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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.
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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
QuickTime™ and aTIFF (LZW) decompressor
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TIFF (LZW) decompressorare needed to see this picture.
QuickTime™ and aTIFF (LZW) decompressor
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QuickTime™ and aTIFF (LZW) decompressor
are needed to see this picture.