The Journal of Neuroscience, April 14, 2004, ():
Defining a Molecular Atlas of the Hippocampus Using DNA Microarrays and High-Throughput In Situ Hybridization
J. Neurosci. Lein et al.
24: 3879
Supplemental data
Supplemental figures and tables
Files in this Data Supplement:
- Supplemental Fig. 1
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Supplemental Figure 1. Dissection of hippocampal subregions. Areas CA1, CA3, and the DG were isolated from one another as shown in A-F. The hippocampus (B, C, arrows) is clearly visible once the overlying neocortex is peeled back (B), and it can be removed as an intact structure (C). The boundaries of the DG can be seen in the dissected hippocampus (D, E, arrows), allowing the isolation of CA1 (E) and CA3 (F). Rostral is to the left in A-F. G-I, Coronal views of the hippocampus at three planes of section along the rostrocaudal axis in cresyl violet-stained cryostat sections. Dashed lines in G indicate approximate regions dissected. CA1, CA3, Pyramidal cells of Ammon's horn; Sub, subiculum; fi, fimbria; cp, choroid plexus.
- Supplemental Fig. 2
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Supplemental Figure 2. Genes enriched in the dentate gyrus. In situ hybridization for Dsp (A,E), Igfbp5 (B,F), P311 (C,G), Mcmd6 (D,H), Dgat2 (Q,U), Ptpro (R,V), Ehd1 (S,W), and calretinin (T,X) on coronal sections through the hippocampus at low magnification (A-D, Q-T) and high magnification (E-H, U-X). Bisbenzimide staining of the same sections is shown in I-L and Y-BB, and gene chip data for each gene are shown in M-P and CC-FF. Arrowheads in E-L and U-BB delimit the boundaries of CA1. Arrow in X denotes the hilus of the dentate gyrus. Scale bars, 1 mm.
- Supplemental Fig. 3
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Supplemental Figure 3. Genes enriched in regions CA1-CA3. In situ hybridization for Mrg1b (A,D), Siat8e (B,E), AA611744 (C,F), AA717225 (M,P), Sez6 (N,Q), and Lpl (O,R) on coronal sections through the hippocampus at low magnification (A-C, M-O) and high magnification (D-F, P-R). Bisbenzimide staining of the same sections is shown in G-I and S-U, and gene chip data for each gene are shown in J-L and V-X. Arrowheads in D-I and P-U delimit the boundaries of CA1. Scale bars, 1 mm.
- Supplemental Fig. 4
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Supplemental Figure 4. Genes enriched in CA3 or CA2/3. In situ hybridization for Bok (A,E), Prkcd (B,F), AA212774 (C,G), Socs2 (D,H), Spock1 (Q,U), Ly6e (R,V), Sgk (S,W), and Cadps (T,X) on coronal sections through the hippocampus at low magnification (A-D, Q-T) and high magnification (E-H, U-X). Bisbenzimide staining of the same sections is shown in I-L and Y-BB, and gene chip data for each gene are shown in M-P and CC-FF. Arrowheads delimit the boundaries of CA1 (E-L, U-BB) and the boundary between CA2 and CA3 (E-G, I-K). Scale bars, 1 mm.
- Supplemental Fig. 5
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Supplemental Figure 5. Genes enriched in the dentate gyrus and CA1. In situ hybridization for calbindin (A,E), Ngef (B,F), Btg1 (C,G), and Itpr1 (D,H) on coronal sections through the hippocampus at low magnification (A-D) and high magnification (E-H). Bisbenzimide staining of the same sections is shown in I-L, and gene chip data for each gene are shown in M-P. Arrowheads delimit the boundaries of CA1 (E-L). Scale bars, 1 mm.
- Supplemental Fig. 6
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Supplemental Figure 6. Genes enriched in CA1. A-F, In situ hybridization for Nov (A,D), Etv1 (B,E), and AA591428 (C,F) on coronal sections through the hippocampus at low magnification (A-C) and high magnification (D-F). Bisbenzimide staining of the same sections is shown in G-I, and gene chip data for each gene are shown in J-L. Arrowheads in D-I delimit the boundaries of CA1. Scale bars, 1 mm.
- Supplemental Fig. 7
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Supplemental Figure 7. Genes enriched in the dentate gyrus and CA2/3. A-H, In situ hybridization for Tgfb2 (A,E), Frzb (B,F), Golph2 (C,G), and Nmyc1 (D,H) at low magnification (A-D) and high magnification (E-H). Bisbenzimide staining of the same sections is shown in I-L, and gene chip data for each gene are shown in M-P. Arrowheads in E-L delimit the boundaries of CA1. Scale bars, 1 mm.
- Supplemental Fig. 8
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Supplemental Figure 8. Genes enriched in the dentate gyrus and CA2. A-H, In situ hybridization for Ntf3 (A,E), Tiam1 (B,F), AA087715 (C,G), and Pcp4 (D,H) on coronal sections through the hippocampus at low magnification (A--D) and high magnification (E-H). Bisbenzimide staining of the same sections is shown in I-L, and gene chip data for each gene are shown in M-P. Arrowheads in E-L delimit the boundaries of CA1 and CA2. Scale bars, 1 mm.
- Supplemental Fig. 9
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Supplemental Figure 9. Genes enriched in CA1 and CA3. A-H, In situ hybridization for Tyro3 (A,E), Man2a1 (B,F), Prss19 (C,G), and Man1a (D,H) on coronal sections through the hippocampus at low magnification (A-D) and high magnification (E-H). Bisbenzimide staining of the same sections is shown in I-L, and gene chip data for each gene are shown in M-P. Arrowheads in E-L delimit the boundaries of CA1 and CA2. Scale bars, 1 mm.
- Supplemental Fig. 10
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Supplemental Figure 10. Genes expressed in fimbrial oligodendrocytes and the choroid plexus. A-F, M-R, In situ hybridization for Mobp (A,D), Cldn11 (B,E), Enpp2 (C,F), Lbp (M,P), Msx1 (N,Q), and the Slc31a1 (O,R) on coronal sections through the hippocampus at low magnification (A-C, M-O) and high magnification (D-F, P-R). Bisbenzimide staining of the same sections is shown in G-I and S-U, and gene chip data for each gene are shown in J-L and V-X. Arrowheads in D-I mark the fimbria, and arrows in F, I, and P-U label the choroid plexus. Scale bars, 1 mm.
- Supplemental Fig. 11
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Supplemental Figure 11. Genes expressed in the subiculum. A-D, In situ hybridization for Fn1 (A), R74641 (B), Rbp4 (C), and Prss12 (D) on coronal sections through the caudal hippocampus. Bisbenzimide staining of the same sections is shown in E-H, and gene chip data for each gene are shown in I-L. Arrowheads in A-H mark the boundaries of the subiculum. CA1, Pyramidal cells of the CA1 region. Scale bar, 1 mm.
- Supplemental Fig. 12
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Supplemental Figure 12. Extremely restricted gene expression in the dentate gyrus. A, B, In situ hybridization for Dsp (A) and AA087715 (B) on parasagittal sections through the hippocampus. Expression is limited to dentate gyrus granule cells (and low levels in CA2 for AA087715) with the exception of light labeling of several brainstem nuclei in B. Scale bar, 1 mm.
- Supplemental Clone information
- Supplemental Table 1
