{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Antonios Papadakis"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16217"],"description":["The goal of this study is to investigate the biological role of the podocyte-specific long non-coding RNA Wt1os (human ortholog WT1-AS) and its contribution to glomerular health and disease.  We generated a Wt1os loss-of-function mouse model and assessed kidney morphology and function using histological techniques and high-resolution microscopy. Glomerular transcriptomes were profiled by total RNA sequencing. This dataset contains total RNA-Seq data from 3 wild type and 3 Wt1os loss-of-function mutant mice."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated from pelleted glomeruli using the Direct-zol RNA Kit (Zymo Research, USA) according to the manufacturer’s protocol. RNA concentrations were measured with the Qubit™ RNA Broad Range assay kit (Invitrogen), and RNA integrity was validated using the Tape Station system (Agilent).","Library Construction - Sequencing libraries were prepared with the Illumina Stranded TruSeq Ribo Zero protocol","Sample Collection - Mice were sacrificed by cervical dislocation. Both kidneys were collected with the abdominal aorta attached. Kidneys were perfused through the renal arteries with magnetic beads (Dynabeads M-450 Tosylactivated, Thermo Fisher Scientific) in HBSS. Perfused kidneys were minced and incubated in digesting solution (1 mg/mL collagenase type II, 0.75 mg/mL pronase E, and 100 U/mL DNase I in HBSS) for 15 minutes at 37°C. Digested tissue was filtered through a 100-μm strainer twice. Glomeruli were isolated using magnetic separation, washed twice in HBSS, pelleted, and stored at -80°C.","Sequencing - Paired end sequencing on Illumina NovaSeq 6000, 100 bp"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw sequencing reads were processed using the nf-core/rnaseq pipeline version 3.13.2 (doi:10.5281/zenodo.1400710) with Nextflow version 23.04.1.5866, executed within a Singularity container. Quality and adapter trimming were performed using Trim Galore with default parameters.  Transcript-level quantification was performed using Salmon with the following parameters: --numBootstraps 100, --validateMappings, --gcBias, and --seqBias. These parameters were applied to improve quantification accuracy and reduce potential biases related to sequence composition and fragment GC content."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Antonios Papadakis"],"additional_accession":[]},"is_claimable":false,"name":"Wt1os lncRNA as a Novel Regulator of Podocyte Function (RNA-Seq of mouse glomeruli)","description":"The goal of this study is to investigate the biological role of the podocyte-specific long non-coding RNA Wt1os (human ortholog WT1-AS) and its contribution to glomerular health and disease.  We generated a Wt1os loss-of-function mouse model and assessed kidney morphology and function using histological techniques and high-resolution microscopy. Glomerular transcriptomes were profiled by total RNA sequencing. This dataset contains total RNA-Seq data from 3 wild type and 3 Wt1os loss-of-function mutant mice.","dates":{"release":"2026-06-01T00:00:00Z","modification":"2026-06-01T01:00:56.262Z","creation":"2025-11-20T02:14:48.891Z"},"accession":"E-MTAB-16217","cross_references":{"ENA":["ERP185359"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}