|
Status |
Public on Mar 06, 2019 |
Title |
M0_1h_1 |
Sample type |
SRA |
|
|
Source name |
Bone marrow-derived macrophage
|
Organism |
Mus musculus |
Characteristics |
strain/background: C57BL/6 genotype/variation: Wild type cell type: Bone marrow-derived macrophage treatment: No stimulus control 1h time point: 1h
|
Treatment protocol |
BMMs were stimulated in complete RPMI supplemented with CSF-1 for indicated times with a combination of 20 or 100 ng/mL LPS (SIGMA), 50 ng/mL IFNg or 20 ng/mL IL-4 (all Peprotech) 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 |
Total RNA was extracted with the RNAqueous-Micro Total RNA Isolation Kit (Thermo Fisher Scientific) and quantified using Qubit 2.0 (Thermo Fisher Scientific) following the manufacturer’s instructions. Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HiSeq 3000 (Illumina).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
Description |
mRNA
|
Data processing |
Sequenced libraries were processed with the Galaxy platform and deepTools (Afgan et al., 2016; Ramírez et al., 2016). STAR (Dobin et al., 2013) for trimming and mapping. featureCounts (Liao et al., 2014) to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 (Love et al., 2014) to determine differentially expressed genes and generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute). Genome_build: GRCm38 Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw read counts for every sample.
|
|
|
Submission date |
Dec 10, 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 (1) |
GSE123596 |
Collateral DNA damage and NAD+ dependence caused by reactive oxygen species signaling in inflammatory macrophages |
|
Relations |
BioSample |
SAMN10577491 |
SRA |
SRX5124372 |