Welcome to SpatialBrain


A platform to view integrated data from the Wade-Martins Laboratory of Molecular Neurodegeneration.


Results and data from:

Kilfeather P, Khoo JH, Wade-Martins R. Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease. Cell Rep. 2024 Mar 26;43(3):113784. doi: 10.1016/j.celrep.2024.113784. Epub 2024 Feb 21. PMID: 38386560.


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




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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 cells

FDR-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

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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

Select a gene to view its splicing profile