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| Status |
Public on May 07, 2019 |
| Title |
Multi Omics analysis of fibrotic kidneys in two mouse models [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Kidney fibrosis represents an urgent unmet clinical need due to the lack of effective therapies and inadequate understanding of the molecular pathogenesis. We have generated a comprehensive and integrated multi-omics data set (proteomics, mRNA and small RNA transcriptomics) of fibrotic kidneys that is searchable through a user-friendly web application. Two commonly used mouse models were utilized: a reversible chemical-induced injury model (folic acid (FA) induced nephropathy) and an irreversible surgically-induced fibrosis model (unilateral ureteral obstruction (UUO)). mRNA and small RNA sequencing as well as 10-plex tandem mass tag (TMT) proteomics were performed with kidney samples from different time points over the course of fibrosis development. The bioinformatics workflow used to process, technically validate, and integrate the single data sets will be described. In summary, we present temporal and integrated multi-omics data from fibrotic mouse kidneys that are accessible through an interrogation tool to provide a searchable transcriptome and proteome for kidney fibrosis researchers.
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| Overall design |
mRNA and small RNA sequencing (n=3 per time point, respectively) as well as proteomics (n=2 per time point) with kidney samples from different time points (day 1, 2, 3, 7 and 14) over the course of fibrosis development in two mouse models. Kidneys from day 0 were used as normal control samples i.e. as reference.
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| Contributor(s) |
Pantano L, Pavkovic M |
| Citation(s) |
31201317 |
| |
| Submission date |
Aug 09, 2018 |
| Last update date |
Aug 06, 2019 |
| Contact name |
Lorena Pantano |
| E-mail(s) |
lpantano@iscb.org
|
| Organization name |
Harvard Chan School of Public Health
|
| Department |
Biostatistics
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| Lab |
Bioinformatic Core
|
| Street address |
655 Huntington Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE118341 |
Multi Omics analysis of fibrotic kidneys in two mouse models |
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| Relations |
| BioProject |
PRJNA485264 |
| SRA |
SRP156882 |
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