red, blue, purple, yellow, and grey) with distinct copy-number states.(C)CHISEL infers a pair of allele-specific copy numbers for each cluster by determining whether the allele-specific copy numbers of the largest balanced (BAF~0.5) cluster are equal to{1, 1}(diploid),{2, 2}(...
barcode_min_quality integer Minimum allowed nucleotide-level quality score in the extracted/uncorrected barcode sequence. Values equal or higher to this this will be considered 'high-quality' and used for generating the barcode whitelist. 15 barcode_max_ed integer Maximum allowable edit distance betwee...
Dropdownlist - Set datatextfield equal to multiple columns DropdownList and Setting Selected Value DropDownList binding get Databinding methods such as Eval(), XPath(), and Bind() can only be used in the context of a databound control exception DropDownList default SelectedValue dropdownlist does n...
Cells were then washed 3 times in staining buffer (2% BSA, 0.01% Tween in PBS) and filtered using a 40 μm Flowmi filter in PBS and pooled in equal proportions. Cells were loaded into 8 lanes of a 10x Genomics Chip B, at 45,000 cells per lane using the 10x Genomics 3′ v3 GEM...
Table S1. Previous single-cell studies; donor characteristics; snRNA-seq and snATAC-seq data and quality control metrics, related to Figures 1 and 5 Table S2. Subcluster membership in major clusters and developmental trajectories; hotspot modules; and IN subcluster investigation, related to Figures...
Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation ...
[82] is an algorithm that aims to select a representative subset of cells that preserves the overall transcriptional heterogeneity of the full dataset. By approximating the underlying geometry of the data through a plaid covering of equal volume hypercubes, geometric sketching is able to evenly ...
line graph. The Kruskal–Wallis test was used for comparisons among multiple independent samples, and Dunn’s test was used for pairwise comparison. A difference was considered statistically significant if the p value of the Kruskal–Wallis test or Dunn’s test was less than or equal to 0.05....