Project description:Transcriptomic analysis of the temporal changes induced in mouse bone marrow derived macrophages (BMDMs) by the cytokine Interferon-beta over a timecourse of 0 to 24 hours of treatment. We set out to study the transcriptional events in mouse macrophages over time following stimulation with Interferon-beta. Mouse bone marrow derived macrophages were stimulated for 1, 2, 4, 8 and 24 hours with 10U/mL mouse interferon-beta or left untreated.
Project description:ATAC-seq profiling of Nfat5 KO and wild type macrophages derived from bone marrow (primary cells), treated or not with Lipopolysaccharide (LPS).
Project description:The systematic temporal gene expression analysis of primary macrophages activated under immune (interferon-gamma) and productive viral infection with murine cytomegalovirus (mCMV). The primary objective of the study is to define, in an unbiased manner, cause-and-effect relationships in the program of gene activation in this cellular system. The even spacing and time intervals (every 30 minutes) makes this study amenable to modelling of gene networks in the system. A kinetic analysis of mCMV infection on the gene expression of murine (BALB/c) bone marrow-derived macrophages (BMDMs) over the first 12 hours, sampling every 30 minutes. Agilent mouse genome arrays were used to determine the differences in gene expression between mock and mCMV infected. The 25 samples collected for the mock infected were pooled and treated as a pooled control. Pooled control was labelled with Cy3 dye and hybridised with every other sample (labelled with Cy5 dye) = 25 dual-dye array hybridisations. The reference channel of the dual-channel hybridisations was only used to normalise the expression of the test channel, rather than used to calculate ratio data. Thus, the normalised data represent log2 single-channel data.
Project description:Bone marrow-derived macrophages, Unstimulated DMSO Bone marrow-derived macrophages, Unstimulated + I-BET (GSK525762A) Bone marrow-derived macrophages, LPS 1h DMSO Bone marrow-derived macrophages, LPS 1h + I-BET (GSK525762A) Bone marrow-derived macrophages, LPS 2h DMSO Bone marrow-derived macrophages, LPS 2h + I-BET (GSK525762A) Bone marrow-derived macrophages, LPS 4h DMSO Bone marrow-derived macrophages, LPS 4h + I-BET (GSK525762A) LPS (100 ng/mL) was purchased from Sigma. Bone Marrow-derived macrophages (BMDMs) were differentiated from C57BL/6 bone marrow using 5 ng/mL each of recombinant M-CSF and IL-3 (Peprotech) for 7 days as described (Jeffrey et al, Nature Immunology, 2006). 2 x10^6 BMDMs were treated with DMSO or 1 μM of I-BET for 30 minutes before the addition of LPS (100 ng/mL) for 1, 2 or 4h. Unstimulated control samples were incubated with I-BET only for 1 hour. 500 ng of total RNA from 3 independent samples per group was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) and hybridized to Illumina MouseRef-8 v2.0 expression BeadChip kits. The chips were scanned using Illumina BeadArray Reader. 3 biological replicates and 4 timepoints