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Series GSE58310 Query DataSets for GSE58310
Status Public on Sep 26, 2014
Title Epigenetic programming during monocyte to macrophage differentiation and trained innate immunity
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Monocyte differentiation into macrophages represents one of the cornerstone processes in innate host defense. In addition, immunological imprinting of either tolerance or trained immunity after an initial infection determines the functional fate of innate immune cells and the susceptibility of the host to secondary infections. Here we comprehensively characterize the epigenetic profiles of these functional states relative to healthy adult naïve monocytes. Inflammatory and metabolic pathways are strongly modulated in the derived macrophages, including decreased activation of inflammasome components. The cAMP-dependent signaling pathway is remodeled and adrenergic signaling was functionally implicated in trained innate immunity induction in vivo. Interestingly, -Glucan trains innate immune cells through extensive remodeling of distal regulatory region-bound histone acetylation, resulting in a sizeable exclusive epigenomic signature. Accordingly, genome-wide transcription factor footprint analysis reveals a specific transcription factor repertoire at trained cell-specific enhancers when recouped with epigenetic data, forming a rich hypothesis generator to manipulate innate immunity.
Overall design Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum. Monocytes were collected at different time points (0 h and 6 d after treatment) and counted before further treatment for chromatin immunoprecipitation, RNA or DNaseI treatment. Different donor Buffycoats (BC) were used as independent replicates. Replicates were generated for all the profiles including ChIPseq,RNAseq and DNaseIseq.
Contributor(s) Saeed S, Quintin J, Rao NA, Kerstens H, Aghajanirefah A, Matarese F, Cheng S, Ratter J, Berentsen K, van der Ent M, Sharifi N, Janssen-Megens E, Ter Huurne M, Mandoli A, Ng A, Burden F, Downes K, Frontini M, Kumar V, Giamarellos-Bourboulis EJ, Ouwehand WH, van der Meer JW, Joosten LA, Wijmenga C, Martens JH, Xavier RJ, Logie C, Netea MG, Stunnenberg HG
Citation(s) 25258085
Submission date Jun 09, 2014
Last update date May 15, 2019
Contact name Hindrik Kerstens
Organization name Radboud University
Department Molecular Biology
Lab Stunnenberg
Street address Geert Grooteplein Zuid 26
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (64)
GSM1406294 Blueprint_S00NJBH1_H3K4me3
GSM1406295 Blueprint_S00NJBH1_H3K27ac
GSM1406296 Blueprint_S00NJBH1_H3K4me1
BioProject PRJNA251977
SRA SRP043033

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Supplementary file Size Download File type/resource
GSE58310_BGall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed.gz 3.5 Mb (ftp)(http) BED
GSE58310_Buffy101112Day0merge.hg19.hotspot.twopass.fdr0.01.bed.gz 1.8 Mb (ftp)(http) BED
GSE58310_GeneExpression.csv.gz 3.2 Mb (ftp)(http) CSV
GSE58310_LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed.gz 2.2 Mb (ftp)(http) BED
GSE58310_RAW.tar 3.0 Gb (http)(custom) TAR (of BED, WIG)
GSE58310_RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed.gz 2.4 Mb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file

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