Spatial Transcriptomic Atlas of Adult Human Basal Ganglia: H22.30.001.CX.13
[ BIL ID: ace-irk-sag ]
Dataset Citation:
Allen Institute for Brain Science, Lein, Ed, Zeng, Hongkui, Close, Jennie, McMillen, Delissa, Martin, Naomi, Valera Cuevas, Nasmil, Olsen, Paul, Campos, Jazmin, VanNess, Marshall, Nagra, Josh. (2024). Spatial Transcriptomic Atlas of Adult Human Basal Ganglia: H22.30.001.CX.13 [Dataset/Microscopy]. Brain Image Library.
Abstract:
This dataset is part of a whole-brain atlas effort for human and non-human primate. The data collected for this submission represent spatial transcriptomics data from core human basal ganglia regions collected using a gene panel designed to identify all known cell types identified in the snRNAseq dataset from human generated from similar regions. When mapped based on these key genes to determine cell type locations, these data should provide a cluster-level cellular map of human basal ganglia.
Methods:
Our methods for the treatment and processing of human tissue with the MERSCOPE platform are described in this manuscript: https://doi.org/10.1038/s41593-024-01774-5
Contributors and Roles:
Allen Institute for Brain Science ( ResearchGroup )
;
Lein, Ed ( ProjectLeader ),
Allen Institute for Brain Science
;
Zeng, Hongkui ( ProjectLeader ),
Allen Institute for Brain Science
;
Close, Jennie ( ProjectLeader ),
Allen Institute for Brain Science
;
Waters, Jack ( Other ),
Allen Institute for Brain Science
;
McMillen, Delissa ( DataCollector ),
Allen Institute for Brain Science
;
Kruse, Lauren ( ProjectManager ),
Allen Institute for Brain Science
;
Martin, Naomi ( DataCollector ),
Allen Institute for Brain Science
;
Valera Cuevas, Nasmil ( DataCollector ),
Allen Institute for Brain Science
;
Olsen, Paul ( DataCollector ),
Allen Institute for Brain Science
;
Campos, Jazmin ( DataCollector ),
Allen Institute for Brain Science
;
VanNess, Marshall ( DataCollector ),
Allen Institute for Brain Science
;
Nagra, Josh ( DataCollector ),
Allen Institute for Brain Science
Funding:
National Institutes of Health
( 1-UM1-MH130981-01 ) Functionally guided adult whole brain cell atlas in human and NHP
Technical Information:
spatial transcriptomics (Modality)
/ MERFISH (Technique)
These represent raw data. Internally these data were segmented and mapped to a reference snRNAseq taxonomy to reveal cell type locations for analysis.
Instrument Metadata
Specimen Metadata
| localid | H22.30.001 |
| species | human |
| ncbitaxonomy | NCBI:txid9606 |
| age | 50.0 |
| ageunit | Years |
| sex | Female |
| genotype | |
| organlocalid | H22.30.001.CX |
| organname | Brain |
| samplelocalid | H22.30.001.CX.13 |
| atlas | AllenHuman34yrsWholeBrain |
| locations | Subcortex |
| linkage | [{'class': 'xref', 'type': 'cubie_tissue', 'relationship': 'slab', 'xid': 'SL-FXXJXQ303825'}, {'class': 'xref', 'type': 'cubie_tissue', 'relationship': 'donor', 'xid': 'DO-FXXJ3038'}] |
Image Metadata
| xaxis | left-to-right |
| obliquexdim1 | |
| obliquexdim2 | |
| obliquexdim3 | |
| yaxis | left-to-right |
| obliqueydim1 | |
| obliqueydim2 | |
| obliqueydim3 | |
| zaxis | anterior-to-posterior |
| obliquezdim1 | |
| obliquezdim2 | |
| obliquezdim3 | |
| landmarkname | |
| landmarkx | |
| landmarky | |
| landmarkz | |
| number | NA |
| displaycolor | NA |
| representation | |
| flurophore | DAPI |
| stepsizex | 0.108 |
| stepsizey | 0.108 |
| stepsizez | 1.5 |
| stepsizet | |
| channels | 3.0 |
| slices | 7.0 |
| z | 1.0 |
| xsize | |
| ysize | |
| zsize | |
| gbytes | |
| files | |
| dimensionorder |
Documented By:
License:
Data:
Data location on the Brain Image Library Analysis Ecosystem:
/bil/data/a6/b2/a6b296ab78fed4dd/H22.30.001.CX.13
Dataset download link:
https://download.brainimagelibrary.org/a6/b2/a6b296ab78fed4dd/H22.30.001.CX.13
Metadata download link:
https://api.brainimagelibrary.org/retrieve?bildid=ace-irk-sag
Manifest download link:
/bil/pscstaff/icaoberg/bil-inventory/datasets/json/ace-irk-sag.json