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Series GSE139107 Query DataSets for GSE139107
Status Public on Jun 08, 2020
Title Cell profiling of acute kidney injury reveals conserved cellular responses to injury
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary After acute kidney injury (AKI), patients either recover or alternatively develop fibrosis and chronic kidney disease. Interactions between injured epithelia, stroma and inflammatory cells determine whether kidneys repair or undergo fibrosis, but the molecular events that drive these processes are poorly understood. Here, we use single nucleus RNA sequencing of a mouse model of AKI to characterize cell states during repair from acute injury. We identify a distinct proinflammatory and profibrotic proximal tubule cell state that fails to repair. Deconvolution of bulk RNA-seq datasets indicates that this “failed-repair proximal tubule cell” or FR-PTC, state can be detected in other models of kidney injury, increasing in the aging rat kidney and over time in human kidney allografts. We also describe dynamic intercellular communication networks and discern transcriptional pathways driving successful vs. failed repair. Our study provides a detailed description of cellular responses after injury and suggests that the FR-PTC state may represent a therapeutic target to improve repair.
Overall design 10X Chromium was used to profile mouse AKI kidneys
Contributor(s) Humphreys BD
Citation(s) 32571916, 33850129, 36310237
Submission date Oct 18, 2019
Last update date Nov 16, 2022
Contact name Tetsuro Kusaba
Organization name Graduate School of Medical Science, Kyoto Prefectural University of Medicine
Department Department of Nephrology
Street address 465 Kajii-cho, Kamigyo-ku
City Kyoto
State/province Kyoto
ZIP/Postal code 6028566
Country Japan
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (24)
GSM4131050 IRIsham1_1
GSM4131051 IRIsham1_2
GSM4131052 IRIsham2
BioProject PRJNA578393
SRA SRP226225

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139107_MouseIRI.metadata.txt.gz 767.2 Kb (ftp)(http) TXT
GSE139107_MouseIRI_12hours.dge.txt.gz 19.7 Mb (ftp)(http) TXT
GSE139107_MouseIRI_14days.dge.txt.gz 21.4 Mb (ftp)(http) TXT
GSE139107_MouseIRI_2days.dge.txt.gz 22.1 Mb (ftp)(http) TXT
GSE139107_MouseIRI_4hours.dge.txt.gz 13.7 Mb (ftp)(http) TXT
GSE139107_MouseIRI_6weeks.dge.txt.gz 23.2 Mb (ftp)(http) TXT
GSE139107_MouseIRI_control.dge.txt.gz 26.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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