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SRX365451: GSM1242511: M1_72h_rep3_miRNAseq; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiScanSQ) run: 1.7M spots, 40.1M bases, 33.9Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Transcriptome-based network analysis reveals a spectrum model of human macrophage activation [miRNA-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: Since transcriptional programs are further modulated on several levels including miRNAs we assessed the global spectrum of miRNA expression by miRNA-Seq in macrophages stimulated with IFN?, IL4 or with the combination of TNFa, PGE2 and P3C
Sample: M1_72h_rep3_miRNAseq
SAMN02378218 • SRS491825 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina HiScanSQ
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: size fractionation
Layout: SINGLE
Construction protocol: 5x106 -2x107 MΦ were harvested and total RNA including small RNAs was isolated. Small RNA libraries were generated from 1 μg total RNA with the TruSeq Small RNA Sample Preparation Kit (Illumina). After successful ligation of 3’ and 5’ adapters to RNA molecules, RNA was reverse-transcribed using SuperScript II reverse transcriptase (Invitrogen). cDNA was amplified by 11 PCR cycles with high-fidelity Phusion Polymerase (Finnzymes). cDNA with the size of miRNAs plus ligated adapters was purified on a pre-cast 6% Tris/Borate/EDTA polyacrylamide gel electrophoresis gel (Invitrogen).
Experiment attributes:
GEO Accession: GSM1242511
Links:
External link:
Runs: 1 run, 1.7M spots, 40.1M bases, 33.9Mb
Run# of Spots# of BasesSizePublished
SRR10134381,655,73340.1M33.9Mb2014-02-13

ID:
522394

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