337-Isoe-BrainRegion

Project

Title
3D medaka brain visualized clonally related units in the pallium
Description
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, the authors 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). They found that pallial anatomical regions, including Dd2, are formed by mutually exclusive clonal units, and that each pallium compartment exhibits a distinct epigenetic landscape.
License
CC BY
Released at
2026-02-06
Updated at
Funding
NIBB Collaborative Research Program 16-522 (HT), KAKENHI 16H06987 (YI), KAKENHI 16KT0072 (HT), KAKENHI 20K20303 (YK), JP21K06013 (RN), Grant-in-Aid for Scientific Research on Innovative Areas JP21H00245 (RN), 18-513 (HT), 17-513 (HT)
# of image datasets
89

Papers

Papers
Paper information: Isoe Y, Nakamura R, Nonaka S, Kamei Y, Okuyama T, Yamamoto N, Takeuchi H, Takeda H. Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium. Elife. 2023 Jul 25;12:e85093. doi: 10.7554/eLife.85093.,
Pubmed ID: 37489039,
PMCID: PMC10368422,
DOI: https://doi.org/10.7554/eLife.85093,
URL: https://pubmed.ncbi.nlm.nih.gov/37489039/

Contacts

Contacts
Yasuko Isoe (Contact) , Department of Molecular and Cellular Biology , Harvard University
Ryohei Nakamura (Imaging Contributor) , Department of Biological Sciences , The University of Tokyo

Biosamples

Organisms
Strains
Cells
Cell lines

Anatomical information

UBERON
brain (UBERON_0000955)
Anatomical entities

Gene ontology

GO: Biological processes
GO: Cellular components
GO: Molecular functions

Molecular biological information

Gene names
Protein names
Genetic methods
Protein tags
Probes
Oligo Primer
Genotype

Reagent or Compound

Reagent or Compound
Concentration
Fold Dilution

Imaging information

Dimensions
298x262x484x3x1, 291x270x535x3x1, 869x660x325x3x1, 362x323x303x3x1, 238x179x673x3x1, 305x265x484x3x1, 321x362x411x3x1, 334x258x304x3x1, 237x181x597x3x1, 474x245x504x2x1, 662x485x187x3x1, 362x322x306x3x1, 369x297x263x3x1, 774x555x221x3x1, 306x245x484x3x1, 537x794x257x3x1, 834x597x190x3x1, 317x258x416x3x1, 240x181x404x3x1, 361x322x307x3x1, 329x269x309x3x1, 309x244x405x3x1, 333x278x501x3x1, 360x170x302x3x1, 483x245x128x3x1, 323x267x305x3x1, 182x203x303x3x1, 322x361x445x3x1, 267x339x489x3x1, 240x240x494x3x1, 517x823x254x3x1, 325x361x414x3x1, 361x322x490x3x1, 322x361x448x3x1, 567x871x168x3x1, 280x244x485x3x1, 1131x569x218x3x1, 480x246x532x3x1, 281x321x411x3x1, 327x247x309x3x1, 313x283x486x3x1, 312x234x497x3x1, 296x253x515x3x1, 523x874x189x3x1, 600x436x189x3x1, 360x325x307x3x1, 300x250x319x1x1, 345x247x312x3x1, 324x361x406x3x1, 360x275x538x3x1, 764x524x310x3x1, 756x514x311x3x1, 342x277x417x3x1, 362x324x493x3x1, 331x274x407x3x1, 277x198x307x3x1, 322x361x490x3x1, 274x302x402x3x1, 163x180x528x3x1, 231x213x526x3x1, 316x231x484x3x1, 538x837x183x3x1, 302x224x495x3x1, 323x3360x407x3x1, 286x255x618x3x1, 359x322x306x3x1, 499x361x414x3x1, 180x194x506x3x1, 559x796x188x3x1, 362x324x312x3x1, 313x235x488x3x1, 361x324x300x3x1, 328x360x405x3x1, 565x393x198x3x1, 360x271x559x3x1, 204x204x539x3x1, 844x549x184x3x1, 217x163x531x3x1, 321x363x486x3x1, 305x267x492x3x1, 354x323x519x2x1, 354x335x522x3x1, 328x361x304x3x1, 289x226x306x3x1, 311x288x493x3x1, 361x324x306x3x1, 726x499x217x3x1, 294x253x415x3x1,
X scales
NA, 5.1692 micrometer/pixel,
Y scales
NA, 5.1692 micrometer/pixel,
Z scales
NA, 2.6 micrometer/slice,
T scales
NA,
Channels
3 channel, 2 channel, 1 channel,

Biological Imaging Methods Ontology

Microscopy types
Detection methods
Visualization methods
Illumination methods
Sources of contrast
Contrast enhancing methods
Resolution enhancing methods
Imaged parameters
Sample preparation methods

Instruments

Datasets

Dataset name
Organism
Gene / Protein
Dimensions
File size
SSBD:OMERO
Download
362x324x493x3x1
347MB
322x361x445x3x1
155MB
286x255x618x3x1
135MB
291x270x535x3x1
126MB
231x213x526x3x1
77.7MB
204x204x539x3x1
67.4MB
483x245x128x3x1
45.4MB
499x361x414x3x1
224MB
180x194x506x3x1
106MB
240x181x404x3x1
52.7MB
163x180x528x3x1
46.5MB
474x245x504x2x1
176MB
354x323x519x2x1
178MB
322x361x448x3x1
156MB
240x240x494x3x1
85.4MB
217x163x531x3x1
56.4MB
480x246x532x3x1
189MB
360x275x538x3x1
160MB
360x271x559x3x1
164MB
362x324x312x3x1
110MB
361x324x306x3x1
107MB
277x198x307x3x1
50.6MB
360x170x302x3x1
106MB
360x170x302x3x1
55.4MB
362x322x306x3x1
106MB
359x322x306x3x1
106MB
289x226x306x3x1
60MB
345x247x312x3x1
79.8MB
329x269x309x3x1
82.1MB
361x324x300x3x1
105MB
361x322x307x3x1
107MB
328x361x304x3x1
216MB
362x323x303x3x1
106MB
360x325x307x3x1
108MB
334x258x304x3x1
78.6MB
327x247x309x3x1
74.9MB
328x360x405x3x1
144MB
324x361x406x3x1
143MB
325x361x414x3x1
146MB
321x362x411x3x1
143MB
323x3360x407x3x1
142MB
317x258x416x3x1
102MB
342x277x417x3x1
119MB
309x244x405x3x1
91.7MB
281x321x411x3x1
111MB
331x274x407x3x1
111MB
294x253x415x3x1
82.7MB
274x302x402x3x1
99.8MB
321x363x486x3x1
170MB
361x322x490x3x1
171MB
322x361x490x3x1
171MB
267x339x489x3x1
133MB
313x283x486x3x1
129MB
311x288x493x3x1
133MB
280x244x485x3x1
99.5MB
333x278x501x3x1
139MB
296x253x515x3x1
116MB
298x262x484x3x1
113MB
305x267x492x3x1
120MB
305x265x484x3x1
117MB
306x245x484x3x1
109MB
316x231x484x3x1
106MB
313x235x488x3x1
108MB
312x234x497x3x1
109MB
302x224x495x3x1
101MB
369x297x263x3x1
86.5MB
237x181x597x3x1
76.9MB
323x267x305x3x1
78.9MB
238x179x673x3x1
86.1MB
182x203x303x3x1
33.6MB
869x660x325x3x1
559MB
565x393x198x3x1
132MB
662x485x187x3x1
180MB
844x549x184x3x1
256MB
538x837x183x3x1
247MB
567x871x168x3x1
249MB
559x796x188x3x1
251MB
523x874x189x3x1
260MB
537x794x257x3x1
329MB
517x823x254x3x1
324MB
764x524x310x3x1
372MB
756x514x311x3x1
363MB
774x555x221x3x1
285MB
834x597x190x3x1
284MB
600x436x189x3x1
148MB
1131x569x218x3x1
421MB
726x499x217x3x1
236MB