Male C57BL/6J D079-4L whole-hemisphere BARseq ,enucleated at birth
[ BIL ID: ace-dim-orb ]
Dataset Citation:
Chen, Xiaoyin, Rue, Mara, Zhang, Aixin. (2023). Male C57BL/6J D079-4L whole-hemisphere BARseq ,enucleated at birth [Dataset/Microscopy]. Brain Image Library.
Abstract:
This dataset is spatial transcriptomic data covering a whole mouse hemi-cortex from a an animal enucleatd at birth (P1), data from this brain are paired with sham littermate control DO79-3L. These data were used as part of the enucleated group in analysis. The 104 gene panel is optimized for distinguishing cortical cell types. We analalyzed changes in gene expression and transcriptomic cell types from a total of eight experimental brains (comparing four sham control and four enucleated littermates) to ask how gene expression and cell types change after bilateral enucleation.
Methods:
A full protocol describing this work is available at protocols.io: https://dx.doi.org/10.17504/protocols.io.81wgbp4j3vpk/v5
Contributors and Roles:
Chen, Xiaoyin ( ProjectLeader ),
Allen Institute for Brain Science
;
Rue, Mara ( ProjectMember ),
Allen Institute for Brain Science
;
Zhang, Aixin ( ProjectMember ),
Allen Institute for Brain Science
;
Fischer, Stephan ( ProjectMember ),
Institut Pasteur
Funding:
National Institutes of Health
( 1-U19-MH114830-01 ) A comprehensive whole-brain atlas of transcriptomic cell types in the mouse
Technical Information:
spatial transcriptomics (Modality)
/ other (Technique)
See https://doi.org/10.1101/2022.11.06.515381 for data processing details.
Instrument Metadata
| microscopetype | Confocal |
| microscopemanufacturerandmodel | NikonTi2E with Crest Xlight v3 |
| objectivename | Nikon |
| objectiveimmersion | Air |
| objectivena | 0.7 |
| objectivemagnification | 20x |
| detectortype | CMOS |
| detectormodel | Photometrics Kinetix |
| illuminationtypes | SolidState |
| illuminationwavelength | |
| detectionwavelength | |
| sampletemperature |
Specimen Metadata
| localid | D079-4L |
| species | Mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 28.0 |
| ageunit | Days |
| sex | Male |
| genotype | Strain_Name='C57BL/6J' |
| organlocalid | D079-4L |
| organname | Brain |
| samplelocalid | D079-4L |
| atlas | AllenMouseV3 |
| locations | Brain |
| linkage | [] |
Image Metadata
| xaxis | right-to-left |
| obliquexdim1 | |
| obliquexdim2 | |
| obliquexdim3 | |
| yaxis | inferior-to-superior |
| obliqueydim1 | |
| obliqueydim2 | |
| obliqueydim3 | |
| zaxis | anterior-to-posterior |
| obliquezdim1 | |
| obliquezdim2 | |
| obliquezdim3 | |
| landmarkname | |
| landmarkx | |
| landmarky | |
| landmarkz | |
| number | 1,2,3,4 |
| displaycolor | (Cyan,Yellow,Magenta,Gray) |
| representation | (G,T,A,C) |
| flurophore | (tdTomato,EGFP) |
| stepsizex | 0.32um |
| stepsizey | 0.32um |
| stepsizez | 1.5um |
| stepsizet | |
| channels | 4.0 |
| slices | 21.0 |
| z | 1.0 |
| xsize | |
| ysize | |
| zsize | |
| gbytes | |
| files | |
| dimensionorder |
Cited By:
License:
Data:
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/23/3e/233eb9bd2df10f2e/20230328_VisReorg_D079_4L
Dataset download link:
https://download.brainimagelibrary.org/23/3e/233eb9bd2df10f2e/20230328_VisReorg_D079_4L
Metadata download link:
https://api.brainimagelibrary.org/retrieve?bildid=ace-dim-orb
Manifest download link:
/bil/pscstaff/icaoberg/bil-inventory/datasets/json/ace-dim-orb.json