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Status |
Public on Mar 03, 2023 |
Title |
aMDM-Blood1 |
Sample type |
SRA |
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Source name |
activated monocyte-derived macrophages
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Organism |
Homo sapiens |
Characteristics |
individual: 1 tissue: blood cell type: pan monocyte treatment: Activated
|
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.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
sample name in manuscript: act. MDM Monocytes from blood 1 were exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF, 100 ng/mL) to induce their differentiation. After 5 days of differentiation, macrophages were activated with IFN-gamma (20 ng/mL) and LPS (100 ng/mL) during 24 hours. D367T02
|
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
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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 |
SAMN16667012 |
SRA |
SRX9434530 |