bulk mRNA seuqencing control
To investigate how CDK5 knockdown affects gene expression of MHC-I-driving transcription factors, we extracted RNA from EO771.Br3.shCtl (duplicates), EO771.Br3.shCDK5 #1 and EO771.Br3.shCDK5 #2. Cells were cultured until 80% confluent in 10 cm dishes. RNA was extracted using TRI reagent and quality-checked with use of an Agilent RNA 6000 Pico Kit by Agilent Bioanalyzer 2100. RNA with an integrity number of greater than 7 was used for library preparation.