chromatin immunoprecipitation followed by microarray hybridization (chip-chip) assay protocol  (NimbleGen Systems GmbH)

Journal: Cell reports

Article Title: IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages

doi: 10.1016/j.celrep.2018.09.002

Figure Lengend Snippet: (A) Control and IFIT1-depleted THP1 cells were stimulated with 100 ng/mL LPS for 1, 2, 4, 6, and 24 hr, and transcriptional responses were measured by microarray. The upper heatmap shows genes with substantial expression increases in WT cells compared to their expression level in IFIT1-depleted cells. The lower heatmap shows the sum of the expression difference between WT and IFIT1-depleted cells across the time course . (B and C) The network connections of genes that showed (B) enhanced expression (group 1; ) or (C) reduced expression (group 2; ) in IFIT1-depleted cells, as determined by IPA. (D) Transfection of siRNA into IFIT1 shRNA-expressing cells sustains a stable suppression of IFIT1 induction in response to 100 ng/mL LPS. (E and F) Control and IFIT1-depleted THP1 cells (E) or human primary macrophages (F) were stimulated with 100 ng/mL LPS, and secreted IFN-β protein was measured by ELISA. Data are representative of two (A) or three (D–F) independent experiments. Data in (D)–(F) are expressed as mean SD; *p < 0.05, **p < 0.01 (two-way ANOVA followed by Sidak’s multiple comparison test). See also and , , and .

Article Snippet: Each condition was represented by two biological replicates. cRNA amplification and labeling were performed using the Illumina TotalPrep RNA Amplification Kit (Ambion), microarray hybridization and scanning protocols followed standard Illumina protocols.

Techniques: Microarray, Expressing, Transfection, shRNA, Enzyme-linked Immunosorbent Assay

Journal: Cell reports

Article Title: IFIT1 Exerts Opposing Regulatory Effects on the Inflammatory and Interferon Gene Programs in LPS-Activated Human Macrophages

doi: 10.1016/j.celrep.2018.09.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Each condition was represented by two biological replicates. cRNA amplification and labeling were performed using the Illumina TotalPrep RNA Amplification Kit (Ambion), microarray hybridization and scanning protocols followed standard Illumina protocols.

Techniques: Recombinant, Microarray, shRNA, Software