{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Leng jiajie"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16586"],"description":["This dataset contains RNA sequencing data from mouse cardiac tissue collected 28 days after myocardial infarction (MI). The study investigates the effect of dietary erucic acid supplementation on post-MI cardiac fibrosis. All animals underwent MI surgery. The experimental group (MIEru, n=4) received a diet containing 20% erucic acid for the entire 28-day post-operative period. The control group (CON, n=4) received a standard diet without erucic acid supplementation following MI. RNA was extracted from whole heart tissue (with a focus on the fibrotic region/infarct border zone) and subjected to standard Illumina library preparation and paired-end sequencing. The data can be used to explore the transcriptional profile associated with post-MI remodeling and the impact of erucic acid on pathways related to fibrosis, inflammation, and metabolism."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The experimental diet was formulated by supplementing a standard rodent chow with erucic acid (cis-13-docosenoic acid, purity >99%) at a concentration of 20% by weight. The control group received an isocaloric diet with an equivalent amount of a standard fat source (e.g., soybean oil) replacing erucic acid. Both diets were produced by a specialized animal diet provider (e.g., Research Diets Inc.). Mice in the treatment group were provided with the 20% erucic acid diet ad libitum immediately after MI surgery, and the diet was continued for the entire 28-day duration until tissue collection.","Sample Collection - Total RNA was isolated from approximately 20-30 mg of snap-frozen left ventricular tissue. The tissue was homogenized in 1 mL of TRIzol Reagent (Thermo Fisher Scientific) using a mechanical homogenizer. RNA extraction followed the manufacturer's standard protocol. Briefly, after phase separation with chloroform, RNA was precipitated from the aqueous phase with isopropanol, washed with 75% ethanol, and dissolved in RNase-free water. RNA concentration and purity were assessed using a NanoDrop spectrophotometer, and RNA integrity was verified by agarose gel electrophoresis or Bioanalyzer (RIN > 7.0).","Nucleic Acid Extraction - RNA-seq libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, 1 µg of total RNA was used for poly(A) mRNA selection using oligo-dT beads. The enriched mRNA was fragmented, followed by first and second strand cDNA synthesis. The double-stranded cDNA was end-repaired, adenylated at the 3' ends, and ligated to Illumina-compatible adapters. Ligated fragments were then amplified by PCR (12-15 cycles) with index primers to generate final libraries. Library quality and size distribution were checked using an Agilent Bioanalyzer High Sensitivity DNA chip.","Library Construction - The final libraries were quantified by qPCR, pooled in equimolar amounts, and sequenced on an Illumina NovaSeq 6000 platform (Novogene Co., Ltd. or specify your sequencing facility). Sequencing was performed in a 150-base pair paired-end (PE150) configuration to a target depth of approximately 40 million reads per sample, following the manufacturer's standard sequencing protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequencing reads (FASTQ files) were first subjected to quality control using FastQC (v0.11.9). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39) with parameters: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The cleaned reads were then aligned to the mouse reference genome (GRCm39/ mm39) using the splice-aware aligner HISAT2 (v2.2.1). The resulting SAM files were sorted and converted to BAM format using SAMtools (v1.12). Gene-level read counts were generated from the aligned reads using featureCounts (part of Subread package v2.0.3) against the Ensembl gene annotation (release 105). Finally, the raw count matrix was normalized to generate Transcripts Per Million (TPM) values and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for downstream differential expression analysis."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Leng jiajie"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq analysis of cardiac fibrosis in mouse hearts 28 days post-myocardial infarction with (MIEru) or without (CONMI) dietary erucic acid supplementation","description":"This dataset contains RNA sequencing data from mouse cardiac tissue collected 28 days after myocardial infarction (MI). The study investigates the effect of dietary erucic acid supplementation on post-MI cardiac fibrosis. All animals underwent MI surgery. The experimental group (MIEru, n=4) received a diet containing 20% erucic acid for the entire 28-day post-operative period. The control group (CON, n=4) received a standard diet without erucic acid supplementation following MI. RNA was extracted from whole heart tissue (with a focus on the fibrotic region/infarct border zone) and subjected to standard Illumina library preparation and paired-end sequencing. The data can be used to explore the transcriptional profile associated with post-MI remodeling and the impact of erucic acid on pathways related to fibrosis, inflammation, and metabolism.","dates":{"release":"2026-03-25T00:00:00Z","modification":"2026-03-25T02:03:18.549Z","creation":"2026-02-16T07:42:56.6Z"},"accession":"E-MTAB-16586","cross_references":{"ENA":["ERP189157"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}