Droplets containing damaged cells: high nuclear fraction score and low UMI count Installation You can install DropletQC with: # install.packages("devtools") devtools::install_github("powellgenomicslab/DropletQC", build_vignettes = TRUE) Calculating the nuclear fraction There are two functions which...
In this analysis cells consist of three distinct cell types: tumour cells, T cells and all other stromal cells. bottom: Schematic of how this same process works when focussing on the TCRA gene in relation to V(D)J recombination and TRECs, the lower right panel indicates an increased number...
In the NGS data analysis for each sample, all referenced chromosomes were divided into segments of the same size (20 kb) bins. The number of unique reads and GC content (rounded to 0.1%) in each 20-kb bin were determined. We then filtered bins without any reads or bins with ‘N’...
The sample includes cell-free DNA fragments originating from maternal cells and fetal cells. For each of a plurality of DNA fragments: one or more sequence reads is received, including both ends of the DNA fragment; the sequence reads are aligned to a reference genome to obtain aligned ...
In vitro characterization of intestinal barrier The barrier function of the gut epithelial cell layer was assessed using epithelial cells, that were isolated from fresh colon samples. About 6 cm of colon were used for cell isolation. Tissue was rinsed with ice-cold phosphate-based saline (PBS) ...
Neurons are cells in the nervous system that send and receive messages throughout your body, allowing your brain to control everything you do. They're even involved inhow your brain processes eating. Since there are about 86 billion neurons in the brain, the synapses that connect them look ...
cells (CDCs) and their exosomes to improve left ventricular structure, function and overall outcome. Administration of CDCs led to improved LV relaxation, lower LV end-diastolic pressure, decreased lung congestion and enhanced survival. Lower risk of arrhythmias in HFpEF was also observed following ...
In patients with cancer, the cfDNA in plasma is derived from both tumor and normal cells, in particular white blood cells [7]. cfDNA tumor fraction, defined as the fractional proportion of tumor DNA relative to total cfDNA, is dependent on multiple factors, including disease extent (localized ...
in the allele frequency of somatic mutations7. To characterise the clonal composition of a tumour, the variant allele frequency (VAF) must be converted to a cancer cell fraction (CCF), the fraction of cancer cells within which the variant is present. Events appearing in all cancer cells (CCF...
in the allele frequency of somatic mutations7. To characterise the clonal composition of a tumour, the variant allele frequency (VAF) must be converted to a cancer cell fraction (CCF), the fraction of cancer cells within which the variant is present. Events appearing in all cancer cells (CCF...