biostudies-arrayexpressAntonios PapadakisMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16254The 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. The experimental workflow integrates both in vivo and cell culture approaches. We generated a Wt1os loss-of-function mouse model and assessed kidney morphology and function using histological techniques and high-resolution microscopy. Promoter activity was evaluated through CUT&Tag analysis of H3K27ac histone marks. This dataset contains CUT&TAG data from 3 wild type and 3 Wt1os loss-of-function mutant mice.biostudies-arrayexpressLibrary Construction - To determine library PCR cycle number, a parallel CUT&Tag reaction was tested with 5 µl DNA, 1 µl Universal i5 primer (10 µM), 1 µl Barcoded i7 primer (10 µM), 1.25 µl SYBR Green, 12.5 µl NEBNext HiFi PCR mastermix (NEB, USA), and 4.25 µl nuclease-free water. Libraries were amplified on a QuantStudio 5 system (Applied Biosystems) with 5 min at 72 °C, 30 s at 98 °C, then 39 cycles of 98 °C for 10 s and 63 °C for 10 s, followed by 72 °C for 1 min.Sequencing - Libraries were sequenced on Illumina NovaSeq 6000. The sequencing was paired-end.Sample Collection - Nuclei were isolated from freshly isolated glomeruli using Nuclei EZ Prep buffer (Sigma-Aldrich) supplemented with protease inhibitors. Isolated nuclei were bound to 10 µl activated Concanavalin A beads (Polysciences, Warrington, USA) per sample for subsequent CUT&Tag processing.Nucleic Acid Extraction - Nuclei were incubated overnight at 4 °C with anti-H3K27ac antibody or Normal Rabbit IgG control at 1:50 dilution in Wash150A buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.1% BSA, 2 mM EDTA, protease inhibitors). A secondary anti-rabbit IgG antibody was added for 30 min at room temperature at 1:100 in Wash150 buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin, 5 mM sodium butyrate, protease inhibitors). pAG-Tn5 (1:20) in Wash300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 5 mM sodium butyrate, protease inhibitors) was incubated with nuclei for 1 h at room temperature. Tagmentation was carried out for 1 h at 37 °C in Wash300 buffer. Reactions were stopped with 10% SDS, 0.5 M EDTA, and 20 mg/ml Proteinase K, followed by incubation at 1 h at 55 °C. DNA was purified using ChIP DNA Clean & Concentrator (Zymo).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw CUT&Tag sequencing reads were processed using the nf-core/cutandrun pipeline (version 3.2.1, Git commit 2727de3) executed with Nextflow (version 23.04.1) and Singularity containerization. Briefly, read quality was assessed using FastQC, and adapter sequences were trimmed using Trim Galore. Reads were aligned to the mouse reference genome (GRCm38/mm10, Ensembl release 102) using Bowtie2 with parameters optimized for CUT&Tag data. Alignments with mapping quality scores below 20 were filtered out. PCR duplicates were removed using Picard Mark. Peak calling was performed using MACS2 with a genome size parameter of 2.7×10⁹ bp. Consensus peak sets were generated by requiring peaks to be present in at least 1 replicate per condition with a minimum peak overlap of 20% between replicates. Peaks were further filtered by requiring a minimum fraction of reads in peaks (FRiP) overlap of 20%UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000DNA-seqMus musculusAntonios PapadakisfalseWt1os lncRNA as a Novel Regulator of Podocyte Function (CUT&TAG of mouse glomeruli)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. The experimental workflow integrates both in vivo and cell culture approaches. We generated a Wt1os loss-of-function mouse model and assessed kidney morphology and function using histological techniques and high-resolution microscopy. Promoter activity was evaluated through CUT&Tag analysis of H3K27ac histone marks. This dataset contains CUT&TAG data from 3 wild type and 3 Wt1os loss-of-function mutant mice.2026-06-01T00:00:00Z2026-06-01T01:00:59.265Z2025-11-21T14:55:37.443ZE-MTAB-16254ERP185484EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0003816EFO_0004184