{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Liwu Zeng"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15816"],"description":["Mouse bone marrow-derived macrophages were extracted from the tibia, fibula and femur of C57BL/6J mice and cultured in DMEM medium containing 10% fetal bovine serum (FBS) (Gibco), 1% penicillin-streptomycin and 20ng/ml M-CSF for 7 days. BMDM was either continuously treated with 10ng/ml LPS for 7 hours or pretreated with 10 mM ITA or Mesa for 4 hours, followed by stimulation with 10 ng/mL LPS for 3 hours. After that, the culture medium was discarded and 1ml of RNAiso Plus was added to each well. The samples were stored at -80℃ and quantitatively analyzed using the sequencing platform of the Beijing Institute of Genomics."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols.","Nucleic Acid Extraction - RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.","Sample Collection - WT BMDMs were inoculated in 6-well plates. First, they were pretreated with 10 mM itaconate or mesaconate for 4 hours, then treated with 10ng/ml LPS for 3 hours. After that, the culture medium was discarded and 1ml of RNAiso Plus was added to each well. The samples were stored at -80℃ and quantitatively analyzed using the sequencing platform of the Beijing Institute of Genomics.","Sequencing - Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter- Quality limit. 0.05). Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomicbenchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost. 3 length fraction.0.8 similarity fraction: 0.8). Read count extraction and normalization were performed using CLC genomic benchwork"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - To enable comparisons of transcript abundance both within and between samples, raw read counts were normalized to account for sequencing depth and gene length. The normalized values are reported as Fragments Per Kilobase of transcript per Million mapped fragments (FPKM)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Liwu Zeng"],"additional_accession":[]},"is_claimable":false,"name":"Mesaconate Attenuates LPS/D-GalN-Induced Acute Liver Failure by Enhancing HIF-1α-Mediated AXL-Dependent Efferocytosis","description":"Mouse bone marrow-derived macrophages were extracted from the tibia, fibula and femur of C57BL/6J mice and cultured in DMEM medium containing 10% fetal bovine serum (FBS) (Gibco), 1% penicillin-streptomycin and 20ng/ml M-CSF for 7 days. BMDM was either continuously treated with 10ng/ml LPS for 7 hours or pretreated with 10 mM ITA or Mesa for 4 hours, followed by stimulation with 10 ng/mL LPS for 3 hours. After that, the culture medium was discarded and 1ml of RNAiso Plus was added to each well. The samples were stored at -80℃ and quantitatively analyzed using the sequencing platform of the Beijing Institute of Genomics.","dates":{"release":"2025-11-15T00:00:00Z","modification":"2026-05-28T09:55:22.574Z","creation":"2025-10-22T13:43:30.848Z"},"accession":"E-MTAB-15816","cross_references":{"ENA":["ERP182703"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}