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Whole-cortex cell typing using BARseq: XC199

ace-cry-zip Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) Brain Initiative Cell Census Network (BICCN)

Cite this dataset

Chen, Xiaoyin. (2023). Whole-cortex cell typing using BARseq: XC199 [Dataset/Microscopy]. Brain Image Library.

Abstract

BARseq was used to interrogate cortex-wide cell type distribution over one mouse hemisphere. The dataset includes 40 hemi coronal sections with 200 um spacing and encompass the whole forebrain. The dataset reveals that cell type compositions distinguish cortical areas and further reveal a modular cell type organization that is consistent with modular connectivity across cortical areas.

Contributors

Funding

Technical Information
Modality
spatial transcriptomics
Technique
other

Instrument

microscopetype Spinning disk confocal
microscopemanufacturerandmodel Olympus IX81 with Crest Xlight v2
objectivename Olympus UCPLFLN20X
objectiveimmersion Air
objectivena 0.7
objectivemagnification 20x
detectortype sCMOS
detectormodel Photometrics Prime BSI
illuminationtypes Laser
illuminationwavelength
detectionwavelength
sampletemperature

Specimen

localid XC199
species mouse
ncbitaxonomy NCBI:txid10090
age 8.0
ageunit Weeks
sex Male
genotype
organlocalid
organname Brain
samplelocalid XC199L
atlas AllenMouseV3
locations Forebrain
linkage []

Image

xaxis superior-to-inferior
obliquexdim1
obliquexdim2
obliquexdim3
yaxis left-to-right
obliqueydim1
obliqueydim2
obliqueydim3
zaxis anterior-to-posterior
obliquezdim1
obliquezdim2
obliquezdim3
landmarkname
landmarkx
landmarky
landmarkz
number 1,2,3,4,5,6
displaycolor (0,1,1),(1,1,0),(1,0,1),(1,1,1),(0,0,0) for sequencing cycles;(0,1,1),(1,1,0),(1,0,1),(1,1,1),(0,0,1),(0,0,0) for hybridization cycles
representation (G,T,A,C, DIC) for sequencing cycles; (GFP,YFP,TxRed,Cy5,DAPI,DIC) for hybridization cycles
flurophore Illumina Miseq for sequencing; Alex488,Alex532,Alex594,Alex594,DAPI for hybiridization
stepsizex 0.34 um
stepsizey 0.34 um
stepsizez 1.5
stepsizet NA
channels 4.0
slices
z
xsize
ysize
zsize
gbytes
files
dimensionorder

Related Works

Additional references

Data

Analysis Ecosystem path
/bil/data/10/a1/10a11616e97eb617
Download
https://download.brainimagelibrary.org/10/a1/10a11616e97eb617
Metadata
https://api.brainimagelibrary.org/retrieve?bildid=ace-cry-zip