Whole-cortex cell typing using BARseq: XC199
[ BIL ID: ace-cry-zip ]
Dataset Citation:
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 and Roles:
Chen, Xiaoyin ( ContactPerson ),
Allen Institute for Brain Science
;
Zador, Anthony ( ProjectLeader ),
Cold Spring Harbor Laboratory
Funding:
National Institutes of Health
( 5-U19-MH114821-04 ) Tool and Technology Development Core
Technical Information:
spatial transcriptomics (Modality)
/ other (Technique)
Instrument Metadata
| 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 Metadata
| localid | XC199 |
| species | mouse |
| ncbitaxonomy | NCBI:txid10090 |
| age | 8.0 |
| ageunit | Weeks |
| sex | Male |
| genotype | |
| organlocalid | |
| organname | Brain |
| samplelocalid | XC199L |
| atlas | AllenMouseV3 |
| locations | Forebrain |
Image Metadata
| 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 |
Additional References:
License:
Data:
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/10/a1/10a11616e97eb617
Dataset download link:
https://download.brainimagelibrary.org/10/a1/10a11616e97eb617
Metadata download link:
https://api.brainimagelibrary.org/retrieve?bildid=ace-cry-zip
Manifest download link:
https://download.brainimagelibrary.org/inventory/c6f0c5ad-f6e4-53a9-b3b4-63103004478b.json