|
| Status |
Public on Jan 16, 2019 |
| Title |
M0.bigwig |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
stimulation: No stimulus control
|
| 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 |
SAMN09954304 |
| SRA |
SRX4639846 |
