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. 2024 Apr 16:54:110431.
doi: 10.1016/j.dib.2024.110431. eCollection 2024 Jun.

Spatially resolved metabolomic dataset of distinct human kidney anatomic regions

Haikuo Li  1 , Benjamin D Humphreys  1   2
Affiliations

Spatially resolved metabolomic dataset of distinct human kidney anatomic regions

Haikuo Li et al. Data Brief. .

Abstract

Cortex, medulla and papilla are three major human kidney anatomic structures and they harbour unique metabolic functions, but the underlying metabolomic profiles are largely unknown at spatial resolution. Here, we generated a spatially resolved metabolomics dataset on human kidney cortex, medulla and papilla tissues dissected from the same donor. Matrix-Assisted Laser Desorption/Ionization-Imaging Mass Spectrometry (MALDI-IMS) was used to detect metabolite species over mass-to-charge ratios of 50 -1500 for each section at a resolution of 10 × 10 µm2 pixel size. We present raw data matrix of each sample, feature annotations, raw AnnData merged from three samples and processed AnnData files after quality control, dimensional reduction and data integration, which contains a total of 170,459 spatially resolved metabolomes with 562 features detected. This dataset can be either visualized through an interactive browser or further analyzed to study metabolomic heterogeneity across regional human kidney anatomy.

Keywords: Imaging mass spectrometry; Kidney anatomy; MALDI; Metabolism; Nephrology; Omics.

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Figures

Fig. 1
Fig. 1
Spatial feature plot of two metabolite species across human kidney anatomic regions. (A) MALDI-IMS intensities of sphingomyelin (d18:0/16:1(9Z)) with its chemical structure shown on the left. (B) MALDI-IMS intensities of phosphatidylcholine (16:0/18:1(11Z)) with its chemical structure shown on the left.
Fig. 2
Fig. 2
Quality control metrics of the presented AnnData. (A) Number of features per pixel (left), number of counts per pixel (middle) and total number of metabolomes of each kidney anatomic region (right) in the processed AnnData. (B) Number of features and counts per pixel in the raw AnnData (left) and number of features and counts per pixel after quality control.
Fig. 3
Fig. 3
UMAP presentation of 170,459 spatially resolved metabolomes, colored by curated Leiden clusters (left) or kidney anatomic regions (right).
Fig. 4
Fig. 4
Projection of the 16 Leiden clusters (presented in Fig. 3) onto sections of the three human kidney anatomic regions.
See this image and copyright information in PMC

References

    1. Li H., Li D., Ledru N., Xuanyuan Q., Wu H., Asthana A., Byers L.N., Tullius S.G., Orlando G., Waikar S.S., Humphreys B.D. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. Cell Metab. 2024 doi: 10.1016/J.CMET.2024.02.015. Online ahead of print. - DOI - PMC - PubMed
    1. Palmer A., Phapale P., Chernyavsky I., Lavigne R., Fay D., Tarasov A., Kovalev V., Fuchser J., Nikolenko S., Pineau C., Becker M., Alexandrov T. FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry. Nat. Methods. 2016:57–60. doi: 10.1038/nmeth.4072. 2016 141 14. - DOI - PubMed
    1. Gallardo P.A., Vio C.P. Functional anatomy of the kidney. Ren. Physiol. Hydrosaline Metab. 2022 doi: 10.1007/978-3-031-10256-1_2. - DOI
    1. Kalim S., Rhee E.P. An overview of renal metabolomics. Kidney Int. 2017;91:61. doi: 10.1016/J.KINT.2016.08.021. - DOI - PMC - PubMed
    1. Li H., Humphreys B.D. Single cell technologies: beyond microfluidics. Kidney. 2021;360(2):1196–1204. doi: 10.34067/kid.0001822021. - DOI - PMC - PubMed

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