Untitled Flashcards Set

What is Bisulfite Conversion?

Bisulfite conversion is a chemical treatment of DNA that selectively converts unmethylated cytosine bases to uracil, while 5-methylcytosine remains unchanged.

What are the common steps involved in Bisulfite Conversion?

The steps include DNA denaturation, bisulfite treatment, desulfonation, and PCR amplification.

In what context is Bisulfite Conversion commonly used?

It's commonly used in epigenetics research to map DNA methylation sites in studies such as Whole-Genome Bisulfite Sequencing.

What are the key advantages of using Bisulfite Conversion?

Key advantages include single-base resolution, widespread adoption, and compatibility with NGS.

What are the major limitations or challenges of Bisulfite Conversion?

Limitations include DNA degradation, incomplete conversion, and CpG bias.

Why is Bisulfite Conversion considered an essential technique in epigenetics?

It allows for precise distinction between methylated and unmethylated cytosines, essential for understanding DNA methylation's role in gene regulation.

What specific type of information does Bisulfite Conversion reveal about DNA?

It reveals specific locations and patterns of 5-methylcytosine modifications within a DNA sequence.

What is DNA Methylation?

DNA methylation is the addition of a methyl group to a DNA base, primarily affecting cytosine residues within CpG dinucleotides, influencing gene expression.

What is PCR Amplification?

PCR amplification is a technique used to generate millions of copies of a specific DNA segment from a small initial sample.

What are the common steps involved in PCR Amplification?

The steps are denaturation, annealing, and extension.

In what context is PCR Amplification commonly used?

It's widely used in forensic science, medical diagnostics, and genetics research.

What are the key advantages of using PCR Amplification?

Advantages include high sensitivity, specificity, speed, and versatility.

What are the major limitations or challenges of PCR Amplification?

Limitations include contamination risk, primer design sensitivity, and limited amplicon size.

Why is PCR Amplification considered an essential technique?

It's indispensable for studying specific DNA sequences from limited samples.

What specific type of information does PCR Amplification reveal about DNA?

It reveals the presence or absence of specific DNA sequences.

What is Next Generation Sequencing (NGS)?

NGS refers to high-throughput sequencing technologies that sequence millions of DNA fragments simultaneously.

What are the common steps involved in Next Generation Sequencing (NGS)?

Steps include library preparation, cluster generation, sequencing by synthesis, and data analysis.

In what context is Next Generation Sequencing (NGS) commonly used?

NGS is used for whole-genome sequencing, RNA sequencing, and metagenomics.

What are the key advantages of using Next Generation Sequencing (NGS)?

Advantages include high throughput, cost-effectiveness, speed, and versatility.

What are the major limitations or challenges of Next Generation Sequencing (NGS)?

Limitations include computational demands, short read lengths, and complexity of workflows.

Why is Next Generation Sequencing (NGS) considered an essential technique?

It enables unprecedented insights into genomic, transcriptomic, and epigenomic studies.

What specific type of information does Next Generation Sequencing (NGS) reveal about DNA and RNA?

NGS reveals comprehensive genomic information and gene expression levels.

What is qPCR (quantitative Polymerase Chain Reaction)?

qPCR is a technique that quantifies DNA or RNA amplification in real-time during the PCR process.

What are the common steps involved in qPCR (quantitative Polymerase Chain Reaction)?

Steps include reverse transcription (if starting with RNA), reaction setup, thermocycling, and fluorescence detection.

In what context is qPCR (quantitative Polymerase Chain Reaction) commonly used?

qPCR is used in medical diagnostics, gene expression studies, and GMO evaluation.

What are the key advantages of using qPCR (quantitative Polymerase Chain Reaction)?

Advantages include quantification, speed, high sensitivity, and reduced contamination risk.

What are the major limitations or challenges of qPCR (quantitative Polymerase Chain Reaction)?

Limitations include potential inhibitors, standard curve dependency, and high costs.

Why is qPCR (quantitative Polymerase Chain Reaction) considered an essential technique?

It offers precise quantification and sensitivity in detecting nucleic acids.

What specific type of information does qPCR (quantitative Polymerase Chain Reaction) reveal about nucleic acids?

qPCR reveals the initial concentration of a specific DNA or RNA sequence.

What is CRISPR/Cas9?

CRISPR/Cas9 is a gene editing technology that allows precise modifications to DNA.

What are the common steps involved in CRISPR/Cas9 gene editing?

Steps include gRNA design, delivery, targeting and cleavage, and DNA repair.

In what context is CRISPR/Cas9 commonly used?

It's explored for therapeutics, creating GMOs, and gene function studies.

What are the key advantages of using CRISPR/Cas9?

Advantages include precision, ease of use, versatility, and cost-effectiveness.

What are the major limitations or challenges of CRISPR/Cas9?

Limitations include off-target effects, delivery challenges, and ethical concerns.

Why is CRISPR/Cas9 considered an essential technology?

It offers unparalleled tools for precise genome engineering.

What specific type of information does CRISPR/Cas9 reveal or allow us to obtain?

CRISPR/Cas9 allows the modification of genetic sequences and reveals functional consequences.

What is siRNA (Small Interfering RNA)?

siRNA are short RNA molecules that mediate gene silencing by targeting mRNA.

What are the common steps involved in siRNA-mediated gene silencing?

Steps include delivery, RISC loading, target recognition, and mRNA cleavage.

In what context is siRNA (Small Interfering RNA) commonly used?

siRNA is used to study gene function and as a potential therapeutic agent.

What are the key advantages of using siRNA (Small Interfering RNA)?

Advantages include specificity, broad applicability, and reversibility.

What are the major limitations or challenges of siRNA (Small Interfering RNA)?

Limitations include off-target effects, delivery challenges, and transient effects.

Why is siRNA (Small Interfering RNA) considered an essential tool?

It provides specific methods for transient gene expression reduction.

What specific type of information does siRNA (Small Interfering RNA) reveal?

siRNA allows researchers to infer the function of specific genes.

What is Chromatin Immunoprecipitation (ChIP)?

ChIP is a technique used to study protein-DNA interactions in living cells.

What are the common steps involved in Chromatin Immunoprecipitation (ChIP)?

Steps include cross-linking, chromatin fragmentation, immunoprecipitation, washing, and DNA purification.

In what context is Chromatin Immunoprecipitation (ChIP) commonly used?

ChIP is used to identify transcription factor binding sites and histone modifications.

What are the key advantages of using Chromatin Immunoprecipitation (ChIP)?

Advantages include genome-wide mapping and direct interaction identification.

What are the major limitations or challenges of Chromatin Immunoprecipitation (ChIP)?

Limitations include antibody quality and computational complexity.

Why is Chromatin Immunoprecipitation (ChIP) considered an essential technique?

It provides direct evidence of protein-DNA interactions in native chromatin.

What specific type of information does Chromatin Immunoprecipitation (ChIP) reveal about protein-DNA interactions?

ChIP identifies specific genomic regions bound by proteins.

What is Whole Genome Sequencing (WGS)?

WGS is a laboratory process that determines the complete DNA sequence of an organism's genome.

What are the common steps involved in Whole Genome Sequencing (WGS)?

Steps include DNA library preparation, clonal amplification, sequencing, and data analysis.

In what context is Whole Genome Sequencing (WGS) commonly used?

WGS is used in clinical diagnostics and public health to identify genetic variations.

What are the key advantages of using Whole Genome Sequencing (WGS)?

Advantages include comprehensive information and future-proofing.

What are the major limitations or challenges of Whole Genome Sequencing (WGS)?

Limitations include high cost and interpretation complexity.

Why is Whole Genome Sequencing (WGS) considered an essential technique?

WGS offers comprehensive views of an organism's genetic makeup.

What specific type of information does Whole Genome Sequencing (WGS) reveal?

WGS reveals the entire DNA sequence of an organism's genome.

What is Digital PCR (dPCR)?

dPCR is a nucleic acid quantification technique that provides absolute quantification of targets.

What are the common steps involved in Digital PCR (dPCR)?

Steps include sample partitioning, PCR amplification, and digital readout.

In what context is Digital PCR (dPCR) commonly used?

dPCR is used for liquid biopsy assays and precise quantification.

What are the key advantages of using Digital PCR (dPCR)?

Advantages include absolute quantification and high sensitivity.

What are the major limitations or challenges of Digital PCR (dPCR)?

Limitations include lower throughput and higher cost per sample.

Why is Digital PCR (dPCR) considered an essential technique?

dPCR offers unparalleled precision for absolute quantification.

What specific type of information does Digital PCR (dPCR) reveal about nucleic acids?

dPCR reveals the precise concentration of target nucleic acids.

What is Sanger Sequencing?

Sanger sequencing is a technique that determines the precise nucleotide sequence of DNA.

What are the common steps involved in Sanger Sequencing?

Steps include reaction setup, chain termination, capillary electrophoresis, and sequence generation.

In what context is Sanger Sequencing commonly used?

Sanger sequencing is used for sequencing specific genes and confirming NGS variants.

What are the key advantages of using Sanger Sequencing?

Advantages include high accuracy and long read lengths.

What are the major limitations or challenges of Sanger Sequencing?

Limitations include low throughput and high cost for large projects.

Why is Sanger Sequencing considered an essential technique?

It offers unmatched accuracy for validating variants.

What specific type of information does Sanger Sequencing reveal about DNA?

It reveals the precise nucleotide sequence of a specific DNA fragment.

What is LAMP (Loop-mediated Isothermal Amplification)?

LAMP is a nucleic acid amplification technique that operates at a constant temperature.

What are the common steps involved in LAMP (Loop-mediated Isothermal Amplification)?

Steps include reaction setup, isothermal incubation, self-priming and amplification, and detection.

In what context is LAMP (Loop-mediated Isothermal Amplification) commonly used?

LAMP is used for point-of-care diagnostics and environmental monitoring.

What are the key advantages of using LAMP (Loop-mediated Isothermal Amplification)?

Advantages include simplicity, rapidity, and high sensitivity.

What are the major limitations or challenges of LAMP (Loop-mediated Isothermal Amplification)?

Limitations include primer design complexity and potential carry-over contamination.

Why is LAMP (Loop-mediated Isothermal Amplification) considered an essential technique?

LAMP offers rapid and robust nucleic acid amplification for accessible diagnostics.

What specific type of information does LAMP (Loop-mediated Isothermal Amplification) reveal?

LAMP reveals the presence of specific DNA or RNA target sequences.

What is ATAC-seq?

ATAC-seq is a technique for investigating genome-wide chromatin accessibility.

What are the common steps involved in ATAC-seq?

Steps include cell lysis, tagmentation, PCR amplification, and sequencing.

In what context is ATAC-seq commonly used?

ATAC-seq is used to identify active regulatory elements and study chromatin accessibility.

What are the key advantages of using ATAC-seq?

Advantages include high resolution and low cell input requirements.

What are the major limitations or challenges of ATAC-seq?

Limitations include sample handling and computational demands.

Why is ATAC-seq considered an essential technique?

ATAC-seq provides rapid insights into gene regulation and chromatin dynamics.

What specific type of information does ATAC-seq reveal about chromatin?

ATAC-seq reveals regions of open, accessible chromatin across the genome.

What is Immunofluorescence (IF)?

Immunofluorescence is a microscopy technique that uses antibodies to visualize proteins.

What are the common steps involved in Immunofluorescence (IF)?

Steps include sample preparation, blocking, antibody incubation, and imaging.

In what context is Immunofluorescence (IF) commonly used?

IF is used to study protein localization, cellular processes, and diagnose diseases.

What are the key advantages of using Immunofluorescence (IF)?

Advantages include high specificity and resolution, multiplexing capability.

What are the major limitations or challenges of Immunofluorescence (IF)?

Limitations include antibody quality and quantification challenges.

Why is Immunofluorescence (IF) considered an essential technique?

IF allows direct visualization of proteins within tissue architecture.

What specific type of information does Immunofluorescence (IF) reveal about proteins?

IF reveals the localization and abundance of specific proteins within cells.

What is ELISA (Enzyme-Linked Immunosorbent Assay)?

ELISA is a plate-based assay for detecting and quantifying proteins or analytes.

What are the common steps involved in ELISA (Enzyme-Linked Immunosorbent Assay)?

Steps include plate coating, blocking, sample addition, detection, and signal measurement.

In what context is ELISA (Enzyme-Linked Immunosorbent Assay) commonly used?

ELISA is used in clinical diagnostics and research for quantifying biomolecules.

What are the key advantages of using ELISA (Enzyme-Linked Immunosorbent Assay)?

Advantages include high sensitivity, specificity, and quantification capabilities.

What are the major limitations or challenges of ELISA (Enzyme-Linked Immunosorbent Assay)?

Limitations include antibody quality and sample matrix effects.

Why is ELISA (Enzyme-Linked Immunosorbent Assay) considered an essential technique?

ELISA offers precise and quantitative detection of analytes in biological samples.

What specific type of information does ELISA (Enzyme-Linked Immunosorbent Assay) reveal about analytes?

ELISA reveals the concentration of specific antibodies, proteins, or other analytes.

What is Mass Spectrometry (MS)?

MS is an analytical technique that measures the mass-to-charge ratio of ions.