Female C57BL/6J D076-1L whole-hemisphere BARseq

ace-dim-owl Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)

Cite this dataset

Chen, Xiaoyin, Rue, Mara, Zhang, Aixin. (2023). Female C57BL/6J D076-1L whole-hemisphere BARseq [Dataset/Microscopy]. Brain Image Library.

Abstract

This dataset is spatial transcriptomic data covering a whole mouse hemi-cortex from a sham littermate control for DO76-4L. These data were used as part of the control 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/v7

Contributors

Chen, Xiaoyin ORCID Allen Institute for Brain Science ProjectLeader
Rue, Mara ORCID Allen Institute for Brain Science ProjectMember
Zhang, Aixin ORCID Allen Institute for Brain Science ProjectMember
Fischer, Stephan ORCID Institut Pasteur ProjectMember

Funding

National Institutes of Health 1-U19-MH114830-01 A comprehensive whole-brain atlas of transcriptomic cell types in the mouse

Technical Information

Modality

spatial transcriptomics

Technique

other

Details

See https://doi.org/10.1101/2022.11.06.515381 for data processing details.

Instrument

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

localid	D076-1L
species	Mouse
ncbitaxonomy	NCBI:txid10090
age	28.0
ageunit	Days
sex	Female
genotype	Strain_Name='C57BL/6J'
organlocalid	D076-1L
organname	Brain
samplelocalid	D076-1L
atlas	AllenMouseV3
locations	Brain
linkage	[]

Image

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

Related Works

Cited by

Chen, X., Fischer, S., Zhang, A., Gillis, J., & Zador, A. (2022). Modular cell type organization of cortical areas revealed by in situ sequencing. BioRxiv, 2022-11. DOI: https://doi.org/10.1101/2022.11.06.515380

Data

Analysis Ecosystem path

/bil/data/23/3e/233eb9bd2df10f2e/20230402_VisReorg_D076_1L

Download

https://download.brainimagelibrary.org/23/3e/233eb9bd2df10f2e/20230402_VisReorg_D076_1L

Metadata

https://api.brainimagelibrary.org/retrieve?bildid=ace-dim-owl