SSBD:database

Summary of 337-Isoe-BrainRegion

SSBD:database
337-Isoe-BrainRegion
SSBD:database URL
https://ssbd.riken.jp/database/337-Isoe-BrainRegion/
Title
3D medaka brain visualized clonally related units in the pallium
Description
-
Relase date
2024-12-14
Updated date
-
License
CC BY
Kind
Image data based on Experiment
Number of Datasets
89 ( Image datasets: 89, Quantitative data datasets: 0 )
Size of Datasets
12.4 GB ( Image datasets: 12.4 GB, Quantitative data datasets: 0 bytes )
Organism(s)
Oryzias latipes
Strain(s)
HuC:loxp-DsRed-loxp-GFP, HSP-Cre
Datatype
-
Molecular Function (MF)
Biological Process (BP)
neuron migration, neurogenesis
Cellular Component (CC)
Biological Imaging Method
light-sheet microscopy
X scale
5.1692 micrometer/pixel, NA
Y scale
5.1692 micrometer/pixel, NA
Z scale
2.6 micrometer/slice, NA
T scale
-
Image Acquisition
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
-
Microscope model
-
Detector model
-
Objective model
-
Filter set
-
Related paper(s)

Yasuko Isoe, Ryohei Nakamura, Shigenori Nonaka, Yasuhiro Kamei, Teruhiro Okuyama, Naoyuki Yamamoto, Hideaki Takeuchi, Hiroyuki Takeda (2023) Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium., eLife, Volume 12

Published in 2023 Jul 25 (Electronic publication in July 25, 2023, midnight )

(Abstract) The dorsal telencephalon (i.e. the pallium) exhibits high anatomical diversity across vertebrate classes. The non-mammalian dorsal pallium accommodates various compartmentalized structures among species. The developmental, functional, and evolutional diversity of the dorsal pallium remain unillustrated. Here, we analyzed the structure and epigenetic landscapes of cell lineages in the telencephalon of medaka fish (Oryzias latipes) that possesses a clearly delineated dorsal pallium (Dd2). We found that pallial anatomical regions, including Dd2, are formed by mutually exclusive clonal units, and that each pallium compartment exhibits a distinct epigenetic landscape. In particular, Dd2 possesses a unique open chromatin pattern that preferentially targets synaptic genes. Indeed, Dd2 shows a high density of synapses. Finally, we identified several transcription factors as candidate regulators. Taken together, we suggest that cell lineages are the basic components for the functional regionalization in the pallial anatomical compartments and that their changes have been the driving force for evolutionary diversity.
Contact
Yasuko Isoe , Harvard University , Department of Molecular and Cellular Biology , Department of Molecular and Cellular Biology
Contributors
Ryohei Nakamura

Dataset List of 337-Isoe-BrainRegion

#
Dataset ID
Kind
Size
4D View
SSBD:OMERO
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# 11829
Datast ID Video1_ReferenceBrain
Dataset Kind Image data
Dataset Size 22.9 MB
4D view
SSBD:OMERO
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# 11830
Datast ID Video2_pallium
Dataset Kind Image data
Dataset Size 331.1 MB
4D view
SSBD:OMERO
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# 11831
Datast ID Video3_subpallium
Dataset Kind Image data
Dataset Size 177.3 MB
4D view
SSBD:OMERO
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# 11832
Datast ID Brain_1
Dataset Kind Image data
Dataset Size 148.0 MB
4D view
SSBD:OMERO
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# 11833
Datast ID Brain_2
Dataset Kind Image data
Dataset Size 129.0 MB
4D view
SSBD:OMERO
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# 11834
Datast ID Brain_3
Dataset Kind Image data
Dataset Size 120.3 MB
4D view
SSBD:OMERO
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# 11835
Datast ID Brain_5
Dataset Kind Image data
Dataset Size 74.1 MB
4D view
SSBD:OMERO
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# 11836
Datast ID Brain_6
Dataset Kind Image data
Dataset Size 64.2 MB
4D view
SSBD:OMERO
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# 11837
Datast ID Brain_7
Dataset Kind Image data
Dataset Size 43.3 MB
4D view
SSBD:OMERO
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# 11838
Datast ID Brain_8
Dataset Kind Image data
Dataset Size 213.4 MB
4D view
SSBD:OMERO
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# 11839
Datast ID Brain_9
Dataset Kind Image data
Dataset Size 101.3 MB
4D view
SSBD:OMERO
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# 11840
Datast ID Brain_10
Dataset Kind Image data
Dataset Size 50.3 MB
4D view
SSBD:OMERO
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# 11841
Datast ID Brain_11
Dataset Kind Image data
Dataset Size 44.4 MB
4D view
SSBD:OMERO
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# 11842
Datast ID Brain_12
Dataset Kind Image data
Dataset Size 167.5 MB
4D view
SSBD:OMERO
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# 11843
Datast ID Brain_13
Dataset Kind Image data
Dataset Size 169.8 MB
4D view
SSBD:OMERO
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# 11844
Datast ID Brain_14
Dataset Kind Image data
Dataset Size 149.0 MB
4D view
SSBD:OMERO
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# 11845
Datast ID Brain_15
Dataset Kind Image data
Dataset Size 81.5 MB
4D view
SSBD:OMERO
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# 11846
Datast ID Brain_16
Dataset Kind Image data
Dataset Size 53.8 MB
4D view
SSBD:OMERO
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# 11847
Datast ID Brain_17
Dataset Kind Image data
Dataset Size 179.9 MB
4D view
SSBD:OMERO
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# 11848
Datast ID Brain_19
Dataset Kind Image data
Dataset Size 152.4 MB
4D view
SSBD:OMERO
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# 11849
Datast ID Brain_20
Dataset Kind Image data
Dataset Size 156.1 MB
4D view
SSBD:OMERO
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# 11850
Datast ID Brain_21
Dataset Kind Image data
Dataset Size 104.7 MB
4D view
SSBD:OMERO
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# 11851
Datast ID Brain_22
Dataset Kind Image data
Dataset Size 102.4 MB
4D view
SSBD:OMERO
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# 11852
Datast ID Brain_23
Dataset Kind Image data
Dataset Size 48.2 MB
4D view
SSBD:OMERO
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# 11853
Datast ID Brain_24
Dataset Kind Image data
Dataset Size 101.2 MB
4D view
SSBD:OMERO
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# 11854
Datast ID Brain_25
Dataset Kind Image data
Dataset Size 52.9 MB
4D view
SSBD:OMERO
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# 11855
Datast ID Brain_26
Dataset Kind Image data
Dataset Size 101.4 MB
4D view
SSBD:OMERO
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# 11856
Datast ID Brain_27
Dataset Kind Image data
Dataset Size 101.2 MB
4D view
SSBD:OMERO
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# 11857
Datast ID Brain_28
Dataset Kind Image data
Dataset Size 57.2 MB
4D view
SSBD:OMERO
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# 11858
Datast ID Brain_29
Dataset Kind Image data
Dataset Size 76.1 MB
4D view
SSBD:OMERO
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# 11859
Datast ID Brain_30
Dataset Kind Image data
Dataset Size 78.3 MB
4D view
SSBD:OMERO
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# 11860
Datast ID Brain_31
Dataset Kind Image data
Dataset Size 100.4 MB
4D view
SSBD:OMERO
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# 11861
Datast ID Brain_32
Dataset Kind Image data
Dataset Size 102.1 MB
4D view
SSBD:OMERO
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# 11862
Datast ID Brain_33
Dataset Kind Image data
Dataset Size 206.1 MB
4D view
SSBD:OMERO
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# 11863
Datast ID Brain_34
Dataset Kind Image data
Dataset Size 101.4 MB
4D view
SSBD:OMERO
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# 11864
Datast ID Brain_35
Dataset Kind Image data
Dataset Size 102.8 MB
4D view
SSBD:OMERO
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# 11865
Datast ID Brain_36
Dataset Kind Image data
Dataset Size 75.0 MB
4D view
SSBD:OMERO
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# 11866
Datast ID Brain_37
Dataset Kind Image data
Dataset Size 71.4 MB
4D view
SSBD:OMERO
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# 11867
Datast ID Brain_38
Dataset Kind Image data
Dataset Size 136.9 MB
4D view
SSBD:OMERO
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# 11868
Datast ID Brain_39
Dataset Kind Image data
Dataset Size 135.9 MB
4D view
SSBD:OMERO
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# 11869
Datast ID Brain_40
Dataset Kind Image data
Dataset Size 139.0 MB
4D view
SSBD:OMERO
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# 11870
Datast ID Brain_41
Dataset Kind Image data
Dataset Size 136.7 MB
4D view
SSBD:OMERO
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# 11871
Datast ID Brain_43
Dataset Kind Image data
Dataset Size 135.4 MB
4D view
SSBD:OMERO
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# 11872
Datast ID Brain_44
Dataset Kind Image data
Dataset Size 97.4 MB
4D view
SSBD:OMERO
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# 11873
Datast ID Brain_45
Dataset Kind Image data
Dataset Size 113.1 MB
4D view
SSBD:OMERO
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# 11874
Datast ID Brain_46
Dataset Kind Image data
Dataset Size 87.4 MB
4D view
SSBD:OMERO
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# 11875
Datast ID Brain_47
Dataset Kind Image data
Dataset Size 106.1 MB
4D view
SSBD:OMERO
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# 11876
Datast ID Brain_48
Dataset Kind Image data
Dataset Size 105.7 MB
4D view
SSBD:OMERO
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# 11877
Datast ID Brain_49
Dataset Kind Image data
Dataset Size 88.4 MB
4D view
SSBD:OMERO
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# 11878
Datast ID Brain_50
Dataset Kind Image data
Dataset Size 95.2 MB
4D view
SSBD:OMERO
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# 11879
Datast ID Brain_52
Dataset Kind Image data
Dataset Size 162.1 MB
4D view
SSBD:OMERO
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# 11880
Datast ID Brain_53
Dataset Kind Image data
Dataset Size 163.0 MB
4D view
SSBD:OMERO
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# 11881
Datast ID Brain_54
Dataset Kind Image data
Dataset Size 163.0 MB
4D view
SSBD:OMERO
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# 11882
Datast ID Brain_55
Dataset Kind Image data
Dataset Size 126.7 MB
4D view
SSBD:OMERO
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# 11883
Datast ID Brain_56
Dataset Kind Image data
Dataset Size 123.2 MB
4D view
SSBD:OMERO
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# 11884
Datast ID Brain_57
Dataset Kind Image data
Dataset Size 126.4 MB
4D view
SSBD:OMERO
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# 11885
Datast ID Brain_58
Dataset Kind Image data
Dataset Size 94.9 MB
4D view
SSBD:OMERO
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# 11886
Datast ID Brain_59
Dataset Kind Image data
Dataset Size 132.8 MB
4D view
SSBD:OMERO
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# 11887
Datast ID Brain_60
Dataset Kind Image data
Dataset Size 110.6 MB
4D view
SSBD:OMERO
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# 11888
Datast ID Brain_61
Dataset Kind Image data
Dataset Size 108.2 MB
4D view
SSBD:OMERO
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# 11889
Datast ID Brain_62
Dataset Kind Image data
Dataset Size 114.7 MB
4D view
SSBD:OMERO
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# 11890
Datast ID Brain_63
Dataset Kind Image data
Dataset Size 112.0 MB
4D view
SSBD:OMERO
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# 11891
Datast ID Brain_64
Dataset Kind Image data
Dataset Size 103.9 MB
4D view
SSBD:OMERO
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# 11892
Datast ID Brain_65
Dataset Kind Image data
Dataset Size 101.1 MB
4D view
SSBD:OMERO
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# 11893
Datast ID Brain_66
Dataset Kind Image data
Dataset Size 102.8 MB
4D view
SSBD:OMERO
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# 11894
Datast ID Brain_67
Dataset Kind Image data
Dataset Size 103.9 MB
4D view
SSBD:OMERO
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# 11895
Datast ID Brain_69
Dataset Kind Image data
Dataset Size 95.9 MB
4D view
SSBD:OMERO
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# 11896
Datast ID Brain_70
Dataset Kind Image data
Dataset Size 82.5 MB
4D view
SSBD:OMERO
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# 11897
Datast ID Brain_71
Dataset Kind Image data
Dataset Size 73.3 MB
4D view
SSBD:OMERO
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# 11898
Datast ID Brain_72
Dataset Kind Image data
Dataset Size 75.3 MB
4D view
SSBD:OMERO
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# 11899
Datast ID Brain_73
Dataset Kind Image data
Dataset Size 82.1 MB
4D view
SSBD:OMERO
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# 11900
Datast ID Brain_74
Dataset Kind Image data
Dataset Size 32.1 MB
4D view
SSBD:OMERO
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# 11901
Datast ID Brain_75
Dataset Kind Image data
Dataset Size 533.4 MB
4D view
SSBD:OMERO
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# 11902
Datast ID Brain_76
Dataset Kind Image data
Dataset Size 125.9 MB
4D view
SSBD:OMERO
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# 11903
Datast ID Brain_77
Dataset Kind Image data
Dataset Size 171.9 MB
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SSBD:OMERO
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# 11904
Datast ID Brain_78
Dataset Kind Image data
Dataset Size 244.0 MB
4D view
SSBD:OMERO
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# 11905
Datast ID Brain_78_rotate
Dataset Kind Image data
Dataset Size 235.8 MB
4D view
SSBD:OMERO
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# 11906
Datast ID Brain_79
Dataset Kind Image data
Dataset Size 237.4 MB
4D view
SSBD:OMERO
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# 11907
Datast ID Brain_80
Dataset Kind Image data
Dataset Size 239.4 MB
4D view
SSBD:OMERO
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# 11908
Datast ID Brain_81
Dataset Kind Image data
Dataset Size 247.2 MB
4D view
SSBD:OMERO
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# 11909
Datast ID Brain_82_left
Dataset Kind Image data
Dataset Size 313.6 MB
4D view
SSBD:OMERO
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# 11910
Datast ID Brain_82_right
Dataset Kind Image data
Dataset Size 309.3 MB
4D view
SSBD:OMERO
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# 11911
Datast ID Brain_83_left
Dataset Kind Image data
Dataset Size 355.2 MB
4D view
SSBD:OMERO
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# 11912
Datast ID Brain_83_right
Dataset Kind Image data
Dataset Size 345.9 MB
4D view
SSBD:OMERO
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# 11913
Datast ID Brain_84
Dataset Kind Image data
Dataset Size 271.7 MB
4D view
SSBD:OMERO
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# 11914
Datast ID Brain_85_left
Dataset Kind Image data
Dataset Size 270.7 MB
4D view
SSBD:OMERO
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# 11915
Datast ID Brain_85_right
Dataset Kind Image data
Dataset Size 141.5 MB
4D view
SSBD:OMERO
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# 11916
Datast ID Brain_86_left
Dataset Kind Image data
Dataset Size 401.5 MB
4D view
SSBD:OMERO
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# 11917
Datast ID Brain_86_right
Dataset Kind Image data
Dataset Size 225.0 MB
4D view
SSBD:OMERO
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