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Sample GSM4880560 Query DataSets for GSM4880560
Status Public on Mar 03, 2023
Title naMDM-Blood6
Sample type SRA
 
Source name monocyte-derived macrophages
Organism Homo sapiens
Characteristics individual: 6
tissue: blood
cell type: pan monocyte
treatment: Unactivated
Treatment protocol Monocytes were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to generate their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours.
Growth protocol Peripheral blood samples were collected from healthy donors. Pan monocytes were sorted using microbeads (negative sorting) according to the manufacturer's instructions (Miltenyi Biotec, Somerville, MA, USA), cultured in RPMI 1640 with glutamine (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum.
Extracted molecule total RNA
Extraction protocol RNA extracted using the RNeasy mini kit (QIAGEN)
RNA sequencing libraries were prepared from 1 µg total RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit, which allows strand specific sequencing to be performed. A first step of polyA selection using magnetic beads was performed to allow sequencing of polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Sequencing was carried out on a NovaSeq 6000 instrument from Illumina based on a 2*100 cycle mode (paired-end reads, 100 bases).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description sample name in manuscript:
MDM
Monocytes from blood 6 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) during 6 days to induce their differentiation.
D367T25
Data processing Raw sequencing reads were aligned on the human hg38 reference genome using the STAR mapper [7] (2.5.3a), up to the generation of a raw count table per gene (Gencode annotation v26). Expressed genes (TPM>=1 in at least one sample) have then been selected for downstream analysis.The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3) functions were applied to detect genes with differential expression between untreated and EGF samples. Genes with an adjusted pvalue < 0,05 were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts
 
Submission date Nov 04, 2020
Last update date Mar 03, 2023
Contact name Nicolas Servant
E-mail(s) Nicolas.Servant@curie.fr
Organization name Institut Curie
Street address 26 rue d'ulm
City Paris Cedex 05
ZIP/Postal code 75248
Country France
 
Platform ID GPL18573
Series (2)
GSE160862 Gene expression analysis in inflammatory macrophages [batch1]
GSE160864 Discovery of a druggable copper-signaling pathway that drives inflammation
Relations
BioSample SAMN16667019
SRA SRX9434537

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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