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Series GSE99339 Query DataSets for GSE99339
Status Public on Aug 12, 2017
Title Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts [glomeruli]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Accumulating evidence suggests that dysregulation of hypoxia-regulated transcriptional mechanisms is involved in development of chronic kidney diseases (CKD). However, it remains unclear how hypoxia-induced transcription factors (HIFs) and subsequent biological processes contribute to CKD development and progression. In our study, genome-wide expression profiles of more than 200 renal biopsies from patients with different CKD stages revealed significant correlation of HIF-target genes with eGFR in glomeruli and tubulointerstitium. These correlations were positive and negative and in part compartment-specific. Microarrays of proximal tubular cells and podocytes with stable HIF1α and/or HIF2α suppression displayed cell type-specific HIF1/HIF2-dependencies as well as dysregulation of several pathways. WGCNA analysis identified gene sets that were highly coregulated within modules. Characterization of the modules revealed common as well as cell group- and condition-specific pathways, GO-Terms and transcription factors. Gene expression analysis of the hypoxia-interconnected pathways in patients with different CKD stages revealed an increased dysregulation with loss of renal function. In conclusion, our data clearly point to a compartment- and cell type-specific dysregulation of hypoxia-associated gene transcripts and might help to improve the understanding of hypoxia, HIF dysregulation, and transcriptional program response in CKD.
 
Overall design Kidney biopsies were microdissected and hybridized on Affymetrix HGU133A and HGU133 Plus 2 arrays. The expression data was normalized using RMA and CustomCDF v 18 ENTREZG in batches, as indicated. Batch correction was performed using ComBat in GenePattern. The disease groups are Diabetic Nephropathy (DN, n=14), Focal and Segmental Glomerulosclerosis (FSGS, n=22), Focal and Segmental Glomerulosclerosis and Minimal Change Disease (FSGS&MCD, n=6), Hypertensive Nephropathy (HT, n=15), IgA Nephropathy (IgA, n=26), Minimal Change Disease (MCD, n=13), Membranous Glomerulonephritis (MGN, n=21), Rapidly Progressive Glomerulonephritis (RPGN, n=23), Systemic Lupus Erythematosus (SLE, n=30), Thin Membrane Disease (TMD, n=3), and Tumor Nephrectomies (TN, n=14). This dataset has substantial overlap with GEO datasets GSE47184,GSE35489, GSE37463
 
Contributor(s) Shved N, Warsow G, Eichinger FH, Hoogewijs D, Brandt S, Wild P, Kretzler M, Cohen CD, Lindenmeyer MT
Citation(s) 28819298
Submission date May 26, 2017
Last update date Jul 25, 2021
Contact name Felix Eichinger
E-mail(s) eichinge@umich.edu
Organization name The University of Michigan
Department Division of Nephrology
Street address 1150 W. Medical Center Drive
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
 
Platforms (2)
GPL19109 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray HGU133Plus2_Hs_ENTREZG_v18]
GPL19184 [HG-U133A] Affymetrix Human Genome U133A Array [Custom Brainarray v18 ENTREZG CDF]
Samples (187)
GSM2642291 Diabetic Nephropathy [H1-Glom-DN1]
GSM2642292 Diabetic Nephropathy [H1-Glom-DN2]
GSM2642293 Diabetic Nephropathy [H1-Glom-DN5]
This SubSeries is part of SuperSeries:
GSE99340 Transcriptome-based network analysis reveals renal cell type-specific dysregulation of hypoxia-associated transcripts
Relations
BioProject PRJNA388165

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
GSE99339_RAW.tar 685.0 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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