{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jay Cao"],"organism":["Mus musculus"],"software":["HISAT2, Samtools"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16172"],"description":["Hypoxia-inducible factor 1α (HIF-1α) broadly orchestrates metabolic reprogramming in inflammatory macrophages.  However, how HIF-1α is activated in the earliest events following pattern recognition receptor activation remains unclear. We found that HIF-1α is functionally active shortly after macrophage inflammatory stimulation via a Rubicon (RUBCN)-NADPH-oxidase (NOX2) reactive oxygen species (ROS) axis, driving glycolysis, cytokine production, and bacterial killing before increased protein accumulation. Early HIF-1α stabilization primes inducible nitric oxide synthase (iNOS) expression and nitric oxide (NO) production, which subsequently suppresses electron transport chain function and induces mitochondrial dysfunction independently of RUBCN. These findings elucidate a temporally-coordina"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - RNA samples from bone marrow-derived macrophages (BMDMs) from unstimulated (control) and M(LPS+γ) macrophages after 6 hours and 24 hours of activation in Hif1a+/+ and Hif1a-/- macrophages were used for the experiment.","Nucleic Acid Extraction - BMDMs were lysed for RNA extraction using the RNAeasy kit (Qiagen). RNA integrity was analyzed on a Bioanalyzer RNA Pico 6000 chip at the Core Facility for Scientific Research – University of São Paulo (CEFAP-USP).","Library Construction - Complementary DNA library construction and sequencing were performed by BGI Global Genomics Services using the DNBSeq platform.","Sequencing - Complementary DNA library construction and sequencing were performed by BGI Global Genomics Services using the DNBSeq platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The raw reads were filtered with the SOAPnuke software (-n 0.001 -l 20 -q 0.4 -A 0.25 --cutAdaptor -Q 2 -G --minLen 100). Reads quality control was summarized by FastQC (Andrews, 2017) and visualized using the MultiQC software (Ewels et al., 2016). The reads were mapped to the genome using the HISAT2 software (Kim, et al., 2019) with default parameters. Samtools (Li, et al., 2009) software was used for converting and generating statistics from the SAM/BAM files. The reads were mapped to the genome using the HISAT2 software (Kim, et al., 2019) with default parameters. Samtools (Li, et al., 2009) software was used for converting and generating statistics from the SAM/BAM files."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-G400","Qiagen RNAeasy, Bioanalyzer QubitFluorometer, Agilent 2100, RNA Pico 6000 chip"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Jay Cao"],"additional_accession":[]},"is_claimable":false,"name":"Temporal Control of Macrophage Pro-inflammatory Phenotype by a Biphasic HIF-1α Regulatory Program","description":"Hypoxia-inducible factor 1α (HIF-1α) broadly orchestrates metabolic reprogramming in inflammatory macrophages.  However, how HIF-1α is activated in the earliest events following pattern recognition receptor activation remains unclear. We found that HIF-1α is functionally active shortly after macrophage inflammatory stimulation via a Rubicon (RUBCN)-NADPH-oxidase (NOX2) reactive oxygen species (ROS) axis, driving glycolysis, cytokine production, and bacterial killing before increased protein accumulation. Early HIF-1α stabilization primes inducible nitric oxide synthase (iNOS) expression and nitric oxide (NO) production, which subsequently suppresses electron transport chain function and induces mitochondrial dysfunction independently of RUBCN. These findings elucidate a temporally-coordina","dates":{"release":"2026-07-13T00:00:00Z","modification":"2026-07-13T18:14:22.205Z","creation":"2025-11-18T13:47:55.582Z"},"accession":"E-MTAB-16172","cross_references":{"ENA":["ERP185257"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0004184"]}}