biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsBrian HendrichIllumina NovaSeq 6000RNA-seq of total RNAMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15102This study investigates the role of the chromatin remodeller CHD4 in regulating gene expression. CHD4 was tagged with a mini-AID degron to enable auxin-inducible degradation. RNA-seq was performed at multiple time-points (1, 2, 4 and 24 hours) following auxin treatment to capture changes in gene expression upon CHD4 depletion. For each time point, three biological replicates were processed. This dataset aims to characterise the immediate effects of CHD4 loss on gene expression.biostudies-arrayexpressSample Treatment - For CHD4-mAID depletion, 0.5mM auxin (1:1000 from DMSO stock) was resuspended in pre-warmed culture media and transferred to the cells. Control cells were not treated with auxin (no auxin).Sequencing - Sequencing was performed on the Illumina NovaSeq S1.Sample Collection - Cells were grown in 6-well plates. Upon aspiration of the medium, cells were harvested in 350µl Trizol Reagent (Ambion, 15596026) to each well. The cell lysate was homogenised by pipetting up and down several times before being transferred into a microcentrifuge tube.Library Construction - Ribosomal RNA was removed from the samples using the Illumina Ribo-Zero Plus rRNA Depletion Kit. As input for a 12-cycle PCR using the NEXTFLEX® Rapid Directional RNA-seq kit, 60-100ng of the depleted RNA was used. ERCC spike-in was added during library prep.Growth Protocol - ES cells were cultured on 0.1% gelatin-coated plates in 2i/LIF conditions.Nucleic Acid Extraction - The RNA was purified using the Zymo Direct-zol RNA purification kit. Samples were treated with DNAse I. RNA was collected in 25µL of DNase/RNase-Free water.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesBrian HendrichAndria KoullefalseRNA-seq data of mouse embryonic stem cells treated with auxin for CHD4 depletion against untreated controlThis study investigates the role of the chromatin remodeller CHD4 in regulating gene expression. CHD4 was tagged with a mini-AID degron to enable auxin-inducible degradation. RNA-seq was performed at multiple time-points (1, 2, 4 and 24 hours) following auxin treatment to capture changes in gene expression upon CHD4 depletion. For each time point, three biological replicates were processed. This dataset aims to characterise the immediate effects of CHD4 loss on gene expression.2026-01-15T00:00:00Z2026-01-15T12:57:15.646Z2025-04-29T21:37:37.644ZE-MTAB-15102ERP172090EFO_0002944EFO_0004170EFO_0009653EFO_0003789EFO_0005518EFO_0004184EFO_0003969