[W11] Transcriptomics Flashcards
(18 cards)
What is the transcriptome?
The complete set of RNA transcripts (coding and non-coding) present in a cell, tissue, or organism under specific conditions.
Transcriptomics studies the transcriptome.
What is transcriptomics?
The study of the transcriptome using high-throughput techniques to quantify and analyze RNA expression.
It involves various techniques for measuring gene expression.
What is Northern blotting?
An RNA quantification technique involving:
* RNA isolation
* Denaturing gel electrophoresis
* Transfer to membrane
* Hybridization with a labeled probe
This method allows for the detection of specific RNA sequences.
What is RT-PCR?
Reverse transcription followed by PCR; converts RNA to cDNA for amplification.
It is a crucial technique for studying gene expression.
What is qRT-PCR (real-time PCR)?
A quantitative technique that detects amplified DNA using fluorescent markers during PCR cycles.
It allows for the monitoring of the PCR process in real-time.
What is a DNA microarray?
A chip containing thousands of known DNA probes that hybridize with labeled cDNA to analyze gene expression.
It enables simultaneous analysis of multiple genes.
How are microarrays used in gene expression studies?
Labeled cDNA from samples binds to complementary DNA probes; intensity of signal reflects gene expression level.
This method provides a snapshot of gene expression profiles.
What are the uses of DNA microarrays in medicine?
- Disease gene discovery
- Diagnostics (e.g., tumor typing)
- Drug development and toxicity screening
- Personalized medicine
These applications enhance understanding of diseases and treatment strategies.
What are the limitations of microarrays?
- Requires prior knowledge of gene sequences
- Cross-hybridization artefacts
- Limited quantification precision
These limitations can affect the accuracy of results.
What is RNA-seq?
A deep-sequencing method to quantify and identify all RNA species in a sample, providing detailed expression profiles.
It is a powerful tool for comprehensive transcriptome analysis.
What are the advantages of RNA-seq over microarrays?
- Higher precision
- No need for prior gene knowledge
- Can detect novel transcripts and isoforms
- Greater dynamic range
These advantages make RNA-seq a preferred method for transcriptome analysis.
What is spatial transcriptomics?
A method that retains tissue context while sequencing RNA, revealing where genes are expressed within tissue sections.
This technique provides insights into gene expression at the tissue level.
What is single-cell transcriptomics?
RNA-seq applied to individual cells to analyze cell-specific gene expression and heterogeneity.
It allows for the study of gene expression variability among individual cells.
What is an sQTL?
A genetic variant associated with changes in transcript splicing ratios, linking genotype to alternative splicing.
sQTL analysis helps understand the genetic basis of splicing variation.
What is somatic mosaicism in transcriptomics?
The detection of somatic mutations in RNA that reflect underlying DNA variants and gene expression changes.
This concept is important for understanding cancer and other diseases.
How is RNA-seq used in personalized medicine?
It helps identify individual gene expression profiles for diagnosis, treatment selection, and prognosis.
Personalized medicine aims to tailor treatments based on genetic information.
What are the main approaches to transcriptome analysis?
- Northern blotting
- RT-PCR/qPCR
- DNA microarrays
- RNA-seq
- Spatial/single-cell transcriptomics
Each method has its strengths and applications in transcriptomics.
What major advantage does RNA-seq have over microarrays?
It does not require prior knowledge of transcript sequences and can detect novel variants and isoforms.
This makes RNA-seq a more versatile and comprehensive tool for transcriptomic analysis.
