Key Concepts in RNA Sequencing and Vaccination

A collection of flashcards covering key concepts related to RNA sequencing, cell types, and vaccine types for SARS-CoV-2.

What novel questions can single-cell RNA-seq answer that bulk RNA-seq cannot?

It can uncover rare cell types, distinguish cell-to-cell heterogeneity, track lineage relationships, and analyze cell-specific responses to stimuli.

What are the four general types of vaccines developed for SARS-CoV-2?

mRNA vaccines (e.g., Pfizer, Moderna), viral vector vaccines (e.g., Johnson & Johnson), protein subunit vaccines, and inactivated virus vaccines.

Which vaccines are most commonly used in the U.S.?

mRNA vaccines-Pfizer-BioNTech and Moderna—are the most widely used.

How are phylogenetic analyses used to understand SARS-CoV-2 variation?

They track mutations, identify new variants (e.g., Delta, Omicron), and help classify viral lineages and sublineages (e.g., Pango lineages).

What processes contribute to transcriptional differences across tissues?

Tissue-specific transcription factors, epigenetic modifications, chromatin accessibility, and regulatory elements like enhancers.

What factors influence tissue-specific gene expression?

Cell signaling, developmental cues, transcriptional regulators, and chromatin structure.

How can changes in gene expression lead to phenotypic variation?

Differential expression of genes affects protein levels, influencing traits such as morphology, physiology, and disease susceptibility.

What methods can be used to measure and quantify RNA molecules?

RT-qPCR, microarrays, bulk RNA-seq, and single-cell RNA sequencing.

Why is replication especially important in RNA-seq compared to DNA-seq?

RNA expression levels vary more between samples and conditions, so replication helps capture biological variation and ensures statistical power.

What is chromatin accessibility and why does it matter?

It refers to how open or closed chromatin is; accessible chromatin allows transcription factors and RNA polymerase to bind DNA, enabling gene expression.

How were distinct cell types traditionally defined?

By morphology, function, and expression of a few marker proteins.

How has new sequencing technology changed how we define cell types?

Single-cell RNA-seq allows definition based on full gene expression profiles, revealing finer distinctions between cell states and subtypes.

How can cell types be identified from single-cell RNA-seq data?

By clustering cells with similar gene expression patterns and using known marker genes to label clusters.

What are some limitations of single-cell RNA-seq?

Low sensitivity, dropout events (missing transcripts), technical noise, and limited transcript capture.

Can you detect all expressed transcripts from a single cell using droplet-based technologies?

No, droplet-based methods typically detect only a subset of highly expressed genes due to capture inefficiency and sequencing depth.