51 Questions
What is the purpose of DNA microarray technique?
To analyze the expression of thousands of genes simultaneously
What does mRNA act as in the context of gene expression?
A surrogate marker
Why is it necessary to convert mRNA into a more stable cDNA form?
mRNA is easily degraded
What does global expression profiling offer as an advantage?
The genes examined are not influenced by preselection
Where are many different DNA sequences deposited in DNA microarray technique?
On a small surface, usually a glass slide
What is the role of mRNA in protein synthesis?
It carries genetic information from the cell nucleus to the cytoplasm
What is the main method used to identify DNA fragments on microarrays?
Location and complementary base pairing through hydrogen bonding
What is the purpose of mRNA samples being converted to cDNA and labeled with fluorescent probes in microarray analysis?
To measure gene expression
What is a limitation of microarray technology?
Time-consuming analysis of large data sets
What does DNA sequencing determine?
The order of nucleotides in a DNA strand
What is a characteristic of Sanger sequencing?
It is a PCR-based method that sequences up to 1000 nucleotides in multiple reactions.
What is a characteristic of NGS (Next-Generation Sequencing)?
It is a high-speed, high-throughput method that sequences entire genomes at a reduced cost.
How can microarray analysis be used in drug discovery and development?
To identify disease pathways, validate targets, and screen compounds for mechanisms of action and toxicity.
What can microarray analysis help identify?
Gene expression changes in response to treatment
How can a patient's breast cancer resistance to chemotherapies be investigated?
By comparing gene expression profiles before and after treatment.
What is the purpose of ligation with custom adaptors in library preparation?
To introduce index for sample identification
What is the main method used for sequencing during library preparation?
Bridge PCR
How are nucleotide additions detected during the sequencing reaction?
By measuring changes in electrical conductivity
What is a characteristic of third-generation sequencing (3GS) technologies?
They generate long reads for a more complete genome picture
How does single-molecule real-time (SMRT) sequencing work?
It immobilizes a single DNA molecule on a polymerase enzyme and generates long, continuous reads in real-time
What is the advantage of third-generation sequencing (3GS) over second-generation sequencing?
Generation of long reads that span entire genomic regions
What is the main purpose of microarrays in drug discovery and development?
Identifying disease pathways, validating targets, and screening compounds for mechanisms of action and toxicity
What is a limitation of microarray technology?
Time-consuming analysis of large data sets
What is a characteristic of Sanger sequencing?
It is a PCR-based method that sequences up to 1000 nucleotides in multiple reactions
What does DNA sequencing determine?
The order of nucleotides in a DNA strand
What is the main advantage of NGS over Sanger sequencing?
High-speed, high-throughput sequencing of entire genomes at a reduced cost
How are mRNA samples from reference and experimental samples processed for microarray analysis?
Converted to cDNA and labeled with fluorescent probes
What can microarray analysis help identify?
Gene expression changes in response to treatment and compounds with too many side-effects
What is the role of mRNA in the context of gene expression?
mRNA carries genetic information from DNA to ribosomes for protein synthesis
What is the purpose of converting mRNA into cDNA and labeling it with fluorescent probes in microarray analysis?
To facilitate hybridization with microarray slides for gene expression analysis
What is the purpose of ligation with custom adaptors during library preparation for NGS?
To allow amplification by PCR before sequencing
What is the purpose of ligation with custom adaptors in library preparation?
To enable the sequencing primer binding site
How does single-molecule real-time (SMRT) sequencing work?
It immobilizes a single DNA molecule on a polymerase enzyme and generates long, continuous reads in real-time
What is a characteristic of third-generation sequencing (3GS) technologies?
They generate long reads
How is data analysis involved in the sequencing process?
Processing signals to determine the sequence using assembly consensus and determining coverage
What is the main method used for sequencing during library preparation?
Immobilizing DNA on a polymerase enzyme for real-time reads
What is the advantage of third-generation sequencing (3GS) over second-generation sequencing?
Generating long reads that span entire genomic regions
What does DNA sequencing determine?
The sequence of nucleotides in a DNA molecule
What can microarray analysis help identify?
Global expression profiles of genes
How can third-generation sequencing (3GS) be applied?
For biomarker discovery, clinical trial design, precision medicine, and bioproduction
What is the purpose of nanopore sequencing?
To thread DNA through a tiny pore and measure changes in electrical conductivity as bases pass through
What is the purpose of DNA microarray technique?
To analyze the expression of thousands of genes simultaneously
What is the role of mRNA in protein synthesis?
It carries genetic information from the cell nucleus to the cytoplasm
Why is it necessary to convert mRNA into a more stable cDNA form?
mRNA is easily degraded
What does global expression profiling offer as an advantage?
The genes examined are not influenced by preselection of genes
What can microarray analysis help identify?
Activity of genes within a cell or tissue sample
What is the principle technology behind DNA microarray technique?
Depositing many different DNA sequences on a small surface
What does mRNA act as in the context of gene expression?
A surrogate marker for gene expression
What is an advantage of using DNA microarray technique?
Investigating gene regulation and function within cells or tissues
How does mRNA contribute to assessing genetic information?
By producing many copies corresponding to active genes for protein synthesis
What can be inferred from assessing various mRNAs in terms of gene expression?
Understanding processes behind altered genetic expression
Study Notes
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Library preparation involves fragmenting DNA using enzymes or sonication, followed by ligation with custom adaptors.
-
The adaptors contain a sequencer binding site, index, and sequencing primer binding site.
-
Sequencing is performed using clonal amplification methods, such as droplet or bridge PCR.
-
During the sequencing reaction, each nucleotide addition generates an optical or chemical signal.
-
Data analysis involves processing signals to determine the sequence using assembly consensus and determining coverage.
-
Third-generation sequencing (3GS) generates long reads, providing a more complete picture of the genome.
-
3GS technologies include single-molecule real-time sequencing (SMRT) and nanopore sequencing.
-
SMRT sequencing immobilizes a single DNA molecule on a polymerase enzyme and generates long, continuous reads in real-time.
-
Nanopore sequencing threads DNA through a tiny pore and measures changes in electrical conductivity as bases pass through.
-
3GS advantages include generating long reads that span entire genomic regions, resolving ambiguities, and studying complex genomic regions.
-
3GS is used for biomarker discovery, clinical trial design, precision medicine, and bioproduction.
-
Library preparation involves fragmenting DNA using enzymes or sonication, followed by ligation with custom adaptors.
-
The adaptors contain a sequencer binding site, index, and sequencing primer binding site.
-
Sequencing is performed using clonal amplification methods, such as droplet or bridge PCR.
-
During the sequencing reaction, each nucleotide addition generates an optical or chemical signal.
-
Data analysis involves processing signals to determine the sequence using assembly consensus and determining coverage.
-
Third-generation sequencing (3GS) generates long reads, providing a more complete picture of the genome.
-
3GS technologies include single-molecule real-time sequencing (SMRT) and nanopore sequencing.
-
SMRT sequencing immobilizes a single DNA molecule on a polymerase enzyme and generates long, continuous reads in real-time.
-
Nanopore sequencing threads DNA through a tiny pore and measures changes in electrical conductivity as bases pass through.
-
3GS advantages include generating long reads that span entire genomic regions, resolving ambiguities, and studying complex genomic regions.
-
3GS is used for biomarker discovery, clinical trial design, precision medicine, and bioproduction.
Test your knowledge of genomic and transcriptomic analysis techniques, including the role of mRNA in protein synthesis and gene expression.
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