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Series GSE99084 Query DataSets for GSE99084
Status Public on Feb 04, 2022
Title A Snapshot of RNA Expression in a Single Segment of the Kidney Reveals Stimulus Specific Responses
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The identification of acute kidney disease at the time of patient encounter remains a central problem in clinical medicine. A single analyte, the serum creatinine (sCr) is currently in use as a surrogate for tubular, vascular, or interstitial cellular damage. Nonetheless the sCr test is not specific to kidney injury, but rather might reflect physiological responses to a the primary disease in a distant organ. In addition, while cellular events occur over minutes or hours, sCr requires 24 hours or more to reach a worrisome clinical threshold or demonstrate further deterioration of tissue function and architecture. Here we have adapted the method of Gay et al, Genes Dev. 2013 27(1):98-115. doi: 10.1101/gad.205278.112. to allow cell specific labelling of RNA at the time of our choosing after an injury. The technique involves the cell specific expression of a uracil phosphoribosyltransferase (Uprt) and the subsequent purification of 4-thio-uracil labelled nascent RNAs. Using this technique focused on the collecting duct, we found that a model of volume depletion and a model of ischemic damage, both of which raise the sCr do not activate the same cohort of genes nor the same pathways of gene expression. Hence, a snapshot of newly synthesized RNA reveals the complexity subsumed by diagnostic classifications dependent on sCr (called 'AKI'). We suggest that the Uprt technique will allow characterization of each cell type in the nephron at multiple time points after the onset of injury. These data will replace our current diagnostic strategies with Precision Medicine.
Overall design Examining transcriptional profilesĀ of two models of "acute kidney injury" (iAKI and vAKI), compared to controls, in a single segment of the kidney using cre mediated 4-thio-Uracil tagging of RNA.
Contributor(s) Shen T, Stauber J, Xu K, Barasch J
Citation(s) 35230973
Submission date May 19, 2017
Last update date May 07, 2022
Contact name Jacob Stauber
Organization name Columbia University
Lab Jonathan Barasch
Street address 1150 Saint Nicholas Ave., Russ Berrie Bldg. Rm.408A
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (69)
GSM2632027 iAKI Hoxb7 Pulldown 1
GSM2632028 iAKI Hoxb7 Pulldown 2
GSM2632029 iAKI Hoxb7 Pulldown 3
BioProject PRJNA387238
SRA SRP107378

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Supplementary file Size Download File type/resource
GSE99084_count_matrix.csv.gz 2.1 Mb (ftp)(http) CSV
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