The CD-Tagging Database offers the following information about tagged cell lines:

Gene | Protein Name
The Gene Symbols and Gene Names given here correspond to those designated as official in the National Center for Biotechnology Information Entrez Gene (LocusLink) Database. Entrez Gene derives these symbols from the standardized names established by the MGD Mouse Nomenclature Committee, the Human Gene Nomenclature Committee, and the International Rat Genetic Nomenclature Committee.

Observed Location

This provides a rough description of the location of GFP fluorescence in each of the tagged lines. These are very general categories, and different lines in the same category (e.g., nuclear) may show quite different distributions of fluorescence within the image.

Fluorescence Micrographs
The micrographs of CD-Tagged cell lines shown here were obtained by standard epifluorescence microscopy or by spinning disk confocal fluorescence microscopy, as indicated in the annotation accompanying the individual images.

NCBI GI#
The hyperlink in the CD-Tagging Database will direct the user to the GI record. This is the National Center for Biotechnology Information (NCBI) GenBank “GenInfo Identifier.” The GI number refers to the sequence record used in making CD-Tagging gene assignments.

LocusLink (Entrez Gene) Identifier
The hyperlink in the CD-Tagging Database will direct the user to the Entrez Gene entry for the gene. Entrez Gene (formerly LocusLink) is a curated NCBI database providing information about genetic loci including “official gene names, aliases, sequence accessions, phenotypes, EC numbers, MIM numbers, UniGene clusters, homology, map locations, and related websites.

Ensembl Identifier
The hyperlink in the CD-Tagging Database will direct the user to the Ensembl entry for the gene.

Sequence After GFP
The sequence shown begins with the first nucleotide 3' to the end of the guest exon in the tagged transcript sequence - i.e., it represents the 5' end of the host exon immediately downstream of the guest exon. The sequence was determined by amplifying tagged transcript sequences using nested RT-PCR and then sequencing from a primer inside the guest exon.

Reading Frame
This indicates the reading frame of the coding sequence following the guest exon (listed under “Sequence after GFP“). “0“ indicates that the first nucleotide of the sequence is also the first nucleotide of a codon. “1“ indicates that the second nucleotide of the sequence is the first nucleotide of a codon, and “2“ indicates that the third nucleotide is the first nucleotide of a codon.

The confocal image viewer can be used to display confocal image stacks as well as time-lapse movies produced by the CD-Tagging project. When a stack of images is loaded the z-projection of the series is initially displayed. The following describe the viewerÕs controls:

[Z-Proj] displays the z-projection of the image series. This image has been constructed using a projection algorithm that steps through the image stack in the z dimension and selects the brightest intensity at each x,y position.

[Image Slices] toggles from the z-projection to a view of individual image frames.

[<<] [>>] steps through the images in the series.

[Animate] toggles animation mode on and off. In animation mode the viewer will automatically step through the image series in the forward direction and then repeat. If frame rate problems occur (image flicker or incomplete image display) try decreasing the animation speed.

[Increase Size] [Decrease Size] increases or decreases the image size in increments of 2 in the x and y dimensions. The native resolution of the CD-Tagging images is 1280x1024.

[Increase Animation Speed] [Decrease Animation Speed] adjust the target frame-rate.

Contact Information
For comments or suggestions contact: jarvik@andrew.cmu.edu