title: GSM5288724: 4T1 cells, CHD8_rep2 (RNAseq); Mus musculus; RNA-Seq
library_construction_protocol: RNA was extracted using the RNeasy mini kit (Qiagen). Cell cultures in T25 flasks were first washed with cold PBS, and 350 µl of RLT was added. Cells were scraped, passed through a 20G syringe five times and resuspended in RLT, and RNA was extracted using the RNeasy mini kit (Qiagen) according to manufacturer instructions. RNA was submitted for library preparation by the Wellcome-MRC Cambridge Stem Cell Institute. Initial QC was performed using Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and TapeStation Analysis software (Agilent Technologies). 1000 ng RNA was used for library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB), ERCC spike-ins, and the QIAseq FastSelect RNA Removal Kit (Qiagen). Libraries were subsequently measured using the Qubit system and visualized on a TapeStation D5000. Sequencing was performed as one lane of PE150 using the HiSeq 4000 at the CRUK-CI Genomics Core. RNA-seq, PE150