Kidney_transplant_nephrectomy_scRNAseq

Single cell transcriptomics study of tissue from human kidney transplant nephrectomies Tissue is acquired from kidney transplant nephrectomies, homogenised and disaggregated to a single cell suspension prior to droplet encapsulation single cell RNAseq (10X protocol) or plate based single cell RNAseq (SS2 protocol). Human tissues, including the kidney are seeded with a tissue resident immune cell network throughout life. These cells may self renew in situ or be replaced by circulating precursors which enter the tissue in response to tissue specific niche and inflammatory signals. We are using single cell RNA sequencing of kidney transplant nephrectomy tissue to 1) understand the immune cell populations which are resident within the human kidney 2) identify which of these populations is donor or recipient derived. 3) Uncover the temporal dynamics of donor/recipient chimerism in the the human kidney following transplantation. 4) Understand transcriptional differences between organs removed for a variety of reasons (infection, chronic rejection, vascular emergencies) This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

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

1 Dataset 1 Publication

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
EGAD00001015631	This dataset contains raw single-cell RNA sequencing (scRNA-seq) data for five new kidney allograft nephrectomy samples used to construct the described in the following study: https://www.biorxiv.org/content/10.1101/2022.10.28.514222v2.full. The full description of processing is described in the manuscript. Briefly, samples were digested into a single cell suspension and run according to the 10X Genomics Chromium 5’ single cell kit (v2). Sequencing was performed using an Illumina Novaseq instrument. Samples were designated as TXN2 (EGAN00002519570, mycotic pseudoaneurysm, control dataset), TXN3 (EGAN00002235628, renal vein thrombus, control dataset), TXN5 (EGAN00002519573, chronic transplant rejection), TXN6 (EGAN00002519572, chronic pyelonephritis and renal artery stenosis, non-alloimmune graft injury dataset), TXN7 (EGAN00002519576, recurrent focal segmental glomerulosclerosis, non-alloimmune graft injury dataset).	Illumina HiSeq 4000 Illumina NovaSeq 6000	1

Publications	Citations
Organ-specific features of human kidney lymphatics are disrupted in chronic transplant rejection. Jafree DJ, Stewart BJ, Price KL, Kolatsi-Joannou M, Laroche C, Mohidin B, Davis B, Mitchell H, Russell LG, Del Rey LM, Wang CJ, Mason WJ, Lee BI, Heptinstall L, Subramanian A, Pomeranz G, Moulding D, Wilson L, Wickenden T, Malik SN, Holroyd N, Walsh CL, Chandler JC, Cao KX, Winyard PJ, Woolf AS, Busche MA, Walker-Samuel S, Walker LS, Crompton T, Scambler PJ, Motallebzadeh R, Clatworthy MR, Long DA. J Clin Invest 135: 2025 e168962	3

Publications

Citations

Organ-specific features of human kidney lymphatics are disrupted in chronic transplant rejection.
Jafree DJ, Stewart BJ, Price KL, Kolatsi-Joannou M, Laroche C, Mohidin B, Davis B, Mitchell H, Russell LG, Del Rey LM, Wang CJ, Mason WJ, Lee BI, Heptinstall L, Subramanian A, Pomeranz G, Moulding D, Wilson L, Wickenden T, Malik SN, Holroyd N, Walsh CL, Chandler JC, Cao KX, Winyard PJ, Woolf AS, Busche MA, Walker-Samuel S, Walker LS, Crompton T, Scambler PJ, Motallebzadeh R, Clatworthy MR, Long DA. J Clin Invest 135: 2025 e168962