Gene Pix In Situ and other pictures of gene hybridization at UCSC.

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Gene Pix In Situ and other pictures of gene hybridization at UCSC

Data Sets Paul Gray - ~1000 mouse transcription factor genes - whole embryo & sections. These are in the database now. Other potential sources: –German AxelDB frog in situs –Japanese NIBB frog in situs (have nice browser) –Genepaint.org - mouse stuff –EMAGE and Jackson Lab mouse images From development and other journals, copyright issues. –Nathaniel Heintz BAC expression constructs –Eddy Rubin lab mouse embryos –UCSF cell-localization stuff?

Types of images Whole animal vs. sectioned tissues, vs. single cell. Single vs. multiple probes within same image. Single image vs. image series (movies even). RNA, Antibody, Fusion protein. Mitotic cell 3 stains

Gene Pix Programs genePixLoad - loads SQL database from a well defined format involving a.ra file and a tab separated file. See genePixLoad.doc loadMahoney - converts Paul Gray (Mahoney center) spreadsheet and image directory into genePixLoad format Hg/lib/genePix.c - interface with SQL database. hgGenePix - cgi script to display images knownToGenePix - makes table in mm5 (or other) genome database to connect known genes to genePix Ids.

Gene Pix Database Just a single database for all assemblies of all organisms. A knownToGenePix table in the assembly database.

GenePix tables fileLocation - directory bodyPart - whole, brain etc. sliceType - transverse, sagital treatment - tech details contributor - who done it Journal - scientific journal submissionSet - info about a whole set of images from one author sectionSet - links together separate sections of same specimen. Gene - gene info geneSynonym Antibody - info on an antibody probeType - antibody, RNA, fusion protein Probe - links gene, primers, sequence Ab. probeColor - color probe is imageFile - file containing image Image - a single image. imageProbe links image and probe

Some Anatomy Required

Especially with slices

Edinburgh mouse atlas

Theiler Stages

Later Stages

NIBB Japanese Frog Site

Earlier Stages

GenePix software demo time