Block 3 CFP2 Flashcards
A visual representation of all the chromosomes in a cell’s nucleus when stained by Giemsa. Define by dark bands and light bands giving each chromosome a unique appearance
Cytogenetic Mapping
Genomics
Also known as gene mapping, this technique allows DNA fragments to be assigned a place on a chromosome after overlapping fragments have been created
Physical Clone Map
Genomics
A microarray that allows entire genomes to be analyzed and compared with a single hybridization
CGH
Genomics
using restriction digest to detect mutations and identify them using agarose gel, nitrocellulose/ nylon membrane and radioactive probes
RFLP and southern blotting
Genomics
a microarray that can detect many single nucleotide polymorphisms simulataneously
SNP chips
Genomics
a method of testing for SNP using oligonucleotide probes
ASO technique
Genomics
Use of fluorescent probes on an interphase or metaphase chromosome to detect abnormalities in a DNA sample
FISH
Genomics
a layout of the number and appearance of each chromosome to detect abnormalities in a DNA sample
Karyotype
Genomics
Shotgun Sequencing
- Genomic DNA is extracted
- DNA digested by restriction enzymes
- Fragments are separated by electrophoresis
- Fragments (contigs) are sequenced
- overall sequence is based on fragment overlap
Genomics
Dideoxynucleotides?
Sanger sequencing, terminate DNA synthesis
Genomics
After electrophoresis and blotting unto nylon membranes, radioactive probes specific to a transcript (mRNA) are used to identify a particular mRNA from a sample
Northern Blotting
Transcriptomics
Allows visualization of a specific gene that is being expressed by attaching a reporter gene to its promoter
Reporter genes
Transciptomics
mRNA is converted to cDNA and small pieces of each cDNA are extracted. These sequences are called tags and are joined together to form a strip (concatemer). The concatemer is then sequenced and processed by a computer to determine patterns of mRNA expression. No sequence knowledge required
SAGE
Transcriptomics
mRNA is converted to cDNA, tagged and fluorescently labelled. The cDNA is amplified using PCR, then attached to beads. Each bead can hold about 100,000 copies of single cDNA. Each cDNA is sequenced and identified. Small amounts of transcripts can be accurately identified. No sequence knowledge required
Massively Parallel Signature Sequencing
Transcriptomics
used to compare 2 different samples. Each sample is labelled with a different fluorescent dye and hybridized to the same chip, competing for binding to the same spot.
Two channel microarray
Transcriptomics
a single sample is labelled with a fluorescent dye and hybridized to a microarray chip containing probes
One channel microarray
Transcriptomics
in the expression array, probes are made from DNA sequences across the length of a chromosome, across particular regions of a genome, or the entire genome of an organism. cDNA is allow to hybridize to the probes and in this way it is possible to scan the genome for areas not previously known to contain genes and id chromosomal regions that are transcriptionally active
Tiling Array
Transcriptomics
Separating and retrieving proteins using liquid capillary action, cation exchange or reverse-phase
chromatography
proteomics
the process of peptide ionization followed by separation of ions based on mass and charge
Mass spectrometry
proteomics
Proteins chemically fragmented; fragments sequenced by removing amino acids from the N-terminal; proteins identified using existing databases
Edman Sequencing
proteomics
Labeling of proteins from 2 different sources with different isotopes of an atom. The samples are mixed and then Mass Spec is done to ID the proteins are present in the 2 samples and the quality of these proteins
ICAT
proteomics
Use of transcription factor domains to look for interactions between proteins to influence gene expression
Yeast 2-hybrid system
proteomics
breakdown of proteins using different kinds of enzymes
proteolysis
proteomics
the digestion of proteins using trypsin
Trypsinization
proteomics
insertion of known proteins into phage coats in order to ID interactions with unknown proteins
Phage display approach
proteomics
a measure of the quality of the alignment between the query sequence and the search results
Score Value
Attaching biological information, such as regulation, biochemical function and expression to genomic elements
Functional Annotation
The number of different alignments with scores that are equivalent to or better than alignment scores that are expected to occur by chance
E-value
Identifying genomic elements such as genes and other important sequences like coding regions and regulatory motifs
Structural Annotation
Obtaining biological information from unprocessed sequence data to create a labeled genome
genome annotation
a presentation of 2 compared sequences showing the regions of greatest statistical similarity
Alignment
A sequence to be used in a BLAST search that is made up of amino acids or nucleotides that can be either in FASTA format, Bare sequence or an identifier such as Accession number
Query Sequence
