PLANNING::::::

February 7th: Everyone presents techniques
Discussion: Suzy
Caitlin & Emily do Who-s-Who

February 14th:
Discussion: Caitlin & Emily
Who-s-Who: Josh & Pia
Food: Suzy

February 21st:
Discussion: JOSH & PIA
Who-s-Who: Patrick & Abe
Food: Caitlin & Emily

February 28th:
Discussion: GUEST STAR CHRIS GREGG !

March 7th:
Discussion: PATRICK S. & Abe
Who-s-Who: Rhea & Patrick W.
Food: Josh & Pia

March 14th:
Discussion: RHEA & PATRICK W.
Who-s-Who: Hannah & Rebecca
Food: Patrik S & Abe

March 21st: SPRING BEAK

March 28th:
Discussion: HANNAH & RYAN
Who-s-Who:Michaela & Rebecca
Food: Rhea & Patrick

April 4th:
Discussion: MICHAELA & KATE
Who-s-Who: Erik & Rebecca
Food: Hannah & Ryan

April 11th:
Discussion:ERIK & Rebecca
Who-s-Who: Chrissy & Gus
Food: Michaela & Kate

April 18th:
Discussion: CHRISSY & GUS
Who-s-Who: Amber
Food: Erik & Rebecca

April 25th:
Discussion: AMBER
Who-s-Who: Suzy
Food: Chrissy & Gus

May 2nd:
Discussion: EVERYONE REVIEW PAPERS
Who-s-Who:
Food:

 

 

STUDENT PRESENTATIONS ON GENOMIC TECHNIQUES NEXT WEEK

Given rapid advances in genomic techniques we are now able to assay, at the whole genome level, gene expression level, genomic content and epigenetic state for a broad range of organisms not previously amenable to genetic/genomic techniques.

Student groups will present (in 5- 10 minutes) the basic methods for various genomic techniques that are likely to surface throughout the semester. When possible, students should discuss they type of inference that can be drawn from data generated by each technique. These presentations are not intended to give a comprehensive explanation, simply a rough understanding so that students are sufficiently prepared to select research papers for further discussion. Each week, the methods used for that specific research paper will be presented in more detail by the student discussion leaders.

Microarray (gene expression) = A miroarray is a collection of microscopic DNA spot, often representing known genes, attached to a solid surface. By hybridizing a cDNA sample (reverse transcribed from isolated mRNA)to the array it is possible to quantify the level of expression for each gene on the array.

CGH(structural variation) = Comparative Genomic Hybridization uses a microarray but the labeled sample is genomic DNA. Therefore, the hybridization intensity reflects the copy number for genomic elements.

RNA-seq = Transciptome description by sequencing of reverse transcribed RNA. This technique can be used to identify transcripts or to compare expression level.

microRNA analysis= microRNA's are known to regulate gene expression. Because these RNA molecules are so short, special techniques are developed to capture them for sequencing and expression level analysis.

GWAS = genome-wide association study is an method by which to examine the common genetic variants (using molecular markers, most often SNP's) in different individuals to see if any variant is statisitcally associated with a trait.

ChIP-seq is used to analyze protein interactions (such as transcription factor binding) with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with DNA sequencing to identify the binding sites of DNA-associated with particular proteins.

DNA-methylation(sequencing) (a.k.a. bisulfite sequencing) = When DNA is treated with bisulfite any C that is methylated is converted to a T. Therefore, comparison of sequence for treated and untreated DNA will reveal the methylation state.

QTL = Quantitative Trait Locus analysis is a statistical method that links two types of information—phenotypic data (trait measurements) and genotypic data ( molecular markers such as SNP's or AFLP's)—in an attempt to explain the genetic basis of variation in complex traits

Proteomics is the large-scale study of protein structure and function. This field relies on a range of techniques often including mass-spec.