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Sample GSM3507583 Query DataSets for GSM3507583
Status Public on Mar 06, 2019
Title M2_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: IL-4 stimulation
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 SAMN10577479
SRA SRX5124384

Supplementary file Size Download File type/resource
GSM3507583_M2_1h_1.txt.gz 180.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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