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Series GSE126182 Query DataSets for GSE126182
Status Public on May 07, 2019
Title Multi Omics analysis of fibrotic kidneys in two mouse models (Unilateral ureter obstruction (UUO) model MS data set)
Organism Mus musculus
Experiment type Protein profiling by Mass Spec
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.
 
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.

Raw MS data deposited in PRIDE:
https://www.ebi.ac.uk/pride/archive/projects/PXD010861
 
Contributor(s) Lorena P, Mira P
Citation(s) 31201317
Submission date Feb 06, 2019
Last update date Aug 06, 2019
Contact name Lorena Pantano
E-mail(s) lpantano@hsph.harvard.edu
Organization name Harvard Chan School of Public Health
Department Biostatistics
Lab Bioinformatic Core
Street address 655 Huntington Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL26156 ThermoFisher 10-plex Tandem Mass Tag (TMT) Mass Spectrometry
Samples (10)
GSM3592699 normal_1_uuo
GSM3592700 normal_2_uuo
GSM3592701 uuo-day3-1
This SubSeries is part of SuperSeries:
GSE118341 Multi Omics analysis of fibrotic kidneys in two mouse models
Relations
BioProject PRJNA521249

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

Supplementary file Size Download File type/resource
GSE126182_RAW.tar 1.0 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available on Series record
Processed data provided as supplementary file

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