Introduction Genomics

37 important questions on Introduction Genomics

What is Moore's law?

The observation that the number of transistors on computer chips doubles approximately every two years.

What would happen if genomic DNA sequences were composed of random nucleotides?

All 17-mers would be present once or not at all in any genome.

What is the chance of detecting an A in a random DNA sequence?

1/4
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What is the chance of detecting a 17-mer sequence?

(¼)^17 = 1.72x10^10.

What is more complex to sequence, the natural genome or random DNA sequences?

The natural genome, because there are repetative sequences and it's highly structured.

What is vertical coverage?

The average number of reads that cover each nucleotide in the assembly.

What is the horizontal coverage?

The percentage of the target genome that has been (re)covered in the assembly.

What can you detect with metabolomics?

The reality of the system, which includes effects of post-translational regulation of protein activity.

What advantage does transciptomics have over proteomics?

Nucleic acids are easier to track and they can be amplified.

What molecule transcribes DNA into RNA?

RNA polymerase II

How is mRNA splicing done?

By a RNA-protein complex

How is transcription controlled by proteins?

Transcription factors and transcription cofactors

What is the library preparation?

When adapters are sequenced at the end of the target DNA so it can be sequenced and identified.

What molecule causes chain termination in sequencing?

A dideoxynucleotide (ddNTP)

How can ddNTPs be used to detects nucleotides/sequences?

By tagging them with fluorescent labels

What do primers do in a PCR?

Synthesizing a complimentary copy of the template strand.

What is strand-specific RNA sequencing?

A sequencing method that allows for obtaining information about RNA strand orientation.

What can the data analysis after strand-specific RNA seq determine?

Whether the transcript comes from the sense or antisense strand.

How do you make sure only the first strand is copied in strand-specific RNA seq?

By replacing dTTP with dUTP on the second strand, resulting in degradation

What do the 5' and 3' ends of a DNA sequence indicate?

The directionality of the DNA molecule

What is the antisense strand?

The template strand.

What does it mean when Ensemble or UCSC says a gene is on the forward strand?

It means the gene's coding sequence is on the forward strand.

What is Illumina sequencing?

A sequencing technique that uses sequencing by synthesis to detect individual DNA bases as they are added to a growing strand.

What is used to identify the nucleotides in Illumina sequencing?

Fluorescently-labeled reversible terminator nucleotides

How are the nucleotides identified in Illumina sequencing?

By detecting the fluorescent label, each base has a different colour.

What is Bulk RNA barcoding sequencing?

A RNA sequencing method that uses multiplexing to produce 3' cDNA libraries for dozens of samples.

What do they use to tag the individual RNA samples in BRB?

Barcoded primers.

How can demultiplexing errors arise?

DNA barcodes can be altered during synthesis, primer ligation, DNA amplification or sequencing.

What is an example of one step in the library preparation vulnerable to contamination?

The washing steps to remove enzymes and solutes may introduce cross-contamination.

How could you check the cross-contamination in the library preparation?

Use a negative control that contains no DNA or RNA.

Why is Sanger sequencing the gold standard?

It has a high accuracy, reliability and simplicity, is well established and standardized in diagnosics and produces clear and reliable output.

How can primer mismatches affect PCR yield and specificity?

They can lead to reduced primer binding to the target DNA and may bind non-target sequences.

What is lost in strand-specific RNA sequencing if the library is non-stranded?

The stand of origin, you can't tell which DNA strand the RNA transcript came from.

When would you use the antisense stand in strand specific RNA sequencing?

When resolving overlapping genes on opposite strands to assign reads to the correct genes.

Would you use BRB sequencing or full RNA sequencing for a N=96 cohort with a cost cap?

BRB sequencing, since it has a low cost per sample and is designed for multiplexing samples.

How do repeats break assemblies?

They cause non-specific gene hits and uncertainties in alignment and assembly.

How could you solve repeats in assemblies?

By using long read sequencing, since that can span across entire repeat regions.

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