|
| Status |
Public on Apr 30, 2021 |
| Title |
Macrophage_M2_Succinate_3 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood monocyte derived macrophages
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Succinate
polarisation: M2
donor: 3
|
| Treatment protocol |
M2 macrophages were treated with 500 μM succinate only, or in combination with either a SUCNR1/GPR91 antagonist (NF-56-EJ40, 1 μM) or a Gq inhibitor (YM-254890, 1 μM).
|
| Growth protocol |
CD14+ monocytes were purified from peripheral blood by MACS and differentiated to macrophages over 7 days in R10 supplemented with 50 ng/ml M-CSF. After 7 days, adherent macrophages were polarised to the M1 or M2 state by 24 hours treatment with 50 ng/ml IFN-γ and 10 ng/ml LPS or 20 ng/ml IL-4 and 20 ng/ml IL-13, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Adherent macrophages were lysed directly with TRIzol reagent and total RNA was extracted using the Qiagen RNeasy Micro kit (Qiagen, Hilden Germany).
PolyA-selected, strand-specific RNA-seq libraries were prepared for BGI DNBSEQ-G400 or Illumina HiSeq 4000 sequencing according to standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
Samples were demultiplexed and sequences converted to FASTQ format using bcl2fastq.
Adapter sequences were trimmed using PEAT-1.2.4 before mapping to the hg19 reference genome using STAR 2.6 with default parameters.
Alignments were filtered using samtools 1.9 to retain only uniquely aligned, properly-paired reads.
Gene-level read counts were obtained using featureCounts (from Rsubread 1.32.4) in R, and raw counts were TMM normalised and analysed with edgeR 3.30.3.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix containing raw gene-level read counts for all samples.
|
| |
|
| Submission date |
Apr 29, 2021 |
| Last update date |
Apr 30, 2021 |
| Contact name |
Christopher O'Callaghan |
| E-mail(s) |
chris.ocallaghan@ndm.ox.ac.uk
|
| Phone |
+44 (0)1865 287794
|
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Medicine
|
| Lab |
O'Callaghan Lab - Henry Wellcome Building for Molecular Physiology
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE173611 |
Extracellular Succinate Hyperpolarizes M2 Macrophages through SUCNR1/GPR91-Mediated Gq Signaling |
|
| Relations |
| BioSample |
SAMN18927069 |
| SRA |
SRX10715613 |
