Measuring microRNAs in LCM-isolated nephron segments to determine region-specific expression
To determine nephron specificity of microRNA expression that may be associated as toxicity biomarker seen in the urine, laser-capture microdissection (LCM) was performed on the 4 major segment of the nephron in control rat samples. These samples were sent to Bayer for candidate digital drop PCR measurements, NIEHS for smallRNA-seq measurements, and Abcam for FirePlex measurements. smallRNA-seq measurements were used as global assessment of miRNA expression in these segments. FirePlex and ddPCR were used as medium to low number candidate assessments, respectively, of miRNA candidates, based on seq and urine data. "Data associated with Fig 4" summarizes the ddPCR findings. "Data Associated with Figure 5" and "Data Associated with Figure 6" summarize the smallRNA-seq findings. "Data Associated with Figure 7" summarize the FirePlex findings. "Data associated with Figure 8_9" summarize the correlations of these measurements. The cumlmination of these data determine nephron-specific and enriched expression of miRNAs, that are potential candidates of toxicity markers that could leak into the urine upon chemical exposure.
This dataset is associated with the following publication:
Chorley, B., H. Ellinger-Ziegelbauer, M. Tackett, F. Simutis, A. Harrill, J. McDuffie, E. Atabakhsh, R. Nassirpour, L. Whiteley, J. Léonard, G. Carswell, E. Harpur, C. Chen, and J. Gautier. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 180(1): 1-16, (2021).
Complete Metadata
| accessLevel | public |
|---|---|
| bureauCode |
[
"020:00"
]
|
| contactPoint |
{
"fn": "Brian Chorley",
"hasEmail": "mailto:chorley.brian@epa.gov"
}
|
| description | To determine nephron specificity of microRNA expression that may be associated as toxicity biomarker seen in the urine, laser-capture microdissection (LCM) was performed on the 4 major segment of the nephron in control rat samples. These samples were sent to Bayer for candidate digital drop PCR measurements, NIEHS for smallRNA-seq measurements, and Abcam for FirePlex measurements. smallRNA-seq measurements were used as global assessment of miRNA expression in these segments. FirePlex and ddPCR were used as medium to low number candidate assessments, respectively, of miRNA candidates, based on seq and urine data. "Data associated with Fig 4" summarizes the ddPCR findings. "Data Associated with Figure 5" and "Data Associated with Figure 6" summarize the smallRNA-seq findings. "Data Associated with Figure 7" summarize the FirePlex findings. "Data associated with Figure 8_9" summarize the correlations of these measurements. The cumlmination of these data determine nephron-specific and enriched expression of miRNAs, that are potential candidates of toxicity markers that could leak into the urine upon chemical exposure. This dataset is associated with the following publication: Chorley, B., H. Ellinger-Ziegelbauer, M. Tackett, F. Simutis, A. Harrill, J. McDuffie, E. Atabakhsh, R. Nassirpour, L. Whiteley, J. Léonard, G. Carswell, E. Harpur, C. Chen, and J. Gautier. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 180(1): 1-16, (2021). |
| distribution |
[
{
"title": "Data associated with Figure 4.xlsx",
"mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1519009/Data%20associated%20with%20Figure%204.xlsx"
},
{
"title": "Data associated with Figure 5.xlsx",
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"title": "Data associated with Figure 6.xlsx",
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"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1519009/Data%20associated%20with%20Figure%206.xlsx"
},
{
"title": "Data associated with Figure 7.xlsx",
"mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1519009/Data%20associated%20with%20Figure%207.xlsx"
},
{
"title": "Data associated with Figure 8_9.xlsx",
"mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
"downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1519009/Data%20associated%20with%20Figure%208_9.xlsx"
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|
| identifier | https://doi.org/10.23719/1519009 |
| keyword |
[
"FirePlex",
"LCM",
"RNA-Seq",
"biomarkers",
"ddPCR",
"kidney injury",
"microRNAs",
"safety assessment"
]
|
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2020-06-25 |
| programCode |
[
"020:095"
]
|
| publisher |
{
"name": "U.S. EPA Office of Research and Development (ORD)",
"subOrganizationOf": {
"name": "U.S. Environmental Protection Agency",
"subOrganizationOf": {
"name": "U.S. Government"
}
}
}
|
| references |
[
"https://doi.org/10.1093/toxsci/kfaa181"
]
|
| rights |
null
|
| title | Measuring microRNAs in LCM-isolated nephron segments to determine region-specific expression |
