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Sample GSM4320178 Query DataSets for GSM4320178
Status Public on Jul 04, 2020
Title Stimulated_M1_18h_3
Sample type SRA
 
Source name Macrophage stimulated with IFNy and LPS
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Bone Marrow derived Macrophages
tissue: Bone Marrow
Treatment protocol Resting Macrophages (M0), or Macrophages stimulated with with 50 ng ml–1 IFN-γ and 20 ng ml-1 LPS (γ+LPS), were treated with 50 μM T863 for DGAT1 inhibition
Growth protocol Bone marrow cells were grown in complete medium (RPMI-1640 medium containing 10 mM glucose, 2 mM L-glutamine, 100 U ml–1 penicillin-streptomycin and 10% FCS) with 20 ng ml–1 murine macrophage colony- stimulating factor 1 (CSF-1; Peprotech) for 7 days, and supplemented with CSF-1 on days 3 and 5.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the PureLink RNA Mini kit (Ambion) and quantified using Qubit 2.0.
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced using the HiSeq 3000 (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description Macrophage stimulated with IFNy and LPS
Data processing Sequenced libraries were analyzed with SnakePipes 1.2.0
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: raw read counts matrix containing count for every sample
 
Submission date Feb 19, 2020
Last update date Jul 04, 2020
Contact name Immunometabolism Department
E-mail(s) dsaninp1@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)
GSE145523 Triacylglycerol synthesis enhances macrophage inflammatory function
Relations
BioSample SAMN14134890
SRA SRX7748673

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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