Computational protocol: Selective deletion of PPARβ/δ in fibroblasts causes dermal fibrosis by attenuated LRG1 expression

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Protocol publication

[…] cDNA synthesis was performed using the Applause WT-Amp ST System (NuGEN Technologies, USA). The resulting cDNA was purified with MinElute Reaction Cleanup Kit (Qiagen, USA), followed by fragmentation and labeling using the Encore Biotin Module (NuGEN Technologies, USA). The fragmented and labeled cDNA were mixed with a hybridization master mix (Affymetrix, USA) in accordance to the manufacturer’s protocol, and 90 μL of the resultant mixture were injected into the GeneChip® Mouse Gene 1.0 ST Array gene chips (Affymetrix, USA). The scanned data was collected for analyses using the Partek Genomics Suite v6.6 (Partek Inc., USA). Differences in gene expression between FSPCre-Pparb/d−/− and wild-type samples were identified using the ANOVA function of the Partek Genomics Suite. Microarray datasets from FSPCre-Pparb/d−/− mice were subsequently hierarchically clustered with microarray datasets from tight skin (Tsk) 1 or 2 heterozygous mutant mice (GSE71999), bleomycin-induced fibrosis mice (GSE71999), sclerodermatous graft versus host disease (SGVHD) mice (GSE24410), and human samples of SSc (PMC2481301, GSE9285), downloaded from NCBI Gene Expression Omnibus (GEO) database. We focused our analysis on an intrinsic SSc gene set comprising 995 genes that was previously reported (GSE9285). Gene ontology (GO) analysis of gene subsets was performed using the Ingenuity Pathway Analysis software (Ingenuity Systems Inc., USA). The microarray protocols and data have been deposited in NCBI’s Gene Expression Omnibus (GEO) database accession number GSE71419. […]

Pipeline specifications

Software tools Partek Genomics Suite, IPA
Databases GEO
Application Gene expression microarray analysis
Organisms Mus musculus