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To validate the breadth of fold differences of microarray results, several ORFs were verified by real-time PCR.
According to our qPCR validated microarray results several other genes implicated in UPR were downregulated in larvae overexpressing Manf, such as pancreatic eIF-2α kinase (PERK), Heat shock protein 83 (Hsp83), Ubiquilin (Ubqn), and septin interacting protein 3 (sip3).
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Additionally, the microarray results revealed several fold up-regulation of transcripts encoding for lipoxygenases (Additional file 8: Table S5) including LOX2 and LOX2.1.
Quantitative RT-PCR was performed to corroborate microarray results for several genes.
Our microarray results demonstrated several genes directly involved in cell envelope or outer membrane biogenesis differentially expressed in the bvrR mutant.
This idea is supported by the microarray results as several other genes involved in electron transport were also differentially expressed.
Microarray results revealed several genes with altered expression according to the fold-change ratio (data not shown).
Finally, we compared our Drosophila microarray results to several SOD1 mouse and ALS human patient microarrays to identify genes that may be commonly misregulated.
Consistent with our microarray results, wherein several probes corresponding to C3AR1, CAMP, CCL5 and IFNγ exhibited a down regulation along with up regulation of C4BPA, real time PCR results also matched the microarray expression profile (Supporting Table S2 in Additional file 1).
In addition, and consistent with the microarray results being accurate, several mini-collagen-like proteins were upregulated in the planula.
To confirm the microarray results, we chose several transcripts from category D, cluster 8 (C5 and LBP) and cluster 1 (SERPINA 3 and C4A), and measured their expressions with real-time PCR using the same RNA samples used for microarray studies.
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