Kidney_Single_Cell_Study - EGA European Genome-Phenome Archive

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	1290
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	8
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	32
EGAD00001009005	Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.	HiSeq X Ten Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NovaSeq 6000	15

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	279
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	77
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	61
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	14
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	10
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	12
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	14
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	0
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	6
New insights into fibrotic signaling in renal cell carcinoma. Chen JY, Yiu WH, Tang PM, Tang SC. Front Cell Dev Biol 11: 2023 1056964	0