molecular

Transcriptomics

The total complement of RNA transcripts, including coding mRNA (95%) and noncoding RNAs like rRNA, snRNA, siRNA, miRNA, and lncRNA.

mRNA

A type of RNA that represents the coding sequence of genes, making up about 1% of the cell's contents.

Next Generation Sequencing (NGS)

A method that reads DNA, requiring the conversion of RNA into complementary DNA (cDNA) to analyze RNA transcripts.

Poly(A)-selection

A method for isolating mRNA by binding mRNA molecules to beads with a polyA tail, allowing removal of other RNA types.

rRNA-depletion

A technique for isolating mRNA by filtering out ribosomal RNA (rRNA) while leaving other RNA types in the mix.

cDNA

Complementary DNA synthesized from an RNA template, used in sequencing to analyze gene expression.

Single-Cell RNA-Seq

A technique that captures the transcription profiles of individual cells, allowing analysis of cellular differences and subtypes.

Cluster analysis

A method that identifies sets of genes with similar expression patterns, revealing regulatory relationships among genes.

Microfluidics

A technology that manipulates small volumes of fluids to isolate single cells for RNA analysis within their unique microenvironments.

Ribosome profiling

A technique that examines the translation of mRNA into protein by identifying which mRNAs are associated with ribosomes.

Ribosome seq

A component of ribosome profiling that sequences mRNA associated with ribosomes to determine translation levels.

RNA degradation

The process through which RNA molecules are broken down, regulated by factors such as lncRNA and siRNA.

how does ribosome profiling work?

We don’t check the amount of proteins in the cell; rather check translation by checking which mRNA is on ribosomes and the amount of RNA found on ribosomes (this is the part that uses RNAseq). RNAs are like chains with beads of ribosomes sitting on them. The goal is to extract the mRNA with ribosomes on them. In order to know which parts of the mRNA have ribosomes on them, we add RNase to fragment all of the RNA except for the parts found in the ribosomes (meaning, protects the ribosomes in the process of translation). We then separate the large and small subunits of the ribosomes and sequence the fragment.

Proteasome

A cellular complex responsible for degrading proteins, providing information about protein levels and translation efficiency.

mRNA stability

The tendency of mRNA to remain intact and functional within the cell, which can affect gene expression.

Ribosome enrichment

The process of isolating mRNA with ribosomes, indicating high translation activity and gene expression.

Expression levels

The quantity of gene products (RNA or proteins) produced in a cell, reflecting the activity of specific genes.

Multiplexed Single-Cell CRISPR Screening

A technique that combines barcode-mediated CRISPR with single-cell RNA sequencing (scRNA-seq) to study the effects of gene knockout (KO) or overexpression on gene expression within individual cells.

scRNA-seq

Single-cell RNA sequencing that allows for the analysis of RNA expression levels in individual cells, crucial for understanding the impact of specific gene mutations.

CRISPRi/CRISPR-KO

CRISPR interference (CRISPRi) and CRISPR knockout (CRISPR-KO) are techniques used to create known mutations in genes, allowing researchers to study their effects on cell behavior and gene expression.

Single-Cell Genomics

The analysis of genomes from individual cells, useful for identifying specific mutations and their effects in diseases like cancer or neurological disorders.

Single-Cell Proteomics

The study of proteins at the single-cell level, allowing for detailed analysis of proteasome activity and its implications for cellular functions.

Neurological Diseases and Single-Cell Analysis

Using single-cell sequencing to investigate specific mutations in neurons that may cause diseases such as Parkinson's, preserving resolution lost in bulk sequencing.

Cancer Genetics and Single-Cell Analysis

Applying single-cell techniques to identify gene mutations that contribute to cancer progression and to examine the gene expressions associated with these mutations.