Transcriptomics,Genomics

Dataset Information

22

0-12 hour transcriptional response of mouse bone marrow-derived macrophages to stimulation by LPS


ABSTRACT: Innate immune response to pathogens is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of the response to LPS have been identified, the temporal complexity of gene expression changes strongly suggest that additional layers of regulation remain to be uncovered. This study was done to examine response of mouse bone marrow-derived macrophages to stimulation with LPS over time. Bone marrow-derived macrophages from C57BL/6J mice were incubated in the presence of LPS for 1, 4 or 12 h, while the control group was incubated under same conditions for 4 h in the absence of the LPS. RNA isolated from these macrophages was analyzed using the Affymetrix Mouse Exon Array 1.0 ST. Overall design: Two sets of three female mice (strain C57BL/6J) were sacrificed at 8-12 weeks of age, and macrophages were derived from the femoral bone marrow using rhM-CSF. On day six, macrophages were divided into two treatment groups per animal, for a total of 12 samples. LPS was introduced into the medium for nine samples (one from each animal) at 10 ng/mL on day seven, and after 1, 4 or 12 h of incubation, RNA was isolated using TRIzol. Three sets of un-stimulated macrophages were harvested at 4 h and RNA isolated with TRIzol. Labeled cRNA derived from the RNA samples was hybridized to Affymetrix Mouse Exon Array 1.0 ST GeneChips. Microarray data were processed using Affymetrix power tools and brain-array CDFs (v 18.0)

INSTRUMENT(S): [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [Mm_ENTREZG_v18]

SUBMITTER: Aderem Lab  

PROVIDER: GSE100059 | GEO | 2017-06-16

SECONDARY ACCESSION(S): PRJNA390608

REPOSITORIES: GEO

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Publications

Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.

Askovich Peter S PS   Ramsey Stephen A SA   Diercks Alan H AH   Kennedy Kathleen A KA   Knijnenburg Theo A TA   Aderem Alan A  

PloS one 20170918 9


The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of this response have been identified, the temporal complexity of gene expression changes in response to pathogen-associated molecular pattern receptor stimulation strongly suggest that additional layers of regulation remain to be uncovered. The evolved pathogen response program in mammalian innate immune cells is u  ...[more]

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