Kate Milova MolGen retreat March 24, 2005 1 Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005.

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Kate Milova MolGen retreat March 24, Microarray experiments. Database and Analysis Tools. Kate Milova cDNA Microarray Facility March 24, 2005

Kate Milova MolGen retreat March 24, Outline.  Microarray platforms and services available at AECOM:  cDNA  Long Oligo  Afymetrix  Database ( cDNA & Long Oligo ) structure and content:  Printing information  Chip layout  Annotation  On-line Analysis Tools:  Normalization  Signal filtering  Comparison  Statistical packages and Analysis software  Summary

Kate Milova MolGen retreat March 24, Microarray Platforms at AECOM.

Kate Milova MolGen retreat March 24, How to choose a microarray platform.

Kate Milova MolGen retreat March 24, Before starting your microarray experiment.

Kate Milova MolGen retreat March 24, Microarray’s Experts.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Home page.  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa  Introduction  aaa

Kate Milova MolGen retreat March 24, cDNA Microarray Facility.Services. cDNA Microarray Facility. Services.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Arrays.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Publications.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Database.

Kate Milova MolGen retreat March 24, Database Search.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Database.

Kate Milova MolGen retreat March 24, Pipeline. LOWESS Normalization.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Pipeline. Filtering.

Kate Milova MolGen retreat March 24, cDNA Microarray Facility. Comparison.

Kate Milova MolGen retreat March 24, Annotation sources: NCBI. NCBI Entrez Gene UniGene Refseq & NT databases Blast Search Blast Software Unigene ID  Gene ID  GO ID Unigene ID  Accession Unigene ID  Blast against Unigene clusters

Kate Milova MolGen retreat March 24, Annotation sources: NCBI. NCBI UniGene Unigene ID  Accession Unigene ID  Blast against Unigene clusters  NCBI  UniGene  Unigene ID:  UniGene Id for cDNA arrays is obtained from the Unigene source file for each particular accession number of the clone.  NCBI  UniGene  Blast:  UniGene Id for Long Oligo arrays

Kate Milova MolGen retreat March 24, Annotation sources: NCBI. NCBI Entrez Gene Unigene ID  Gene ID  GO ID

Kate Milova MolGen retreat March 24, Annotation sources: NCBI. NCBI Refseq & NT databases Blast Search Blast Software

Kate Milova MolGen retreat March 24, Annotation sources: Gene Ontology. Gene Ontology Biological process Cellular compartment Molecular function

Kate Milova MolGen retreat March 24, cDNA Microarray Facility home page

Kate Milova MolGen retreat March 24, Summary  Global observables “phase transition”:  Quantity  Quality  Measurement  Systematization  Understanding.  Intriguing and exciting:  / vs. centrality is flat!  / vs. √s NN is consistent with freeze-out temperature and has two distinct regions.  Both dE T /dη and dN ch /dη at mid-rapidity scale with ln(s NN ) over all measured √s NN (factor of 100 for N ch ) landing SIS and RHIC on the same line!  What do √s 0 NN mean?  Centrality shape of dN ch /dη looks to be independent of √s NN at RHIC energies and flattens out at lower.  Something is going on at lower SPS energy!  LHC predictions are on the desk! Let’s see what data says!