1. Web site for step-by-step Instructions

2. Web site for step-by-step Instructions
SPSS Instructions (.pdf)
SPSS_QTL Data_Template

3. Example data only—yours will be different.

4. Not yer data!
Variables Controlled by Regression

5. Example data only—yours will be different.

6. Web site for step-by-step Instructions
Using GeneNetwork_QTL
SPSS_QTL Data_Template

13. Web site for step-by-step Instructions
BXD_geno Markers032609

15. Defining a Peak and looking for SNPs
Peak is defined by a drop of 4.6 in the LRS from maximum
This is about 1 log unit
Pay particular attention to SNPs in our peak or region of interest

16. Clickable track to corresponding display in UCSC Genome Browser.
Each Small colored box represents a known gene
Likelihood ratio statistic
SNP Density
Peak Megabases

17. Web site for step-by-step Instructions
Using UCSC Genome Browser

18. Clickable track to corresponding display in UCSC Genome Browser.

19. Clickable genes!

20. For Gabarapl1, Dr.G’s gene.

21. Gene Chips DNA microarrays
Can use fluorescent cDNAs (mRNAs or RNAs) as probes.
Yield the pattern of gene expression across 2 different conditions.
Can examine many (thousands) of genes at once.
Does not give cell-by-cell resolution.

22. Gene Chip Animation

23. Web site for step-by-step Instructions
Using the Allen Brain Atlas

29. In situ hybridization
Finding out which cell(s) express a gene by probing for mRNA.
Probes to mRNA can be made of antisense DNA or RNA (sense is control).
Probes are labeled.
Probes hybridize with specific mRNAs being made in a cell.
Can only examine expression of one or two genes at a time.

30. Web site for step-by-step Instructions
Using Entrez Gene

36. Web site for step-by-step Instructions
Using PubMed