JUMP TO:
3D tissue imaging and cytometry
Goal:
Understand the kidney in health and disease via 3D imaging and cytometric analyses.
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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
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:
- Preparation
- Isolation of single nuclei from solid tissues
- snDrop-seq
- 10x Genomics snRNA sequequencing for TRA
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.
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Protocol(s)
Metadata standards
- Not yet available
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
JUMP TO:
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
JUMP TO:
Spatial metabolomics
Goal:
Localize the small metabolite markers in tissue sections from human kidneys.

Protocol(s)
- Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometric Imaging (MALDI-MSI)
- Tissue Preparation for Spatial Metabolomics
- Optical Image Collection
Metadata standards
Spatial lipidomics
Goal:
Localize the lipid markers in tissue sections from human kidneys.

Protocol(s)
Metadata standards
Spatial N-glycomics
Goal:
Localize the N-glycan markers in tissue sections from human kidneys

Protocol(s)
Metadata standards
JUMP TO:
CUT&RUN
Goal:
To obtain genome-wide profiles of histone post-translational modifications that define chromatin states of healthy and injured/repairing kidney tissue using Cleavage Under Targets and Release Using Nuclease (CUT&RUN). This technology enables the interrogation of chromatin profiles with limited tissue, such as kidney biopsies.

PROTOCOLS:
METADATA STANDARDS
DNA METHYLATION SEQUENCING
Goal:
The goal of this technology is to uncover methylation signatures of kidney sub-segments that are key determinants of kidney disease progression. This work will result in a comprehensive set of methylation patterns and genotypes to map back to a kidney atlas. This will allow the characterization of methylation signatures of over 20 million CpG sites in individual kidney compartments from both nephrectomies and biopsies using laser microdissection (LMD) methodology with downstream whole-genome bisulfite-sequencing (WGBS).

Workflow: 1) Cryosectioning, 2) LMD processing, 3) DNA isolation, bisulfate conversion, WGBS-sequencing, 4) aligning with the reference genome with Bismark, 5) data analysis in R, and genome program visualization, 6) raw and analyzed data are uploaded to the KPMP data lake.
PROTOCOLS:
METADATA STANDARDS
JUMP TO:
3D tissue imaging and cytometry
Goal:
Understand the kidney in health and disease via 3D imaging and cytometric analyses.
.jpg)
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