Transcriptome profile in RAW264.7 cells in response to LPS stimulation

The lincRNA-Tnfaip3 is an early-primary gene controlled by the NF-κB signaling in murine macrophages. This study aims to measure the impact of lincRNA-Tnfaip3 knockdown on the transcriptome profile in cultured 264.7 macrophages in response to LPS stimulation. Cells were treated with a specific siRNA to knockdown lincRNA-Tnfaip3 and then exposed to LPS for stimulation. Cells treated with a scrambled non-specific siRNA were used as the control. Total RNA was collected for the genome-wide analysis. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4852A) was used for the genome-wide analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A). The RAW264.7 mouse macrophage cells were grown to 80% confluence for four groups: the siRNA control (Group A, cells treated with a non-specific scrambied siRNA control), the LPS-stimulated (Group B, cells treated with the siRNA control plus LPS stimulation), lincRNA-Tnfaip3 siRNA (Group C, cells treated with an siRNA to lincRNA-Tnfaip3), and lincRNA-Tnfaip3 siRNA/LPS stimulated (Group D, cells treated with the lincRNA-Tnfaip3 plus LPS stimulation). Cells were treated with the siRNAs for 24h, followed by additional culture for 4h in the presence or absence of LPS (E. coli LPS, 1 µg/ml). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.