deseq2 normalized count data  (Broad Institute Inc)

Journal: Journal of Neuroinflammation

Article Title: Minocycline counter-regulates pro-inflammatory microglia responses in the retina and protects from degeneration

doi: 10.1186/s12974-015-0431-4

Figure Lengend Snippet: Light exposure and minocycline exert global effects on the retinal transcriptome. a Gene Expression Dynamics Inspector (GEDI) analysis of the complete RNA-seq dataset (Gene Expression Omnibus Series Nr. GSE71025) from control retinas and light-exposed retinas in the absence or presence of minocycline. Biological duplicates were analyzed for each condition and the pseudo-color scale indicates high ( red ) or low ( blue ) expression levels. b , c DESeq2 analysis to determine differential gene expression between the indicated groups using a log2 fold change cutoff of ≥2 and ≤−2. The MA-plots demonstrate that light exposure caused a global induction of 217 genes ( b ), whereas light exposure plus minocycline administration reversed this effect with many counter-regulated transcripts ( c )

Article Snippet: The RNA-seq raw data and normalized DESeq2 counts of this study are publicly available at the National Center for Biotechnology Information Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) as series record GSE71025.

Techniques: Gene Expression, RNA Sequencing, Control, Expressing