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Sample GSM3375040 Query DataSets for GSM3375040
Status Public on Jan 16, 2019
Title M2_Val.bigwig
Sample type SRA
 
Source name bone marrow derived macrophage
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: bone marrow
stimulation: IL-4 and PGE2
Treatment protocol BMMs were stimulated in complete RPMI supplemented with CSF-1 for indicated times with a combination of 20 ng/mL IL-4 (Peprotech), 10 μM PGE2 (SIGMA) or 10 nM valinomycin (SIGMA) under 5% CO2, atmospheric oxygen, at 37°C in a humidified incubator.
Growth protocol Mature bone marrow derived macrophages (BMMs) were obtained at day 7 of culture of bone marrow cells in 20 ng/mL CSF-1 (Peprotech) in RPMI medium containing 10% fetal bovine serum, 4 mM L-glutamine, 100 U/mL penicillin/streptomycin (complete RPMI) (all Gibco).
Extracted molecule total RNA
Extraction protocol 5x10^4 BMMs treated for 6 h as described were washed in PBS and then lysed in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630 (all SIGMA). Nuclei were then spun down and then resuspend in 25 μl TD (2x reaction buffer), 2.5 μL TDE1 (Nextera Tn5 Transposase) and 22.5 μL nuclease-free water, incubated for 30 min at 37°C. DNA was purified with the Qiagen MinElute PCR Purification Kit (Thermo Fisher Scientific).
PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol. Libraries were quantified with the Qubit and submitted for sequencing with a HISeq 3000 (Illumina)
 
Library strategy ATAC-seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Data processing Sequenced samples were trimmed with Trimmomatic (Bolger et al., 2014)
Mapped using Bowtie2 (Langmead and Salzberg, 2012)
Replicate mapped files merged with SAM tools (Li et al., 2009).
Coverage files were generated with deepTools (Ramírez et al., 2016). Open chromatin and differentially regulated chromatin was detected with MACS2 (Zhang et al., 2008) with a p value < 1x10-7 and a q value of less than 0.1 and a 2 fold enrichment threshold.
Genome_build: GRCm38
Supplementary_files_format_and_content: Coverage files in bigwig format
 
Submission date Sep 04, 2018
Last update date Feb 17, 2020
Contact name Immunometabolism Department
E-mail(s) jcurti29@jhmi.edu
Organization name Johns Hopkins University
Department Immunometabolism
Street address 1650 Orleans Street
City Baltimore
State/province Maryland
ZIP/Postal code 21287
Country USA
 
Platform ID GPL21493
Series (2)
GSE119463 Mitochondrial Membrane Potential Regulates Nuclear Gene Expression in Macrophages Exposed to PGE2 (ATAC-seq)
GSE119521 Mitochondrial Membrane Potential Regulates Nuclear Gene Expression in Macrophages Exposed to PGE2
Relations
BioSample SAMN09954302
SRA SRX4639848

Supplementary file Size Download File type/resource
GSM3375040_M2_Val.bigwig 151.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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