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Series GSE118340 Query DataSets for GSE118340
Status Public on May 07, 2019
Title Multi Omics analysis of fibrotic kidneys in two mouse models [miRNA-Seq]
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
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.
 
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@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)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (15)
GSM3325589 normal-1 (miRNA-Seq)
GSM3325590 normal-2 (miRNA-Seq)
GSM3325591 normal-3 (miRNA-Seq)
This SubSeries is part of SuperSeries:
GSE118341 Multi Omics analysis of fibrotic kidneys in two mouse models
Relations
BioProject PRJNA485263
SRA SRP156883

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
GSE118340_RAW.tar 7.3 Mb (http)(custom) TAR (of GTF, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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