Advanced Sequencing Technologies and Genomic Applications

Vocabulary practice flashcards covering advanced genomics and sequencing methodologies, including targeted sequencing, epigenetics, chromatin accessibility, 3D genome conformation, and single-cell approaches.

Exome

All the protein-coding regions (exons) of the genome, which constitute only a small fraction of total genomic DNA.

Exome Sequencing

A targeted sequencing method where genomic DNA is fragmented, and exon regions are captured and enriched using specific probes before sequencing and mapping back to a reference genome.

RAD-tag Sequencing

Restriction-site Associated DNA sequencing; a method used to sequence regions of DNA surrounding restriction enzyme recognition cut sites by ligating adaptors, shearing to size, and adding a second adaptor.

RNA Sequencing (RNA-seq)

A technique used to sequence RNA transcripts to assess gene expression and determine which genes are active or inactive under specific conditions.

Stochastic Gene Expression

Random variation in gene expression observed even among synchronized clones, leading to differing transcript abundance across genetically identical cells.

RNA Capture Sequencing

A method combining exome capture arrays and RNA-seq that uses capture probes to selectively enrich targeted RNA sequences, enabling deep sequencing of low-abundance transcripts.

Bisulfite Sequencing (BS-seq)

An epigenetic sequencing technique where bisulfite treatment converts unmethylated cytosine to uracil ($C \rightarrow U$, read as $T$ during PCR), while methylated cytosine ($^{m}\text{C}$) remains unchanged.

Biological Age Estimation

The process of estimating an individual's physiological age by measuring age-dependent changes in genomic DNA methylation patterns.

TAB Sequencing

TET-assisted bisulfite sequencing; an epigenetic technique combining TET enzyme treatment with bisulfite sequencing to specifically distinguish and detect 5-hydroxymethylcytosine ($5\text{hmC}$) from 5-methylcytosine ($5\text{mC}$).

Tagmentation

A process mediated by the Tn5 transposase where DNA is simultaneously cleaved and tagged with sequencing adaptors.

ATAC-seq

Assay for Transposase-Accessible Chromatin using sequencing; a technique utilizing the hyperactive Tn5 transposase to target and tag open, accessible chromatin regions for sequencing.

ChIP-seq

Chromatin immunoprecipitation sequencing; an approach used to determine genome-wide binding locations of specific proteins or histone modifications using protein-specific antibody pulldown followed by sequencing.

Hi-C Sequencing

A genome-wide method for identifying 3D chromatin conformation and spatial proximity by crosslinking interacting DNA loci, cutting with restriction enzymes, marking with biotin, ligating, and performing paired-end sequencing.

Hi-C Contact Map

A two-dimensional interaction heatmap displaying the frequency of spatial interactions between genomic regions, where darker or redder points indicate higher interaction frequencies.

Single-Cell Sequencing

The sequencing of genetic or transcriptomic material from individual cells, providing high-resolution insight into cellular heterogeneity without averaging signals across a bulk population.

Yeast Two-Hybrid Screen

A molecular screening method used to identify physical protein-protein interactions within cellular networks.

Farncombe HiSeq 1500

A high-throughput sequencing platform utilized to generate large volumes of sequencing data across varied genomics applications.