biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsBrian HendrichIllumina NovaSeq XCUT&RUNMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15607This study investigates the role of the chromatin remodeller CHD4 in regulating transcription factor binging using CUT&RUN. CHD4 was tagged with a mini-AID degron to enable auxin-inducible degradation. CUT&RUN for Nanog and Sox2 was performed at multiple time-points (30 minutes, 1 hour, and 4 hours) following auxin treatment to capture changes in their binding upon CHD4 depletion. For each time point, two biological replicates were processed, each with two technical replicates. This dataset aims to characterise the immediate effects of CHD4 loss on TF binding.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 - 300bp paired-end (2 x 150 bp) sequencing was performed on a NovaSeqX 25B flowcell at the Cambridge Stem Cell Institute and CRUK sequencing facilities.Sample Collection - Cells were cultured on 10cm plates. Cells from all conditions were harvested at the same time using accutase and spun down for 3 min, 600 x g in a swinging bucket rotor at room temperature. Cells were washed in PBS and processed immediately.Nucleic Acid Extraction - MaxExtract tubes were spun down at 1500 x g for 1 minute at room temperature before use. Equal volume of Phenol/chloroform/isoamylalcohol (100µL) was added to each sample. Samples were vortexed for 15 seconds and then transferred into the MaxExtract tubes. Samples were spun down at 16,000 x g for 5 minutes at room temperature. 100µL of chloroform was added, tubes were inverted 10 minutes to mix and then spun down at 16,000 x g for 5 minutes at room temperature. The aqueous phase was transferred into new tubes were 2mg/mL glycogen and 500μl of 100% Ethanol were added. Samples were incubated at -20C for 30 minutes and then spun down at 20,817 x g for 15 minutes at 4C. The ethanol wash step was repeated. Ethanol was removed and samples were left to air-dry before being resuspended in 20µL of nuclease-free water.Growth Protocol - ES cells were cultured on 0.1% gelatin-coated plates in 2i/LIF conditions.Library Construction - Library preparation for sequencing was carried out in the SCI facilities.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesBrian HendrichAndria KoullefalseCUT&RUN data of Nanog and Sox2 in mouse embryonic stem cells treated with auxin for CHD4 depletion against untreated controlThis study investigates the role of the chromatin remodeller CHD4 in regulating transcription factor binging using CUT&RUN. CHD4 was tagged with a mini-AID degron to enable auxin-inducible degradation. CUT&RUN for Nanog and Sox2 was performed at multiple time-points (30 minutes, 1 hour, and 4 hours) following auxin treatment to capture changes in their binding upon CHD4 depletion. For each time point, two biological replicates were processed, each with two technical replicates. This dataset aims to characterise the immediate effects of CHD4 loss on TF binding.2026-01-15T00:00:00Z2026-01-15T12:58:26.938Z2025-09-18T17:33:18.314ZE-MTAB-15607ERP180288EFO_0002944EFO_0009973EFO_0004170EFO_0003789EFO_0005518EFO_0004184EFO_0003969