JUMP TO:


3D tissue imaging and cytometry

Goal:
Understand the kidney in health and disease via 3D imaging and cytometric analyses.

The following image types within this technology are available in the Kidney Tissue Atlas:

  • Composite 3D 8-channel immunofluorescence image volume
    3D volume completely represented as a stack of individual, 8-channel images. Every focal plane image and every channel can be independently inspected.
  • Composite max projection of 8-channel immunofluorescence image volume
    8-channel volume combined into a single maximum projection; composite image consists of 8 channels.
  • RGB max projection of 2-channel (autofluorescence and second harmonic generation) image volume
    Projection of 3D volume collected prior to labeling; channels cannot be controlled.
  • RGB max projection of 8-channel immunofluorescence image volume
    8-channel volume combined into a single maximum projection and converted to RGB color space.

Protocol(s)

Metadata standards

  • Not yet available


CODEX (CO-detection by InDEXing)

Goal:

To build a library of high-resolution phenotypical maps of kidney biopsies with anchor, immune, and functional markers for in situ spatial analysis at single cell resolution in normal and pathological conditions.

Protocol(s)

  • Not yet available

Metadata standards

  • Not yet available

Imaging

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How to customize formatting for each rich text

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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


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.

Protocol(s)

Metadata standards

  • Not yet available

Transcriptomics

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Regional proteomics

Goal:
Characterize the kidney proteome in health and disease to identify protein markers that reflect each segment, matrix, and cell type contained in the tissue.

Protocol(s)

Metadata standards

  • Not yet available

Proteomics

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Spatial metabolomics

Goal:
Localize the small metabolite markers in tissue sections from human kidneys.

Protocol(s)

Metadata standards

  • Not yet available


Spatial lipidomics

Goal:
Localize the lipid markers in tissue sections from human  kidneys.

Protocol(s)

Metadata standards

  • Not yet available

Metabolomics

JUMP TO:


3D tissue imaging and cytometry

Goal:
Understand the kidney in health and disease via 3D imaging and cytometric analyses.

The following image types within this technology are available in the Kidney Tissue Atlas:

  • Composite 3D 8-channel immunofluorescence image volume
    3D volume completely represented as a stack of individual, 8-channel images. Every focal plane image and every channel can be independently inspected.
  • Composite max projection of 8-channel immunofluorescence image volume
    8-channel volume combined into a single maximum projection; composite image consists of 8 channels.
  • RGB max projection of 2-channel (autofluorescence and second harmonic generation) image volume
    Projection of 3D volume collected prior to labeling; channels cannot be controlled.
  • RGB max projection of 8-channel immunofluorescence image volume
    8-channel volume combined into a single maximum projection and converted to RGB color space.

Protocol(s)

Metadata standards

  • Not yet available


CODEX (CO-detection by InDEXing)

Goal:

To build a library of high-resolution phenotypical maps of kidney biopsies with anchor, immune, and functional markers for in situ spatial analysis at single cell resolution in normal and pathological conditions.

Protocol(s)

  • Not yet available

Metadata standards

  • Not yet available

Imaging