Transcriptomics
Single-nucleus, single-cell, regional, and spatial transcriptomics: goals, protocols, and metadata standards.
JUMP TO:
- Regional transcriptomics
- Single-cell RNA-seq
- Single-nucleus RNA-seq
- Single-nucleus (sn) RNA-seq + snATAC-seq (10X Multiome)
- Spatial transcriptomics
Single-nucleus RNA-seq
Goal:
Identify cell types and states associated with normal and injured kidney functions using gene expression profiling. Identify marker genes for cell type/states and any proportion shifts underlying pathology.
Protocols:
METADATA STANDARDS
Single-cell RNA-seq
Goal:
Empirically derive cell subtypes and cell-type-specific gene expression profiles.
Protocol(s)
METADATA STANDARDS
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Regional transcriptomics
Goal:
Generate deep transcriptomic signatures from nephron segments defined spatially by antibody staining using laser microdissection.
Protocol(s)
METADATA STANDARDS
Spatial transcriptomics
Goal:
Capture whole transcriptome mRNA expression with localization to kidney cells and structures.
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Protocol(s)
METADATA STANDARDS
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Single-nucleus (sn) RNA-seq + snATAC-seq (10X Multiome)
Goal:
10X Genomics multiome protocol generates a molecular atlas of the human kidney with comprehensive cell types and minimal processing artifacts. 10X Multiome snATAC-seq + Gene Expression assay allows measurements of chromatin accessibility and transcription from the same cell. This allows direct insights into putative transcription factors or SNPs associated with open chromatin and impact on gene expression.
PROTOCOLS:
METADATA STANDARDS
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