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FAQs
The FAQs page serves as a comprehensive guide to help users navigate and maximize their experience with BrainScope. This section addresses common questions regarding dataset availability, analytical tools, and functionality across different modules. Covering 26 key topics, the FAQs provide clear and structured explanations on how to explore single-cell, bulk RNA-seq, and spatial transcriptomic data, perform pan-dimensional analysis, and utilize advanced bioinformatics tools such as gene set enrichment, protein-protein interaction networks, and evolutionary comparisons. Whether you are a new user looking for an overview or an experienced researcher seeking specific functionalities, this page offers quick and accessible answers to enhance your analysis workflow within BrainScope.
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What is BrainScope?
BrainScope is a comprehensive multi-dimensional platform designed for the integrative analysis of brain-related transcriptomic data. Covering both single-cell and bulk RNA sequencing, as well as spatial transcriptomics, BrainScope enables users to explore gene expression patterns across species, brain regions, developmental stages, and disease conditions.
What types of datasets are available on BrainScope?
BrainScope provides access to single-cell RNA sequencing (scRNA-seq), bulk RNA sequencing (bulk RNA-seq), and spatial transcriptomics (ST) datasets, covering different species, brain regions, developmental stages, and diseases.
How do I explore datasets on BrainScope?
Users can explore datasets through different modules, including AtlasScope (cross-species analysis), RegionScope (brain regions), PathoScope (disease-related data), AgeScope (developmental stages), TissueScope (bulk RNA-seq), and SpaceScope (spatial transcriptomics).
How can I search for a specific dataset?
Each module provides a search function where users can filter datasets by species, brain region, disease, or developmental stage. The dataset table provides metadata, and clicking 'View Data' allows for deeper exploration.
Can I download raw and processed data?
Yes. BrainScope offers raw sequencing data, processed expression matrices, and analytical results for download, allowing users to conduct further research.
What modules are available for single-cell dataset exploration?
The AtlasScope, RegionScope, PathoScope, and AgeScope modules provide access to single-cell transcriptomic datasets, each focusing on a specific aspect: species, brain regions, diseases, and development.
What are SGPDA, GSPDA, and CTPDA?
SGPDA (Single-Gene Pan-Dimensional Analysis) allows users to explore a gene's expression across species, brain regions, developmental stages, diseases, and spatial transcriptomics. GSPDA (Gene-Set Pan-Dimensional Analysis) enables users to investigate curated gene sets across these dimensions. CTPDA (Cell-Type Pan-Dimensional Analysis) allows users to analyze the distribution and proportion of specific cell types across different conditions.
How do I explore the expression of a specific gene?
Use the SGPDA tool in any single-cell module. Enter the gene name, select a dimension (e.g., species, brain region), and visualize its expression pattern in the provided heatmaps.
How can I analyze the expression of a gene set?
Navigate to GSPDA, select a gene set from the provided categories, and view its aggregated expression pattern across different dimensions.
How do I compare the proportion of cell types across datasets?
Use CTPDA to select a specific cell type (e.g., microglia, astrocytes), and view its distribution across species, brain regions, developmental stages, diseases, or spatial transcriptomic datasets.
What is TissueScope?
TissueScope provides bulk RNA-seq datasets from different species and brain tissues, allowing users to analyze gene expression in large-scale transcriptomic datasets.
How can I analyze gene expression in bulk RNA-seq data?
TissueScope offers SGPDA (single-gene analysis) and GSPDA (gene-set analysis) to explore gene expression across species and tissues.
What additional tools are available in TissueScope?
TissueScope provides gene homolog mapping, transcriptome-wide association studies, PCA visualization, and evolutionary gene expression analysis.
What is SpaceScope?
SpaceScope enables the exploration of spatial transcriptomic (ST) datasets, allowing users to analyze gene expression within the anatomical context of the brain.
How do I search for spatial transcriptomics datasets?
Users can filter by species, brain region, or dataset type. Each dataset includes metadata such as sequencing technology, disease condition, and cell count.
How can I visualize gene expression in spatial datasets?
Using SGPDA in SpaceScope, users can select a gene and generate heatmaps that illustrate its spatial expression pattern across brain sections.
Can I analyze gene sets in spatial data?
Yes, GSPDA in SpaceScope allows users to examine curated gene sets and their spatial distribution in different datasets.
What are cPandora, ePandora, and sPandora?
cPandora enables comparative analysis of cell types across species, regions, diseases, development, and spatial datasets. ePandora provides a gene set-based comparative analysis across the same dimensions. sPandora allows single-gene expression comparisons across these dimensions.
How can I analyze a cell type across species?
Use cPandora, select a cell type (e.g., oligodendrocytes), and visualize its proportions in different species, regions, or conditions.
How do I perform evolutionary expression analysis of a gene set?
ePandora allows users to select a gene set and examine its expression across species, highlighting conserved and divergent gene expression patterns.
Can I study disease-specific gene expression patterns?
Yes, users can use sPandora to compare the expression of disease-associated genes across species, brain regions, and developmental stages.
Does BrainScope offer functional enrichment analysis?
Yes. BrainScope includes gene list enrichment, motif analysis, and protein-protein interaction (PPI) network analysis, accessible through different modules.
How can I perform enrichment analysis on a gene list?
Users can select a gene set in the GSPDA tool and run enrichment analyses to identify associated biological pathways and transcription factors.
How do I explore protein-protein interaction networks?
The PPI tool visualizes interactions among genes in a selected dataset, highlighting functional networks.
Can I download figures and processed results?
Yes, all analysis pages provide options to download images, PDFs, and CSV files of heatmaps, stacked bar charts, and expression profiles.
How can I share or cite BrainScope data?
Users can access dataset metadata, journal references, and PMIDs for citation. BrainScope also allows exporting gene lists and analysis results for use in external studies.
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