[HTML][HTML] Principles of spatial transcriptomics analysis: a practical walk-through in kidney tissue

T Noel, QS Wang, A Greka, JL Marshall - Frontiers in Physiology, 2022 - frontiersin.org
… -seqV2 to kidney tissue has enabled us to elucidate spatially … Here, we review spatial
transcriptomic technologies, as well … spatial cell type and transcriptomic characterizations. We take …

Single‐cell RNA‐seq with spatial transcriptomics to create an atlas of human diabetic kidney disease

D Chen, M Shao, Y Song, G Ren, F Guo… - The FASEB …, 2023 - Wiley Online Library
kidney disease worldwide. We used single- cell RNA- sequencing and spatial transcriptomic
analyses of kidney … The DEGs in most kidney parenchymal cells in DKD were primarily …

[HTML][HTML] Integrating spatial transcriptomics with single-cell transcriptomics reveals a spatiotemporal gene landscape of the human developing kidney

H Wu, F Liu, Y Shangguan, Y Yang, W Shi, W Hu… - Cell & Bioscience, 2022 - Springer
… unbiased spatial transcriptomics profile of the fetal kidney, we mounted cryosections of the
embryonic kidneys at two post-conception time points (9 PCW and 18 PCW) on the spatially

[PDF][PDF] High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways

JL Marshall, T Noel, QS Wang, H Chen, E Murray… - Iscience, 2022 - cell.com
… tional complexity, second only to the brain, there is a significant need to develop spatial
transcriptomics from intact kidney tissue both as a reference and to uncover disease-specific …

[HTML][HTML] Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury

RM Ferreira, AR Sabo, S Winfree, KS Collins… - JCI insight, 2021 - ncbi.nlm.nih.gov
spatial distribution of acute kidney injury (AKI) is regional and affects cells heterogeneously.
We first optimized coordination of spatial transcriptomics … the spatial transcriptomic signature …

Spatially resolved transcriptomics and the kidney: many opportunities

EE Dixon, H Wu, E Sulvarán-Guel, J Guo… - Kidney International, 2022 - Elsevier
spatial transcriptomic methods, discuss the advantages and limitations of each method,
and digest the recent applications of spatially resolved transcriptomics on kidney biology. …

[HTML][HTML] Challenges and Opportunities for the Clinical Translation of Spatial Transcriptomics Technologies

KD Smith, DK Prince, JW MacDonald… - Glomerular …, 2024 - karger.com
… In this perspective, we focus on two platforms for spatial transcriptomics, GeoMx and Visium,
and how these platforms have been used to provide novel insight into kidney disease. The …

[HTML][HTML] Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model

EE Dixon, H Wu, Y Muto, PC Wilson… - Journal of the …, 2022 - journals.lww.com
… We used the Visium spatial transcriptomic pipeline from 10× … sequencing with spatial
transcriptomics permitted evaluation … spatial transcriptomic atlas serves as a first step in the spatial

[HTML][HTML] Resident macrophage subpopulations occupy distinct microenvironments in the kidney

MD Cheung, EN Erman, KH Moore, JMP Lever, Z Li… - JCI insight, 2022 - ncbi.nlm.nih.gov
… ) and spatial transcriptomics to demonstrate that KRMs consist of at least 7 major subpopulations
localized to defined zones within the kidney. The distinct transcriptomic programs of …

[HTML][HTML] Deconvolution tactics and normalization in renal spatial transcriptomics

R Melo Ferreira, BJ Freije, MT Eadon - Frontiers in Physiology, 2022 - frontiersin.org
… In an effort to create a spatially anchored atlas of the kidney, analysis of multiple ST samples
is invariably expected. On the VSGE platform, four samples are run in parallel on a single …