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SRX286014: GSM1146439: H3K4me3_M0_Macro_ChIPSeq; Homo sapiens; ChIP-Seq
3 ILLUMINA (Illumina HiScanSQ) runs: 13.2M spots, 603.8M bases, 369.1Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Transcriptome-based network analysis reveals a spectrum model of human macrophage activation [ChIP-Seq]
show Abstracthide Abstract
Macrophage activation is associated with profound transcriptional reprogramming. Although much progress has been made in the understanding of macrophage activation, polarization and function, the transcriptional programs regulating these processes remain poorly characterized. We stimulated human macrophages with diverse activation signals, acquiring a dataset of 299 macrophage transcriptomes. Analysis of this dataset revealed a spectrum of macrophage activation states extending the current M1 versus M2-polarization model. Network analyses identified central transcriptional regulators associated with all macrophage activation complemented by regulators related to stimulus-specific programs. Applying these transcriptional programs to human alveolar macrophages from smokers and patients with chronic obstructive pulmonary disease (COPD) revealed an unexpected loss of inflammatory signatures in COPD patients. Finally, by integrating murine data from the ImmGen project we propose a refined, activation-independent core signature for human and murine macrophages. This resource serves as a framework for future research into regulation of macrophage activation in health and disease. Overall design: To better understand active gene regulation in human macrophages during activation and differentiation in vitro with different stimuli ChIP-sequencing experiments were performed. Enrichment patterns of the permissive histone modification mark trimetylation of histone protein 3 (H3K4me3) and macrophage lineage-specific transcription factor PU.1 were analyzed.
Sample: H3K4me3_M0_Macro_ChIPSeq
SAMN02169215 • SRS428946 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiScanSQ
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Fixed or unfixed chromatin out of primary human macrophage lysates was sheared and histone-DNA or TF-DNA complexes isolated with antibody. Multiplex DNA libraries of both H3K4me3 as well as PU.1 bound DNA were generated using Illumina’s ChIP-Seq Sample Preparation Kit (Illumina; # IP-102-1001) and the Multiplexing Sample Preparation Oligonucleotide Kit (Illumina; # PE-400-1001) using approximately 10 ng DNA following the manufacturer’s instructions. Briefly, purified DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Klenow exo minus polymerase to generate a protruding 3′ A base used for adaptor ligation. Next, size selection of libraries was performed as follows: DNA libraries were agarose gel purified, DNA fragments with approximately 220 bp size excised and eluted using QIAquick Gel Extraction kit (Qiagen). After subsequent adapter ligation to the repaired ends, an amplification step was performed for 5 cycles with PCR primers 1.1 and 2.1 (Illumina; # IP-102-1001). During a second 13 cycles amplification step multiplex PCR primers were added to the DNA libraries to construct multiplex sequencing libraries. For PU.1 DNA libraries multiplex PCR primers were added directly after adapter ligation to the amplification mix and 18 cycles of amplification were performed. After amplification steps DNA was purified.
Experiment attributes:
GEO Accession: GSM1146439
Links:
External link:
Runs: 3 runs, 13.2M spots, 603.8M bases, 369.1Mb
Run# of Spots# of BasesSizePublished
SRR8666284,107,918180.7M119Mb2015-07-22
SRR8666291,460,50078.9M39.8Mb2015-07-22
SRR8666307,647,789344.2M210.3Mb2015-07-22

ID:
403826

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