Post by the Scribe on Jun 10, 2022 10:46:34 GMT
The human kidney atlas
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A new atlas called the Kidney Precision Medicine Project, constructed by researchers at the Icahn School of Medicine at Mount Sinai, Princeton University, the Flatiron Institute in New York, and the University of Michigan School of Medicine in Ann Arbor just dropped this week. Built from biopsies from 56 adults, the reference reveals single cells, shared pathways, and culprit genes for the classification of kidney disease. Science Advances
Fig. 1. Graphic outline of KPMP data integration and harmonization procedures.
The “subway map” representation of the experimental and analytical protocols used within KPMP is shown in operational flow from kidney biopsy to the integrated multimodal data represented in this manuscript. The kidney biopsy, which is processed through three different tissue processing methods, is shared among tissue interrogation sites (TISs) that generate the data. Four key modalities of molecular data are generated: transcriptomic (red), proteomic (blue), imaging (yellow), and metabolomic (green). Biopsy cores 2 and 3 are used for the molecular analysis; biopsy core 1 (not depicted) is used for histological analysis.
RESULTS
The KPMP Consortium conducted different types of omics assays and low-throughput imaging experiments at different sites for these reference atlas studies. Although it is impossible to definitively characterize tissue as healthy, clinical pathologists adjudicated that the specimens used in this study show no structural signs of disease manifestations. Nevertheless, since we use unaffected tissue regions from nephrectomies and biopsies from both living donors and transplant recipients (i.e., surveillance biopsies), we use the general term reference tissue (table S1). In future studies, these can be compared to diseased tissue specimens.
There were four transcriptomic, two proteomic, two imaging-based, and one spatial metabolomics tissue interrogation assays deployed on the shared tissue samples (Fig. 1A). These assays yielded 3 to 48 different datasets obtained from 3 to 22 subjects per assay for a total of 56 different adult human subjects (table S1). The assays and their detailed tissue preanalytical, tissue processing, data acquisition, and analytical data processing pipelines are schematically depicted as a flowchart in Fig. 1B. We also summarize, in the integration segment of our flowchart, the steps by which the datasets from different assays were integrated and harmonized. This is shown on the upper right side of the descriptive map.
life.us14.list-manage.com/track/click?u=c6c016b12d112265802aafd76&id=0f277f6203&e=082b36634c
A new atlas called the Kidney Precision Medicine Project, constructed by researchers at the Icahn School of Medicine at Mount Sinai, Princeton University, the Flatiron Institute in New York, and the University of Michigan School of Medicine in Ann Arbor just dropped this week. Built from biopsies from 56 adults, the reference reveals single cells, shared pathways, and culprit genes for the classification of kidney disease. Science Advances
Fig. 1. Graphic outline of KPMP data integration and harmonization procedures.
The “subway map” representation of the experimental and analytical protocols used within KPMP is shown in operational flow from kidney biopsy to the integrated multimodal data represented in this manuscript. The kidney biopsy, which is processed through three different tissue processing methods, is shared among tissue interrogation sites (TISs) that generate the data. Four key modalities of molecular data are generated: transcriptomic (red), proteomic (blue), imaging (yellow), and metabolomic (green). Biopsy cores 2 and 3 are used for the molecular analysis; biopsy core 1 (not depicted) is used for histological analysis.
RESULTS
The KPMP Consortium conducted different types of omics assays and low-throughput imaging experiments at different sites for these reference atlas studies. Although it is impossible to definitively characterize tissue as healthy, clinical pathologists adjudicated that the specimens used in this study show no structural signs of disease manifestations. Nevertheless, since we use unaffected tissue regions from nephrectomies and biopsies from both living donors and transplant recipients (i.e., surveillance biopsies), we use the general term reference tissue (table S1). In future studies, these can be compared to diseased tissue specimens.
There were four transcriptomic, two proteomic, two imaging-based, and one spatial metabolomics tissue interrogation assays deployed on the shared tissue samples (Fig. 1A). These assays yielded 3 to 48 different datasets obtained from 3 to 22 subjects per assay for a total of 56 different adult human subjects (table S1). The assays and their detailed tissue preanalytical, tissue processing, data acquisition, and analytical data processing pipelines are schematically depicted as a flowchart in Fig. 1B. We also summarize, in the integration segment of our flowchart, the steps by which the datasets from different assays were integrated and harmonized. This is shown on the upper right side of the descriptive map.