Transcriptomics_Flashcards

What is transcriptomics?

The study of the transcriptome, which is the complete set of RNA transcripts produced by a genome under specific conditions.

What percentage of all genes is typically expressed in a cell at a given time?

40-50% of all ~25,000 genes.

What are housekeeping genes?

Genes that are consistently expressed in most cells to maintain basic cellular functions, numbering around 8,000-10,000.

What is bulk RNA-Seq primarily used for?

To measure gene expression levels across a population of cells.

What is the purpose of Poly-A Selection in bulk RNA-Seq?

To selectively capture mature mRNA and remove rRNA and other unwanted RNA types.

What is the significance of random priming in bulk RNA-Seq?

To ensure unbiased reverse transcription and generate cDNA that represents the whole transcriptome.

List one alternative to Poly-A Selection in RNA-Seq library preparation.

rRNA depletion.

What is the purpose of A-tailing in bulk RNA-Seq?

To add a single adenine nucleotide to the 3' end of each DNA fragment to prevent self-ligation and enable efficient adapter ligation.

What is the difference between bulk RNA-Seq and scRNA-Seq?

Bulk RNA-Seq averages gene expression from all cells, while scRNA-Seq analyzes individual cell expression profiles.

What is GSEA used for in transcriptomic analysis?

To determine if a defined set of genes shows statistically significant differences between two biological states.

What does UMI stand for in the context of scRNA-Seq?

Unique Molecular Identifier.

What technique is used to identify pathways enriched for differentially expressed genes?

Pathway analysis.

What are t-SNE and UMAP used for in scRNA-Seq analysis?

Dimensionality reduction techniques to visualize complex datasets.

What type of analysis compares expression analysis across spatial domains in spatial transcriptomics?

Differential Expression Analysis.

Name one method for filtering out low-quality cells in scRNA-Seq analysis?

Total number of genes detected per cell.

What step follows dimensionality reduction in scRNA-Seq analysis?

Clustering to identify groups of similar cells.

What is the main goal of cell-cell communication analysis in single-cell RNA sequencing?

To predict interactions between cell types.

What does the term 'gene set enrichment analysis (GSEA)' refer to?

A computational method to determine if a set of genes shows significant expression changes between biological states.