Illumina Sequencing
Illumina sequencing is primarily used to determine the order of these four DNA building blocks.
What are A, T, G, and C (nucleotides)?
What do histone proteins do?
DNA wraps around histones to form nucleosomes - these form chromatin fragments, and loops of chromatin establish chromosomes
PacBio is known for making these instead of short reads.
What are long reads?
Sequencing that when elongated is terminated after the addition of each NTP.
What is Sanger/First generation sequencing?
The enzyme that adds nucleotides complementary to the DNA template strand.
What is DNA polymerase?
Illumina sequencing is considered a type of this generation of sequencing technology.
What is next-generation sequencing (NGS)?
What is the significance of CpG islands?
Nearly 60% of human gene promoters are located in CpG islands
PacBio HiFi reads can reach about this percent accuracy.
What is 99.9%?
DNA sequence additions are measured by drop in electrical current magnitude.
What is Ion Torrent?
The bond formed between two nucleotides that allows a DNA strand to elongate.
What is a phosphodiester bond?
During Illumina sequencing, each of the four nucleotides is identified using this detectable signal.
What is fluorescence?
What are the two classes of pseudogenes?
Processed and nonprocessed (processed contain counterparts of introns and exons, non processed only have exonic sequences)
SMRT in PacBio SMRT sequencing stands for this.
What is Single Molecule Real-Time sequencing?
Can use either a 2-channel or 4-Channel SBS when detecting nucleotide additions.
What is Illumina?
A template stand, primer with free 3'OH, DNA polymerase and dNTPs.
What are the key requirements for DNA synthesis?
These short DNA sequences are attached to fragments so they can bind to the flow cell.
What are adapters?
What percentage of the human genome contains TEs?
This PacBio method makes HiFi reads by sequencing the same circular DNA molecule multiple times and combining the results into one consensus sequence.
What is circular consensus sequencing or CCS?
Directly reads both DNA and RNA in real time and can be reused multiple times.
What is Oxford Nanopore?
The energy for bond formation during dNTP incorporation.
What is pyrophosphate (PPi)?
Before sequencing begins, DNA fragments are amplified into clusters on a flow cell using this process.
What is bridge amplification?
What are the two major classes of TEs?
Class I retrotransposons (replicate via RNA intermediate ex LINE SINE LTR) and Class II DNA transposons (no RNA intermediate - rare)
Unlike Illumina sequencing, PacBio single-molecule sequencing does not require this step to make many identical copies of each DNA fragment before sequencing.
What is clonal amplification?
The first next-generation sequencing technology that has been mostly phased out.
What is 454 Pyrosequencing?
DNA chain elongation is terminated because a ddNTP lacks the 3′-OH group needed to form a connection with the next nucleotide.
What happens when a ddNTP is incorporated at the 3′ end of a growing DNA strand, and why?