{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Leo Zeef"],"organism":["Mus musculus"],"software":["Bcl2fastq v2.20.0.422"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15467"],"description":["Chronic kidney disease (CKD) is characterised by kidney fibrosis and represents a major public health concern. Alport syndrome, a common monogenic cause of kidney failure caused by genetic variants in the type IV collagen genes COL4A3, COL4A4or COL4A5, leads to abnormal basement membrane remodelling and kidney fibrosis. Understanding the dynamics and mechanisms of kidney matrix remodelling is crucial for directing emerging gene therapies and developing non-invasive biomarkers to detect and stage kidney fibrosis earlier, ultimately enabling risk stratification and timely intervention. To define the temporal and spatial dynamics of kidney matrix remodelling, we applied a multi-omics strategy in a Col4a5-/-mousemodel of X-linked Alport syndrome, integrating stable isotope metabolic labelling, deep proteomicprofiling, bulk RNA sequencing, super-resolution imaging, and bioinformatic prediction.Transcriptomic profiling identified enrichment of extracellular matrix degradation pathways and upregulation of matrix proteases. This being the RNA-seq component."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The care and use of all mice in this study was carried out in accordance with the UK Home Office regulations, UK Animals (Scientific Procedures) Act of 1986 under the Home Office Project Licences: P1AE9A736, PP4262564, PP708858and LO45CA465. Mice were maintained in 12-h light/12-h dark cycleat 20°C to 22°C, humidity of 40-50%, with ad libitumaccess to water. Mice were fed “light diet” (standard rodent chow) or “heavy diet”; Mouse Express L-Lysine (13C6, 99%; MLK-LYS-C) purchased from CK Isotopes Ltd (UK), as per the labelling experimental design. For the pulse-time experiments, wildtype C57BL/6J mice (Charles River, UK) were employed. For the RNA sequencing experiment and Alport proteomics study, Col4a5−/mice were employed. These mice were obtained from the International Mouse Phenotyping Consortium [doi: 10.1038/nature19356]and the line was generated by deletion of the critical exon 36, resulting in the absence of the collagen-α5(IV) protein, using the published allele map [DOI: 10.1038/ng.3901]. Col4a5-/mice were on a C57BL/6J background. Heterozygous females were crossed with wildtype males and hemizygous male offspring were used to study Alport syndrome and wildtype male littermates were used as a control. All mice gained weight in accordance with reference laboratory data for C57BL/6J mice.  Mice were sacrificed by cervical neck dislocation and kidneys were immediately dissected. The surrounding fat, adrenal glands and renal capsule were removed, and kidneys used for RNA sequencing and proteomic experiments were snap frozen and stored at -80oC. Kidneys used for immunofluorescence imaging were embedded in OCT compound (PFM medical UK Ltd, cat ref #PRC/OCT) and stored at -80oC until cryosectioning.","Sequencing - Paired end sequencing","Nucleic Acid Extraction - Total RNA was extracted from 30 mg of kidney tissue using TRIzol reagent (Invitrogen). In brief, 1 ml of TRIzol was added to minced kidney tissue and homogenised with a micro pestle. Following phase separation with 0.2 ml of Chloroform, the aqueous phase was mixed with 0.5 ml of isopropanolol and centrifuged for 10 minutes at 12,000 x g at 4 ºC. RNA precipitate was washed with 75% ethanol. RNA in 100 L of RNase-free H2O was cleaned up using RNeasy mini column (QIAGEN) as per manufacturers protocol. RNA was eluted in nuclease-free water and concentration measured using a NanoDrop 2000 (Thermo Fisher Scientific). The quality of all resuspended mRNA was measured using a QubitTM Fluorometer (Thermo Fisher Scientific) and RNA integrity measured using a 2200 TapeStation (Agilent Technologies) to ensure good quality for downstream analysis.","Library Construction - Illumina stranded mRNA library"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The reads were mapped against the reference human genome (hg38) and counts per gene were calculated using annotation from GENCODE M32  (http://www.gencodegenes.org/) using STAR_2.7.7a (PMID: 23104886).","Data Transformation - Normalisation was with DESeq2 v1.40.2"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Leo Zeef"],"additional_accession":[]},"is_claimable":false,"name":"Basement membrane turnover and circulating matrix biomarkers in kidney disease","description":"Chronic kidney disease (CKD) is characterised by kidney fibrosis and represents a major public health concern. Alport syndrome, a common monogenic cause of kidney failure caused by genetic variants in the type IV collagen genes COL4A3, COL4A4or COL4A5, leads to abnormal basement membrane remodelling and kidney fibrosis. Understanding the dynamics and mechanisms of kidney matrix remodelling is crucial for directing emerging gene therapies and developing non-invasive biomarkers to detect and stage kidney fibrosis earlier, ultimately enabling risk stratification and timely intervention. To define the temporal and spatial dynamics of kidney matrix remodelling, we applied a multi-omics strategy in a Col4a5-/-mousemodel of X-linked Alport syndrome, integrating stable isotope metabolic labelling, deep proteomicprofiling, bulk RNA sequencing, super-resolution imaging, and bioinformatic prediction.Transcriptomic profiling identified enrichment of extracellular matrix degradation pathways and upregulation of matrix proteases. This being the RNA-seq component.","dates":{"release":"2026-05-27T00:00:00Z","modification":"2026-05-27T13:36:10.955Z","creation":"2025-08-08T15:23:07.842Z"},"accession":"E-MTAB-15467","cross_references":{"ENA":["ERP178571"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}