title: RNA-seq data of mouse embryonic stem cells treated with auxin for CHD4 depletion against untreated control
design: RNA-seq data of mouse embryonic stem cells treated with auxin for CHD4 depletion against untreated control
library_construction_protocol: 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. 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. Control cells were not treated with auxin (no auxin). 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. 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.