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Series GSE233512 Query DataSets for GSE233512
Status Public on Dec 01, 2023
Title Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [spatial transcriptomics]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary T cells are important in the pathogenesis of acute kidney injury (AKI), and TCR+CD4-CD8- (double negative-DN) are T cells that have a regulatory role. However, little is understood about these cells in comparison to traditional CD4+ and CD8+ cells. To elucidate the molecular and spatial dynamics of DN T cells during AKI, we performed single-cell RNA sequencing (scRNA-seq) on sorted murine DN, CD4+, and CD8+ cells, combined with spatial transcriptomic profiling of normal and post-AKI mouse kidneys. scRNA-seq revealed distinct transcriptional profiles for DN, CD4+, and CD8+ T cells of mouse kidneys, with enrichment of Kcnq5, Klrb1c, Fcer1g, and Klre1 expression in DN T cells compared to CD4+ and CD8+ T cells in normal kidney tissue. We validated the expression of these genes in mouse and human kidney DN, CD4+ and CD8+ T cells using RT-PCR and in the NIH kidney precision medicine project (KPMP). Spatial transcriptomics in normal and ischemic mouse kidney tissue showed a localized cluster of T cells in the outer medulla expressing DN T cell genes including Fcer1g. These results provide a template for future studies in DN T as well as CD4+ and CD8+ cells in the normal and diseased kidney.
 
Overall design Normal kidneys and kidneys treated with ischemic reperfusion injury were analyzed using spatial transcriptomics.
 
Contributor(s) Gharaie S, Lee K, Noller K, Lo EK, Miller B, Jung H, Newman-Rivera AM, Kurzhagen JT, Singla N, Welling P, Fan J, Cahan P, Noel S, Rabb H
Citation(s) 38017015
Submission date May 25, 2023
Last update date Dec 02, 2023
Contact name Emily Lo
Organization name Johns Hopkins
Street address 733 N Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM7429786 Left kidney, ctrl 1
GSM7429787 Left kidney, ctrl 2
GSM7429788 Left kidney, ischemic reperfusion 1
This SubSeries is part of SuperSeries:
GSE233513 Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys
Relations
BioProject PRJNA976466

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Supplementary file Size Download File type/resource
GSE233512_RAW.tar 144.6 Mb (http)(custom) TAR (of CSV, JSON, MTX, PNG, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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