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1.
Figure 3

Figure 3. Representative examples of RNA ISH data that show gene expression patterns restricted to specific anatomical structures.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

(A) 0610009A07Rik is expressed in the thyroid; (B) 9030227G01Rik in the salivary glands; (C) Tle6 in the pancreas; (D) E130119H09Rik in the eye; (E) 6330406I15Rik in the cerebellum; and (F) Gpr151 in the thalamus. Insets are higher magnification views of expression shown in main panels and show in greater detail the sites of expression. crb, cerebellum; pan, pancreas; sgl, salivary glands; thl, thalamus; thy, thyroid.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.
2.
Figure 2

Figure 2. Snapshot view of the Web-based transcriptome atlas.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

(A) Keyword search results showing a table format including a thumbnail view of an image, and visualizing each embryonic section and associated anatomical annotation, color-coded according to expression strength. (B) Clicking on a particular image allows viewing the annotation associated with the particular image (left panel). Top tabs give additional details and links to other gene expression Web sites and genomic resources. (C) Zoom viewer. The image viewer provides full resolution images with standard zoom and pan capability. In addition, the viewed section can be selected using the 3-D embryo view. The left-hand panel shows the annotation in the context of the anatomy ontology, and the tabs provide additional detail and links to other gene expression and genomic resources.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.
3.
Figure 1

Figure 1. Representative examples of RNA ISH data of E14.5 embryos.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

The expression categories defined by the annotation summary are illustrated by the following examples. (1) Expression not detected: Rassf1 messenger RNA is not detected at this stage. (2) Homogeneous (non-regional) signal: Wdr68 shows hybridization signal in all tissues and structures. (3) Regionally expressed genes: Crmp1, Mir124, Titf1, and 1300010A20Rik. Crmp1 signal is evident in the brain, the V trigeminal ganglion, the spinal cord, and the neural retina. miR124 is restricted to the nervous system. Titf1 expression is detected in the diencephalon, hypothalamus, telencephalon, thyroid, and lung. 1300010A20Rik is an example of a tissue-specific gene with expression limited to the liver. Complete sets of images for 19,411 genes are available at http://www.eurexpress.org.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.
4.
Figure 4

Figure 4. Hierarchical clustering of regionally expressed genes.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

(A) Graphical representation of clusters (listed on the right) with more than eight genes in terms of expression occupancy. The occupancy is calculated as the number of genes in each cluster that are expressed in the anatomical structures (listed at the top) divided by the number of genes in that cluster (normalization). The matrix of occupancy values for each tissue group clusters with tissue distribution. More information on clustering can be found at http://www.eurexpress.org/ee/project/publication/PlosBiol2010.html. (B) Cluster 83, with a Pearson coefficient of 0.73, is composed of eight different genes showing expression in epithelia (oral and nasal cavities, respiratory tract, and middle and internal auditory cavities), choroid plexus, and middle-gut mucosa. (C) Genes in Cluster 83 are also synexpressed in adult tissues. Publicly available microarray data (http://symatlas.gnf.org) were clustered using the MeV program (http://www.tm4.org/mev.html). The figure shows synexpression in intestine, stomach, lacrimal gland, salivary gland, uterus, prostate, mammary gland, placenta, and bladder. Note that some tissues listed on the top of the diagram are duplicated because they represent two independent datasets. Gene symbols are on the right.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.
5.
Figure 5

Figure 5. Expression sites of Wnt signaling components in the E14.5 mouse kidney.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

(A) The matrix shows the level of expression of all 58 regionally expressed genes in ten different renal structures that are defined in (B). Colors represent expression strength: strong (red), moderate (light red), weak (pink), and not detected (white). The Wnt signaling components are grouped into seven blocks (ligands, receptors, extracellular inhibitors, canonical signaling, Ca2+ signaling, PCP signaling, and GO Wnt receptor signaling pathway). (B) The scheme in the center illustrates the ten main anatomical structures characterizing the developing kidney. The image gallery composed of low- and high-power (inset) images reveals that each of the ten structures characteristically expresses a particular Wnt component. 1: Wnt7b; 2: Wnt11; 3: Dkk1; 4: Sfrp2; 5: Lrp6; 6: Slc9a3r1; 7: Tle4; 8: Tcf4; 9: Wnt5a; 10: Rspo3. (C) Wnt signaling components involved in the mesenchyme-to-epithelium transition. Wnt9b is expressed in the ureteric bud (white arrowhead) and acts upstream of WNT4, which is expressed in condensing mesenchyme (black arrowhead). The Wnt receptors FZD3 (black arrowhead) and FZD4 (black arrowhead) are expressed in a way that allows them to function as candidate transducers for WNT9B/WNT4 signaling and could possibly underlie a shift from canonical to noncanonical signaling.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.
6.
Figure 7

Figure 7. Combinatorial analysis of several transcription factors' patterns in the hypothalamus reveals a new model of mammalian hypothalamic organization.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

(A) Foxa1 expression pattern in the basal plate of rhombencephalic, mesencephalic, diencephalic, and caudal hypothalamic neuroepithelium. This pattern is representative of other transcription factors such as Lmx1a, Lmx1b, Barhl1, Dbx1, Pax7, Olig2, Rarb, Dfp3, Lhx1, Lhx5, Irx1, and Irx3, expressed in the prosencephalic basal plate, including hypothalamus, where they were exclusively localized in the caudal regions: mammillar (MM) and/or retromammillar (RM) areas. (B and C) Lhx2 and Dlx1 expression patterns are representative of transcription factors expressed in alar prosencephalic derivatives (telencephalon, prethalamus, and thalamus) showing expression in TM and AH areas (currently described as basal plate hypothalamic domains), as well as in alar hypothalamic regions such as the suprachiasmatic (SCH), paraventricular (PV), and supraopto-paraventricular (SPV) areas. These patterns are representative of other genes expressed in alar derivatives including the TM and AH regions: Lhx6, Lhx9, Dlx1, Dlx2, Dlx5, Unc4, Cited, Rorb, Arx, Foxa2, and Otx2. (D) Photoshop composition to illustrate the alar expression patterns of Lhx2 and Dlx1 (green) and the Foxa1 basal expression (red). (E) Schematic representation of the analyzed patterns suggesting that the mammillar and retromammillar areas show basal plate molecular characteristics, while the TM and AH regions showed alar plate molecular characteristics. (F and G) Representation of the new revised topologic model that incorporates the TM and AH regions into the alar plate (F), compared to the currently accepted prosomeric model (G).The merged color composites are the product of alignment, superposition of sections, and editing using a computer program. A detailed description of the methods used to obtain such figures is included in Text S1. A, amygdale; ac, anterior commissure; Bst, bed nucleus of stria terminalis; Cx, cortex; FF, forel fields; P1Tg, pretectal tegmentum; P2Tg, thalamic tegmentum; PH, posterior hypothalamic area; POA, preoptic area; PT, pretectum; PTh, prethalamus; PV, paraventricular; SCH, suprachiasmatic; Se, septum; SPV, supraopto-paraventricular; ST/Pa, striatum/pallidum; Th, thalamus.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.
7.
Figure 6

Figure 6. High-resolution molecular regionalization in the central nervous system.. From: A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo.

(A) Genes expressed in cells at different radial levels in the anterior pole of the dorsal pallium (presumptive frontal cortex). 2610306H15Rik and Hist1h1d are localized at different apico-basal levels of the ventricular epithelium (VZ); Nhlh1 is expressed at the subventricular zone (SVZ) and intermedial zone (IZ); Nin and Rorb are expressed in cells localized at different radial levels of the mantle layer (ML). Each transcript is depicted with a different color to show how the expression of each gene in pallial cells is complementary to others, with some degree of overlap. MZ, marginal zone. (B) Picture of a mid-sagittal section of the brain from a section series of a Eurexpress assay processed with Cresyl violet. The inserts show the area where the corresponding regions (arrows) have been localized. It is important to note the homogeneity of cellular patterns in the mantle layer of the thalamus and spinal cord, as opposed to the complex molecular patterns observed in (C) and (D). (C) Examples of three genes with a graded expression in the thalamic mantle layer (Th). BC055811 shows strong expression in the caudal pole of the thalamus (close to the retroflexus tract [rf]), becoming weaker towards the anterior pole; Pde10a expression is complementary to that of BC055811, with a strong signal at the anterior pole of the thalamus, showing a sharp edge of its expression domain at the limit with the prethalamus (PTh). The expression of this gene becomes progressively weaker towards the caudal pole. Btbd3 transcripts have a dorso-ventral decreasing gradient, strong at the dorsal thalamus and progressively weaker towards the ventral thalamus. The ventral pole of the thalamic mantle layer is depicted by the expression of Calb1. The merged picture, using a color for each gene (right panel), shows how molecular regionalization allows detection of differences in cell identities in the four areas of thalamic mantle layer: dorsal (DTh), anterior (ATh), ventral (VTh), and posterior (PTh) thalamus. COM, commissural nuclei of pretectum; EPTh, eminentia thalami; ET, epithalamus; MP, medial pallium; PC, precommisural nuclei of pretectum; PThTg, prehalamic tegmentum; PTTg, pretectal tegmentum; TTg, thalamic tegmentum; ZI, zona incerta. (D) Sagittal section of the spinal cord, showing an overlay picture where the expression patterns of four genes have been combined. The picture summarizes the localization of region-specific molecular codes in spinal cord cells. These molecular codes correspond to different structural levels of the developing spinal cord: Adcyap1 is expressed in the gelatinous substance (SG, Rexed's layer 2) and motoneurons (MN); Nhlh1 is expressed in the spinal cord in the central nucleus of the dorsal horn (NP, Rexed's layers 3 and 4); Lrrtm1 is located in the spinal reticular nucleus (Rt, Rexed's layers 5 and 6); and Zdhhc2 is located in visceral motoneurons (vMN). Note that the expression patterns reported above, with the exception of Rorb and Calb, are novel. The merged color composites are the product of alignment, superposition of sections, and editing using a computer program. A detailed description of the methods used to obtain such figures is included in Text S1.

Graciana Diez-Roux, et al. PLoS Biol. 2011 January;9(1):e1000582.

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