Kidney_Single_Cell_Study

We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney.

Type: Transcriptome Analysis
Archiver: European Genome-Phenome Archive (EGA)

4 Datasets 16 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001004304	We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. . This dataset contains all the data available for this study on 2018-08-20.	Illumina HiSeq 2500	1
EGAD00001007854	We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.	Illumina HiSeq 4000 Illumina NovaSeq 6000	5
EGAD00001008345	Using the chromium 3' expression assay, we generated an atlas of neuroblastoma and the human fetal adrenal gland. These data were complemented with whole genome sequencing of normal and tumour DNA from the neuroblastoma samples.	Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina MiSeq Illumina NovaSeq 6000	15
EGAD00001015452	Abstract: Children with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), and via a conserved sequence of mutations. Here, we examined the relationship between the genetic and transcriptional evolution of ML-DS from a rich collection of primary patient samples through single cell mRNA sequencing, complemented by phylogenetic analyses in progressive disease. We distilled the transcriptional consequence of each genetic step in the evolution of ML-DS, showing that TAM-defining GATA1 mutations account for most of the ML-DS transcriptome, including those of progressive disease. This transcriptional backbone may thus represent a common vulnerability in ML-DS. We extracted the transcriptional difference between TAM and ML-DS which, unexpectedly, reflected features shared across childhood leukaemia. Our approach delineates the transcriptional evolution of ML-DS and provides an analytical blueprint for distilling consequences of mutations directly from patient samples.	Illumina HiSeq 4000 Illumina NovaSeq 6000	1

Publications	Citations
Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ, Ferdinand JR, Collord G, Botting RA, Popescu DM, Loudon KW, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Del Castillo Velasco-Herrera M, Guzzo C, Richoz N, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Maxwell PH, Lindsay S, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M, Teichmann SA, Clatworthy M, Behjati S. Science 361: 2018 594-599	571
Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation. Subramanian A, Sidhom EH, Emani M, Vernon K, Sahakian N, Zhou Y, Kost-Alimova M, Slyper M, Waldman J, Dionne D, Nguyen LT, Weins A, Marshall JL, Rosenblatt-Rosen O, Regev A, Greka A. Nat Commun 10: 2019 5462	152
Mapping the immune environment in clear cell renal carcinoma by single-cell genomics. Borcherding N, Vishwakarma A, Voigt AP, Bellizzi A, Kaplan J, Nepple K, Salem AK, Jenkins RW, Zakharia Y, Zhang W. Commun Biol 4: 2021 122	278
Single cell derived mRNA signals across human kidney tumors. Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Nat Commun 12: 2021 3896	41
The Extracellular Matrix Environment of Clear Cell Renal Cell Carcinoma Determines Cancer Associated Fibroblast Growth. Bond KH, Chiba T, Wynne KPH, Vary CPH, Sims-Lucas S, Coburn JM, Oxburgh L. Cancers (Basel) 13: 2021 5873	27
Kidney organoids recapitulate human basement membrane assembly in health and disease. Morais MRPT, Tian P, Lawless C, Murtuza-Baker S, Hopkinson L, Woods S, Mironov A, Long DA, Gale DP, Zorn TMT, Kimber SJ, Zent R, Lennon R. Elife 11: 2022 e73486	28
Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Nat Med 28: 2022 743-751	53
Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers. Li S, Lu C, Zhang Y, Zhao X, Lin K, Kong X, Fox D, Xue L, Sun L, Liu Y, Mao F. iScience 25: 2022 104631	4
A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma. Alchahin AM, Mei S, Tsea I, Hirz T, Kfoury Y, Dahl D, Wu CL, Subtelny AO, Wu S, Scadden DT, Shin JH, Saylor PJ, Sykes DB, Kharchenko PV, Baryawno N. Nat Commun 13: 2022 5747	51
New insights into fibrotic signaling in renal cell carcinoma. Chen JY, Yiu WH, Tang PM, Tang SC. Front Cell Dev Biol 11: 2023 1056964	9
The GPCR-Gα<sub>s</sub>-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS. Nat Immunol 24: 2023 1318-1330	55
Multiomics Data Reveal the Important Role of ANXA2R in T Cell-mediated Rejection After Renal Transplantation. Zhang D, Zhang H, Lu J, Hu X. Transplantation 108: 2024 430-444	0
Sex differences in renal cell carcinoma: a single-cell analysis reveals exhausted CD8<sup>+</sup> T-cells highly infiltrated in males. Ning K, Peng Y, Jiang Y, Li Z, Luo X, Lin L, Deng M, Wu Y, Huang T, Huang Y, Xie Y, Yang X, Zhang M, Xiong L, Zou X, Zhou Z, Zhou F, Dong P, Yu C, Zhang Z. Biol Sex Differ 14: 2023 58	20
Transcriptional signals of transformation in human cancer. Kildisiute G, Kalyva M, Elmentaite R, van Dongen S, Thevanesan C, Piapi A, Ambridge K, Prigmore E, Haniffa M, Teichmann SA, Straathof K, Cortés-Ciriano I, Behjati S, Young MD. Genome Med 16: 2024 8	5
Comparative single-cell transcriptomic profiling of patient-derived renal carcinoma cells in cellular and animal models of kidney cancer. Huang R, Kee L, Gont A, Meens J, Ferens FG, Irwin MS, Ailles L, Yuzwa SA, Robinson CM, Ohh M. FEBS Open Bio 15: 2025 1124-1143	0
Data standards for single-cell RNA-sequencing of paediatric cancer. Xu X, Saxon J, Soon MSF, Lee CY, Tuong ZK. Clin Transl Immunology 14: 2025 e70033	0