Single Cell Analysis Flashcards
Why would someone go for a single cell RNA-sequencing technique instead of a bulk sequencing
The limitation of bulk sequencing of tumor samples is being unable to identify small subjects of tumor tissues. With a SC RNA-seq you will get cell specific info
If you look at a cluster map (clustering normal cells and tumor cells), and you see some overlapping, what cells may those be
Might be immune cells or epithelial cells (for ex. blood vessels)
What does UMAP means and what does it tell us
UMAP= Uniform Manifold Approximation And Projection
It is a helpful way of displaying many types of data and are usually in 3D. The biological variance is not correlated with the distance seperating 2 (or more) clusters, however, within the cluster, the distance does matter for correlation
What does a heatmap show
It shows us the expression levels of specific markers in each cell cluster. It uses a value and gives it a colour. How stronger the colour, the more expressed
What is a violin plot used for
Is used to visualize the distribution of numerical data. Unlike a box plot that can ONLY show summary statistics, violin plots depict summary statistics AND the density of each value
What is Pseudotime analysis
IS a computational technique used in single-cell transcriptomics to determine the pattern of a dynamic process experienced by cells and then arrange cells based on their progression through the process
What is a vocano plot used for
Used for Up/down regulation and displaying the fold change (FC). Left of the volcano is downregulated whereas right is for upregulation. How higher the dots, the more significant differences there was
