{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Menghua Liu"],"organism":["Rattus norvegicus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16261"],"description":["In renal tubulointerstitial fibrosis (TIF), aberrant changes in renal drug transporters severely disrupt systemic drug disposition, leading to reduced therapeutic efficacy or increased toxicity. Although we have previously documented transporter alterations in TIF, the underlying epigenetic mechanisms remain unknown. This study aims to map the DNA methylation landscape of TIF, elucidate the epigenetic network governing transporter dysregulation, and provide mechanistic insights to support safer drug use in CKD."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Raw data were processed and aligned using Bismark software to determine cytosine methylation levels. Differentially methylated regions (DMRs) were identified using the dispersion shrinkage for sequencing data (DSS) algorithm with a Wald test (Bonferroni-adjusted p < 0.00005, Δmethylation ≥ 0.1), and subsequently annotated to their associated genes","Nucleic Acid Extraction - Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) following the manufacturer’s instructions. DNA was quantified with Qubit dsDNA BR and checked for integrity (agarose gel ≥20 kb, 260/280 ≥1.8)","Library Construction - DNA ( ~ 350 bp) was fragmented, end-repaired, A-tailed, and ligated to bisulfite-compatible adaptors, followed by bisulfite conversion. Sequencing libraries were constructed and quality-checked, then sequenced.","Sample Collection - Kidney cortex (~30 mg) was dissected from 8-week-old male Sprague–Dawley rats under isoflurane anesthesia, immediately snap-frozen in liquid nitrogen, and stored at –80 °C until DNA extraction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Paired-end reads were adapter-trimmed and quality-filtered with Trim Galore v0.6.7 (–paired –rrbs). Clean reads were aligned to the Rattus norvegicus Rnor_6.0 genome using Bismark v0.23.1 with default bowtie2 settings. Duplicate reads were removed with deduplicate_bismark. Methylation calls were extracted using the bismark_methylation_extractor module; coverage ≥10× was required for inclusion. CpG-site β-values were calculated as β = methylated_reads / (methylated_reads + unmethylated_reads). β-values were normalized with the SWAN method (minfi v1.40) to correct for probe-type bias. Differential methylation was assessed using limma-voom; sites with |Δβ| ≥0.1 and FDR <0.05 were considered significant. The final normalized β-matrix and DMR list are provided as processed data files."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["methylation profiling by high throughput sequencing"],"species":["Rattus norvegicus"],"pubmed_authors":["Menghua Liu"],"additional_accession":[]},"is_claimable":false,"name":"DNA methylation atlas of rat kidney under tubulointerstitial fibrosis","description":"In renal tubulointerstitial fibrosis (TIF), aberrant changes in renal drug transporters severely disrupt systemic drug disposition, leading to reduced therapeutic efficacy or increased toxicity. Although we have previously documented transporter alterations in TIF, the underlying epigenetic mechanisms remain unknown. This study aims to map the DNA methylation landscape of TIF, elucidate the epigenetic network governing transporter dysregulation, and provide mechanistic insights to support safer drug use in CKD.","dates":{"release":"2025-12-14T00:00:00Z","modification":"2026-05-28T21:13:33.07Z","creation":"2025-11-21T19:19:06.39Z"},"accession":"E-MTAB-16261","cross_references":{"ENA":["ERP185497"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002761","EFO_0005518","EFO_0003816","EFO_0004184"]}}