Welcome to SpatialBrain
A platform to view integrated data from the Wade-Martins Laboratory of Molecular Neurodegeneration.
Results and data from Kilfeather, Khoo, et al. 2023 (Manuscript in review):
Spatial Transcriptomic Analyses:
- Cell Type Markers
- SN/VTA Markers in Dopaminergic Neurons
- Cell Number Changes in Age
TRAP Analyses:
- Dopaminergic Markers
- Dopaminergic Ageing
- Alternative Splicing in Dopaminergic Neurons
Coming soon: Integration with iPS-derived dopaminergic transcriptomic datasets.
Spatial Markers
Select a cell type to view markers...
Select a gene to view its spatial expression
Definitions
LFC: The log2 fold-change in abundance between the cell type of interest and all other cellsFDR-P The P value, adjusted for multiple comparisons (B&H)
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SN/VTA Markers
Label cells above a threshold:
Click on a gene to view the spatial profile...
Definitions
LFC: The log2 fold-change in abundance between the substantia nigra and ventral tegmental area. Positive values indicate enrichment within the substantia nigra.FDR-P The P value, adjusted for multiple comparisons (B&H).
Data Download
Cell Type Numbers with Age
Testing for age-related changes in cell type abundance was performed using MASC in Stereo-Seq samples
Definitions
YOUNG: Mice aged 3-6 months
OLD: Mice aged 18-22 months
FDR-P: The P value, adjusted for multiple comparisons (B&H)
Estimate: Odds ratio for abundance change in aged brains. Positive values indicate an increase in abundance
Select a cell type to view its abundance across age groups
Dopaminergic TRAP Enrichment
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Definitions
LFC: The log2 fold-change in abundance in TRAP samples, compared to TOTAL
FDR-P: The P value, adjusted for multiple comparisons (B&H)
TOTAL: Bulk RNA from ventral midbrain
TRAP: RNA from DAT-TRAP
Select genes above to display information
Dopaminergic Ageing
Testing for age-related differential expression was performed using DESeq2 on gene-level counts derived from TRAP samples.
Definitions
TOTAL: Bulk RNA from ventral midbrain
TRAP: RNA from DAT-TRAP
YOUNG: Mice aged 3-6 months
OLD: Mice aged 18-22 months
LFC: The log2 fold-change in abundance in aged samples, compared to young
FDR-P: The P value, adjusted for multiple comparisons (B&H)
Select a gene to view its expression with age
Dopaminergic Splicing
Evidence for differential transcript usage was assessed using DRIMSeq on transcript-level counts derived from next-generation and long-read sequencing data of TRAP samples.
Definitions
TOTAL: Bulk RNA from ventral midbrain
TRAP: RNA from DAT-TRAP