Spatial Transcriptomics

10X Genomics Visium Spatial Gene Expression Profiling

10X Visium Technology

Experimental Design

Spatial transcriptomics using 10X Genomics Visium platform captures gene expression while preserving spatial context within brain tissue sections.

  • Platform: 10X Genomics Visium Spatial Gene Expression
  • Samples: 8 total (4 P15, 4 P30)
  • Comparisons: GAERS vs Wistar at P15 and P30
  • Analysis: Limma differential expression
  • Resolution: 55 μm spot size, ~10 cells per spot

Sample Groups

GAERS (Epilepsy Model):

  • GA1-P15, GA1-P30
  • GA2-P15, GA2-P30

Wistar (Control):

  • WH1-P15, WH1-P30
  • WH2-P15, WH2-P30
  • WH3-P15, WH3-P30

Sample Overview

Sample ID Group Timepoint Phenotype Description
GA1-P15 GAERS P15 Pre-seizure GAERS rat, postnatal day 15
GA1-P30 GAERS P30 Seizure-onset GAERS rat, postnatal day 30
GA2-P15 GAERS P15 Pre-seizure GAERS rat, postnatal day 15
GA2-P30 GAERS P30 Seizure-onset GAERS rat, postnatal day 30
WH1-P15 Wistar P15 Control Wistar control, postnatal day 15
WH1-P30 Wistar P30 Control Wistar control, postnatal day 30
WH2-P15 Wistar P15 Control Wistar control, postnatal day 15
WH2-P30 Wistar P30 Control Wistar control, postnatal day 30

Differential Expression Summary

P15: GAERS vs Wistar

1,079 Total DEGs
509 Upregulated
570 Downregulated

P30: GAERS vs Wistar

1,079 Total DEGs
565 Upregulated
514 Downregulated

P15 Comparison: GAERS vs Wistar

Pre-seizure developmental stage

Top Differentially Expressed Genes (P15)

P30 Comparison: GAERS vs Wistar

Seizure-onset stage

Top Differentially Expressed Genes (P30)

Spatial Context & Interpretation

Key Observations

  1. Temporal Progression: Both P15 and P30 show extensive transcriptional differences between GAERS and Wistar, with over 1,000 DEGs at each timepoint. This indicates early and persistent molecular dysregulation in the GAERS model.
  2. Balanced Regulation at P15: The P15 comparison shows relatively balanced up/down regulation (509 up, 570 down), suggesting complex developmental differences between GAERS and control.
  3. Shift at P30: By P30, the ratio shifts slightly toward upregulation (565 up, 514 down), potentially reflecting circuit maturation and seizure-associated changes.
  4. Spatial Resolution: The Visium platform preserves tissue architecture, enabling identification of region-specific gene expression patterns critical for understanding thalamocortical circuit dysfunction.

Spatial Advantages

Unlike bulk RNA-seq, spatial transcriptomics reveals:

  • Region-specific dysregulation in thalamus vs cortex
  • Cell type composition differences between GAERS and controls
  • Spatial organization of seizure-related gene expression
  • Anatomically-resolved molecular pathways

Go Beyond Web Visualizations

Explore spatial data interactively with 10X Genomics Loupe Browser

What Loupe Browser Adds

While our web visualizations provide quick insights, Loupe Browser unlocks the full power of spatial transcriptomics:

  • Interactive Tissue Maps: Overlay gene expression on H&E tissue images
  • Query Any Gene: Search and visualize 20,000+ genes on demand
  • Custom Regions: Select specific brain regions and compare expression
  • Spatial Clustering: Discover region-specific expression patterns
  • Differential Expression: Compare cortex vs thalamus, or custom selections
  • Publication Figures: Export high-resolution images

Available Datasets

P15 Pre-Seizure

Baseline spatial expression before seizure onset (ga2p15_2)

275 MB

P30 Seizure-Onset

Spatial expression at absence seizure onset (ga1p30_2)

328 MB

Hybrid Approach

Our website provides fast, pre-computed visualizations for quick data exploration. For in-depth spatial analysis, custom queries, and publication-quality figures, download the .cloupe files and use Loupe Browser's full suite of interactive tools.

Complete Loupe Browser Guide

Download, install, and explore spatial data interactively

Download GAERS Spatial Data (.cloupe files)

P15 Pre-Seizure (ga2p15_2)

File: GAERS_P15_PreSeizure.cloupe

Size: 275 MB

Contains:

  • ~5,000 spatial spots
  • 20,000+ genes
  • H&E tissue image
  • Spatial coordinates
Download P15 Data
File Verification

MD5: 75165a5804a3ccfffa72af6f1232de4f

Use to verify download integrity

P30 Seizure-Onset (ga1p30_2)

File: GAERS_P30_SeizureOnset.cloupe

Size: 328 MB

Contains:

  • ~5,000 spatial spots
  • 20,000+ genes
  • H&E tissue image
  • Spatial coordinates
Download P30 Data
File Verification

MD5: 011b9ca08f1b38f4e8bc3b9de6193f03

Use to verify download integrity

Installation & Setup

1. Download Loupe Browser

Get the free desktop application from 10X Genomics

10X Genomics Downloads

2. Install

Available for:

  • Windows 10/11
  • macOS 10.14+
  • Linux (Ubuntu, CentOS)

Requirements: 8GB RAM minimum, 16GB recommended

3. Load Data

  1. Launch Loupe Browser
  2. File → Open
  3. Select .cloupe file
  4. Start exploring!

Example Workflows for GAERS Data

Workflow 1: Visualize Seizure-Related Genes

  1. Open GAERS_P30_SeizureOnset.cloupe
  2. In Gene Expression panel, search for: Scn1a
  3. View spatial expression pattern on tissue section
  4. Compare cortex vs thalamus expression levels
  5. Add more genes: Cacna1g, Gabrb3
  6. Export high-resolution images for publication

Tip: Use the split-view feature to compare multiple genes side-by-side

Workflow 2: Compare Brain Regions (Cortex vs Thalamus)

  1. Open either P15 or P30 file
  2. In Tissue Viewer, use Lasso Tool to select cortex spots
  3. Right-click → "Create Cluster" → Name: "Cortex"
  4. Repeat for thalamus region
  5. Go to Differential Expression panel
  6. Select: Cortex vs Thalamus
  7. View top differentially expressed genes
  8. Export as CSV for further analysis

Tip: Use the histogram in Tissue Viewer to validate region selection

Workflow 3: Temporal Comparison (P15 vs P30)

  1. Open GAERS_P15_PreSeizure.cloupe
  2. Search for a gene of interest (e.g., Gad1)
  3. Take screenshot or export image
  4. Close and open GAERS_P30_SeizureOnset.cloupe
  5. Search for the same gene
  6. Compare spatial patterns between timepoints
  7. Note changes in expression levels and spatial distribution

Note: Loupe Browser cannot overlay multiple samples simultaneously. Use side-by-side comparison of exported images.

Troubleshooting

Loupe Browser won't open .cloupe file

Possible solutions:

  • Ensure you have the latest Loupe Browser version (check 10X website)
  • Verify file downloaded completely (check file size: P15=275MB, P30=328MB)
  • Verify file integrity using MD5 checksum
  • Try re-downloading the file
  • Check disk space (need ~1GB free for temporary files)
Application is slow or crashing

Possible solutions:

  • Close other memory-intensive applications
  • Ensure at least 8GB RAM available (16GB recommended)
  • Reduce number of genes displayed simultaneously
  • Disable real-time rendering in preferences if available
  • Restart Loupe Browser
Can't find a specific gene

Possible solutions:

  • Gene symbols are case-sensitive - try different capitalizations
  • Try alternative gene names (e.g., "Gad1" vs "GAD1" vs "gad1")
  • Use Ensembl ID instead of symbol
  • Check our Gene Search page to verify gene names in dataset
  • Gene might be filtered out due to low expression (check filtering settings)
How to verify file integrity (MD5 checksum)

On macOS/Linux:

md5sum GAERS_P15_PreSeizure.cloupe
md5sum GAERS_P30_SeizureOnset.cloupe

On Windows (PowerShell):

Get-FileHash GAERS_P15_PreSeizure.cloupe -Algorithm MD5
Get-FileHash GAERS_P30_SeizureOnset.cloupe -Algorithm MD5

Compare output to checksums listed in download cards above.

Can I use Loupe Browser offline?

Yes! Once installed, Loupe Browser works completely offline.

  • No internet connection required after installation
  • All analysis runs locally on your computer
  • Data never leaves your machine
  • Perfect for secure/air-gapped environments

Summary Data Downloads (CSV)

Download curated summary tables for quick analysis and integration

P15 Top DEGs

Top 50 differentially expressed genes at P15 timepoint

  • 25 upregulated genes (highest logFC)
  • 25 downregulated genes (lowest logFC)
  • Full statistics included
Download P15 Top DEGs CSV

~5 KB | 51 rows (header + 50 genes)

P30 Top DEGs

Top 50 differentially expressed genes at P30 timepoint

  • 25 upregulated genes (highest logFC)
  • 25 downregulated genes (lowest logFC)
  • Full statistics included
Download P30 Top DEGs CSV

~5 KB | 51 rows (header + 50 genes)

Summary Statistics

Comparison table: P15 vs P30 overview

  • Total DEGs per timepoint
  • Up/down regulation counts
  • Mean fold-changes
Download Summary Statistics CSV

~1 KB | 3 rows (header + P15 + P30)

CSV Column Descriptions

Top DEGs files contain:

  • Symbol - Gene symbol
  • Gene_Name - Full gene name
  • logFC - Log2 fold change (GAERS vs Wistar)
  • Average_Expression - Mean expression level
  • t_Statistic - T-test statistic
  • P_Value - Raw p-value
  • Adjusted_P_Value - FDR-adjusted p-value
  • Regulation - "Up" or "Down"

Summary statistics file contains:

  • Timepoint, Total_DEGs, Upregulated, Downregulated
  • Percent_Up, Percent_Down, Mean_logFC_Up, Mean_logFC_Down

Access Spatial Data

Download complete differential expression results and spatial coordinates:

Go to Downloads Page → Search Genes →