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Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [scRNA-Seq]

ABSTRACT: Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [scRNA-Seq]

PROVIDER: PRJNA976467 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24742900_1.fastq.gz	Fastqsanger.gz
	SRR24742900_2.fastq.gz	Fastqsanger.gz
	SRR24742901_1.fastq.gz	Fastqsanger.gz
	SRR24742901_2.fastq.gz	Fastqsanger.gz
	SRR24742902_1.fastq.gz	Fastqsanger.gz

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Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [spatial transcriptomics]

Project description: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.

2023-12-01 | GSE233512 | GEO

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys

Project description:Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys

| PRJNA976463 | ENA

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [spatial transcriptomics]

Project description:Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [spatial transcriptomics]

| PRJNA976466 | ENA

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys [scRNA-Seq]

2023-12-01 | GSE233511 | GEO

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys.

Project description:T cells are important in the pathogenesis of acute kidney injury (AKI), and TCR+CD4-CD8- (double negative-DN) are T cells that have regulatory properties. However, there is limited information on DN T cells compared to traditional CD4+ and CD8+ cells. To elucidate the molecular signature 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 four genes in mouse kidney DN, CD4+ and CD8+ T cells using RT-PCR and Kcnq5, Klrb1, and Fcer1g genes with the NIH human 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 normal and diseased kidneys.

| S-EPMC10684868 | biostudies-literature

Single cell and spatial transcriptomics analysis of kidney double negative T lymphocytes in normal and ischemic mouse kidneys

Project description:This SuperSeries is composed of the SubSeries listed below.

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Gene expression profile on ischemic kidneys from wildtype C57BL/10 and TLR4 null C57BL/10ScNJ mice

Project description:TLR4 deficiency attenuates kidney injury after ischemic reperfusion as measured by both renal function and morphology. To better understand the role of TLR4 during the acute kidney injury, we used DNA microarray to identify genes that were differentially expressed on kidneys in wildtype B10 mice and TLR4 null mice during the early stage of injury. A murine ischemic reperfusion injury model was established. After right nephrectomy, the left pedicle was clamped for 23min followed by 4hr reperfusion. Sham mice were used as controls. 6 WT males and 6 TLR4 null males were included with 3 ischemic and 3 shams in each group.

2012-08-15 | E-GEOD-34351 | biostudies-arrayexpress

Gene expression profile on ischemic kidneys from wildtype C57BL/10 and TLR4 null C57BL/10ScNJ mice

2012-08-15 | GSE34351 | GEO

Single cell RNASeq of whole mouse kidneys from Uromodulin/Tamm horsfall protein knock-out mice

Project description:To elucidate changes in cellular populations in the ischemic acute kidney injury, we performed single cell RNAseq on mouse kidneys following ischemic reperfusion injury and a sham surgery. Mice were subjected to bilateral clamping of the renal pedicule for 30 minutes. After 6-7 hours of reperfusion the kidneys were removed and processed by a MACs cell isolation protocol and dead cell removal (PMID:33448928) , sorted on a 10X Chromium platform version 3 and libraries generated. Sequencing was performed on an Illumina NovaSeq 6000.

2021-04-08 | GSE171639 | GEO

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Project description:Transcriptional profiling of mouse embryonic kidneys (E13.5) comparing UB HDAC1,2-/- kidneys with wild type kidneys. Studies in our lab showed that histone deacetylase 1 (HDAC1) and 2 (HDAC2) perform redundant, yet essential functions in the developing mouse ureteric bud (UB) tissue. Double deletion of HDAC1 and HDAC2 in the UB results in impaired UB branching morphogenesis, followed by severe kidney dysgenesis. The goal of the microarray analysis was to identify the genetic pathways controlled by HDAC1 and 2 in the UB.

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