Lecture 13: Introduction to Omics Flashcards
What are -omics?
The branch of molecular sciences concerned with studying the entire complement of some entity or process.
How does Streptococcus Pneumoniae become pathogenic?
The Competence Stimulating Peptide (CSP) activates ComD, which activate the ComE TF. This turns on the ComAB protein (which makes CSP). A positive feedback loop.
Usually, when density of S. Pneumoniae is low, this activity is low.
When density increases, this transcirption machinery becomes more active, making the bacteria pathogenic.
What are the goals in transcriptomics?
Measure expression level of all RNAs
This can be done at a tissue or single cell level
Explain microarray experiments in transcriptomics?
Microarrays: Wash fluorescently tagged mRNA sample of cDNA microarray glass slide. Complimentary nucleic acids will hybridize, and fluorescent signal can be measured.
Microarray experiments can also be performed as a 2-channel experiment, with 2 different fluorescent dyes. Here the color AND intensity is measured.
Affymetrix GeneChip: A more sophisticated and streamlined approach to microarray experiments.
Explain RNA-seq experiments in transcriptomics.
Short reads are mapped onto a reference genome to get counts of gene expression.
The density of exonic reads for a particular genome corresponds directly to the expression level of the gene.
Very low capability to detect low expressed genes.
What is proteomics and what are some of the techniques used?
Proteomics measures the concentration of a protein in tissue, allowing to estimate what protein activities are present in a tissue.
Experimental protocols include: 2D PAGE, Mass Spec, Protein Chips (ELISA).
Explain 2D PAGE experiments in proteomics.
Uses 2 dimensional separation (By isoelectric point and molecular weight).
Computer vision can then be used on the gel to identify proteins. These can then be characterized and identified by Mass Spec.
What is metabolomics and what are some of the techniques used?
A tissue sample is used of all cells together, and is smashed open to end up with small molecules in solution, NMR is then performed.
NMR is the main technique used in this field.
What are some canonical experiments used in -omics?
-Observational
-Time Series
-Cell Type analysis
-Spatial Clustering
What is the protocol for a time series experiment?
Take a cell/tissue sample
Apply environmental changes
Take n samples at given time points
Take measurements and perform analyses
What is the protocol for a cell type experiment?
Take one or more tissue samples
Extract similar cells by either morphology or tagging.
Measure each group of cells and analyze the differences.
What is the protocol for a spatial clustering experiment?
Take a tissue sample
Either perform in-situ hybridization to probes OR microdissection floowed by sequencing.
What is a distance matrix?
An all-against-all comparison, telling you how far two entities are.
All scores on the diagonal are 0
A distance measure can be used as is, but a similarity measure must be inverted in some way.
What are some different tree clustering algorithms?
- Distance based (UPGMA, Neighbor Joining trees)
- Maximum Parsimony Trees
- Maximum Likelihood Trees
What are some distance measures in Biology?
- Raw number of base/amino acid substitutions
- Estimating evolutionary distance by applying a model.
- Geometric distance between feature vectors
What are the properties of the UPGMA tree?
It has time complexity (n^2log(n))
Generates a unique tree, for a given distance matrix
Provides a rooted tree
Provides an ultrametric (all leaves equidistant from the root)
How does an Illumina HiSeq machine work?
The Illumina HiSeq uses sequencing by synthesis (SBS):
Fragment Library is loaded on a flow cell with immobilized oligos.
Each fragment is amplified into a cluster via bridge PCR.
Fluorescently labelled nucleotides are incorporated one base at a time.
A high-res camera detects the fluorescence signal for each cluster.
The machine cycles through multiple rounds, producing millions of short reads in parallel.
