sureprint g3 mouse gene expression v2 microarray 8×60k  (Agilent technologies)

Journal: bioRxiv

Article Title: Histone Deacetylases (HDACs) maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and non-coding loci

doi: 10.1101/2023.04.06.535398

Figure Lengend Snippet: (A) Microarray data from n = 3 biological replicates showing relative expression (log 2 fold-change) of indicated pluripotent genes in Hdac1/2-KO (DKO) and Hdac1-KO; Hdac2-Het cells at 0 (Ctrl) and 3 days post deletion (OHT). (B) Gene set enrichment analysis (GSEA) plot of microarray data showing Ctrl samples are enriched for the Muller Plurinet (ES=0.47; P<0.0001) and pluripotency (ES=0.70; P<0.0001) gene sets compared to Hdac1-KO; Hdac2-Het KO cells. (C) Western blot data for HDAC1, HDAC2, NANOG and POU5F1 proteins in Hdac1/2-KO (DKO) and Hdac1-KO; Hdac2-Het cells at 0 (Ctrl) and 3 days post deletion (OHT). α-Tubulin (α-TUB) was used as a protein loading control.

Article Snippet: Comparative gene expression profiles were generated using the Illumina mouseWG-6, v2 (LBH589 and Hdac1 L/L ; Hdac2 L/wt ) or Agilent SurePrint G3 Mouse Gene Expression v2 8×60K microarray ( Hdac3 L/L ) according to manufacturer’s instructions.

Techniques: Microarray, Expressing, Western Blot, Control

Journal: bioRxiv

Article Title: Histone Deacetylases (HDACs) maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and non-coding loci

doi: 10.1101/2023.04.06.535398

Figure Lengend Snippet: (A) Microarray analysis: the number of genes differentially expressed (1.5-fold; FDR ≤0.05) at the indicated times following LBH589 treatment. (B) Gene set enrichment analysis (GSEA) plot showing enrichment for the defined pluripotency gene set (Kim_Core_Module) in Control versus LBH589 treated ESCs. LBH589 2hr (ES=0.527; P<0.0001), 6hr (ES=0.789; P<0.0001) and 18hr (ES=0.83; P<0.0001). (C) GSEA for Ctrl and LBH589 samples showed equal enrichment for the formation of the primary germ layer (GO:0001704; Germ Layer). (D) Microarray data from n = 3 biological replicates showing relative expression of indicated pluripotent genes in ESCs treated with LBH589 for 2, 6 and 18hrs. The statistical difference was calculated using Benjamini & Hochberg’s false discovery rate (FDR). Asterisk (*) denotes significant changes in expression (≤1.5-fold; FDR≤0.05) relative to untreated control ESCs. (E) RT-qPCR was used to quantify nascent RNA transcription at Nanog, Pou5f1 and Tfcp2l1 . Values represent relative Log 2 mean (± SEM) of n = 3 technical replicates. (F) ChIP-qPCR analysis of H3K27ac enrichment at the indicated regions. Bars represent the mean (± SEM) of n = 3 technical replicates from one immunoprecipitation.

Article Snippet: Comparative gene expression profiles were generated using the Illumina mouseWG-6, v2 (LBH589 and Hdac1 L/L ; Hdac2 L/wt ) or Agilent SurePrint G3 Mouse Gene Expression v2 8×60K microarray ( Hdac3 L/L ) according to manufacturer’s instructions.

Techniques: Microarray, Control, Expressing, Quantitative RT-PCR, Immunoprecipitation

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

Article Title: Suppression of Dynamical Network Biomarker Signals at the Predisease State ( Mibyou ) before Metabolic Syndrome in Mice by a Traditional Japanese Medicine (Kampo Formula) Bofutsushosan

doi: 10.1155/2020/9129134

Figure Lengend Snippet: The numbers of analyzed samples. Samples with insufficient quality for microarray assay were excluded.

Article Snippet: In order to investigate the gene expression profiles of each mouse, the Agilent SurePrint G3 Mouse Gene Expression 8 × 60K Microarray Kit (Agilent Technologies, Santa Clara, CA, USA) was used.

Techniques: Microarray

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

Article Title: Suppression of Dynamical Network Biomarker Signals at the Predisease State ( Mibyou ) before Metabolic Syndrome in Mice by a Traditional Japanese Medicine (Kampo Formula) Bofutsushosan

doi: 10.1155/2020/9129134

Figure Lengend Snippet: The numbers of analyzed samples. Samples with insufficient quality for microarray assay were excluded.

Article Snippet: On completion of the fragmentation reaction, 25 μ l of 2 × Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression 8 × 60K Microarray (Agilent) at 65°C for 17 hours in a rotating Agilent hybridization oven.

Techniques: Microarray