title: WT_C
organism: Mus musculus
description: Protocols: 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 resuspended in ice-cold NE1 buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 0.5mM spermidine, 0.1% Triton X-100, 5% Glycerol, protease inhibitors) with gentle vortexing. After 10 minutes incubation on ice, the pellet was collected by centrifugation for 4 minutes at 1300 x g at 4C in a swinging bucket rotor. Nuclei was washed with 1X PBS before being resuspended in wash buffer with 10% DMSO to a concentration of 1 million cells per mL. Nuclei was aliquoted in cryotubes and frozen overnight at -80oC in Mr. Frosty containers. ES cells were cultured on 0.1% gelatin-coated plates in 2i/LIF conditions. For CHD4-mAID depletion, 0.5mM auxin (1:1000 from DMSO stock) was resuspended in pre-warmed culture media and transferred to the cells. WT cells were not treated with auxin. DNA was extracted using Zymo DNA Clean and Concentrator Kit-5 (Cat. No. D4014). Barcoding for library prep was performed by PCR amplification using NEBNext® High-Fidelity 2X PCR Master Mix (New England Biolabs, Cat. No. 10169146) and NEBNext® index primers for Illumina sequencing.
attributes.tag: ENA first public
attributes.value: 2025-08-01
attributes.tag: INSDC center name
attributes.value: University of Cambridge, Cambridge Stem Cell Institute
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-15037:WT_C
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: embryonic stem cell
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: house mouse
attributes.tag: genotype
attributes.value: Chd4-mAID Adnp-FKBP
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: sample name
attributes.value: E-MTAB-15037:WT_C
attributes.tag: scientific_name
attributes.value: Mus musculus