How to use this site

The “Human Chromosome 21 gene expression atlas” web site collects data derived from a systematic study on chromosome 21 genes. This study identifies the tissues where each chromosome 21 gene is turned on during development and in the adult. It is based on the expression analysis of all identifiable murine orthologues of human chromosome 21 genes by RNA in situ hybridization on whole-mounts (E9.5, E10.5 embryos) and tissue sections (E14.5 embryos), and by RT-PCR on adult tissue.

Under the Scientific Data section, you can access:

1. a Summary table containing all the expression data (see below);
2. Examples of gene expression in specific tissues, with images of expression of some genes in organs affected in Down Syndrome patients, i.e., “Pancreas”, “Gut”, “Limb”, “Heart”, “Thymus”, “Cerebellum”;
3. “Materials and Methods” with a description of the techniques used for these studies.

Summary Table

This table shows all the identified genes on chromosome 21 ordered by their position on human chromosome 21. The third column lists the Human gene accession number and the fourth column the accession number of the murine ortholog gene. Finally, the last column on the right summarizes the Status in the mouse. By clicking on “Status in mouse” a description of the color code will be found. To access the data for each gene you need to click on the gene name. This will take you to a gene card.

• The “Gene characteristics” button will link you to a public database (LocusLink or Genecard) collecting all the available information on this gene.
• The button “Probe” will open a table with 25 genes among which the gene of interest is listed. The table reports the information on the probe used for the expression studies.
• The “RT-PCR“ button opens a table of 25 genes among which the gene of interest is listed. This table reports the primers used for RT-PCR studies and the results obtained using RNA from adult murine tissues such as: brain, heart, kidney, thymus, liver, stomach, muscle, lung, testis, ovary, skin, eyes. RT-PCR data obtained from embryonic RNA  (E8.5, E9.5, E12.5, E19.5) is also shown. “+” was used to report expression in that tissue, no detectable expression is blank.
• By clicking on E9.5 or the small image you can open the image of an E9.5 embryo hybridized with the probe for the gene of interest. Similarly, by clicking on E10.5 or E14.5 you can access to bigger images of the embryos.
• Using the “WholeMountTable” button you will open a table with 25 genes among which the gene of interest is listed. This table summarizes the data obtained from whole mount in situ hybridization experiments using “+” when the gene was detected in a tissue and “++” for strong signal. The tissues listed in this table are: brain, spinal chord (SC), eyes, otocyst, dorsal root ganglia (DRG), branchial arches, heart, gut, kidney, limbs, skin.
• Using the “E14.5MountTable” button you will open a table with 5 genes among which the gene of interest is listed. This table summarizes the data obtained from in situ hybridization experiments on E14.5 embryonic sections. The code used is: (U) ubiquitous (R) regional (i) isolated +++ strong / ++ moderate / + weak signal. The tissues listed in this table are: forebrain, midbrain, hindbrain, cerebellum, spinal cord, cranial ganglia, dorsal root ganglia, parasympathetic ganglia, eye, nasal/olfactory epithelium, cochlea, skeleton (cartilage), lung, atrium, ventricle, arterial system, gut, bladder, kidney, testis, ovary, salivary, spleen, pancreas, adrenal, thyroid, thymus, liver, skin, whisker follicles, muscle, mesenchyme, tongue, limbs, tail.