A molecularly defined and spatially resolved cell atlas of the whole mouse brain
[ DOI: https://doi.org/10.35077/act-bag, BIL ID: act-bag ]
Dataset Citation:
Jung, Won, Zhang, Meng, Zhuang, Xiaowei. (2022). A molecularly defined and spatially resolved cell atlas of the whole mouse brain [Dataset/Microscopy]. Brain Image Library. https://doi.org/10.35077/act-bag
Abstract:
In this project, we used MERFISH to perform in situ gene expression profiling of individual cells in the entire mouse brain, determine the cell-type identity of these cells and map the spatial organization of the cell types. We performed MERFISH imaging on 1124 or 1147 genes in a total of 245 brain slices (217 coronal, 28 sagittal) from a total of 4 animals.
Contributors and Roles:
Jung, Won ( Researcher ),
Harvard University
;
Zhang, Meng ( Researcher ),
Harvard University
;
Zhuang, Xiaowei ( ProjectLeader ),
Harvard University
;
Zhuang, Xiaowei ( ContactPerson ),
Harvard University
Funding:
National Institutes of Health
( 5-U19-MH114830-05 ) A comprehensive whole-brain atlas of transcriptomic cell types in the mouse
Technical Information:
spatial transcriptomics (Modality)
/ MERFISH (Technique)
Instrument Metadata
Specimen Metadata
| localid | Mouse 1 |
| species | mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 57-63 |
| ageunit | Days |
| sex | Male |
| genotype | |
| organlocalid | |
| organname | |
| samplelocalid | Mouse 1 |
| atlas | |
| locations | |
| linkage | [] |
| localid | Mouse 2 |
| species | mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 57-63 |
| ageunit | Days |
| sex | Female |
| genotype | |
| organlocalid | |
| organname | |
| samplelocalid | Mouse 2 |
| atlas | |
| locations | |
| linkage | [] |
| localid | Mouse 3 |
| species | mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 57-63 |
| ageunit | Days |
| sex | Male |
| genotype | |
| organlocalid | |
| organname | |
| samplelocalid | Mouse 3 |
| atlas | |
| locations | |
| linkage | [] |
| localid | Mouse 4 |
| species | mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 57-63 |
| ageunit | Days |
| sex | Male |
| genotype | |
| organlocalid | |
| organname | |
| samplelocalid | Mouse 4 |
| atlas | |
| locations | |
| linkage | [] |
Image Metadata
| xaxis | left-to-right |
| obliquexdim1 | |
| obliquexdim2 | |
| obliquexdim3 | |
| yaxis | left-to-right |
| obliqueydim1 | |
| obliqueydim2 | |
| obliqueydim3 | |
| zaxis | left-to-right |
| obliquezdim1 | |
| obliquezdim2 | |
| obliquezdim3 | |
| landmarkname | |
| landmarkx | |
| landmarky | |
| landmarkz | |
| number | 1.0 |
| displaycolor | single color, gray scale |
| representation | |
| flurophore | |
| stepsizex | 0.109 |
| stepsizey | 0.109 |
| stepsizez | |
| stepsizet | |
| channels | |
| slices | |
| z | |
| xsize | |
| ysize | |
| zsize | |
| gbytes | |
| files | |
| dimensionorder |
License:
Data:
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/29/3c/293cc39ceea87f6d
Dataset download link:
https://download.brainimagelibrary.org/29/3c/293cc39ceea87f6d
Metadata download link:
https://api.brainimagelibrary.org/retrieve?bildid=act-bag
Manifest download link:
/bil/pscstaff/icaoberg/bil-inventory/datasets/json/act-bag.json