This dataset is a systematic study of transcriptional profiles of HAP1 cells under environmental and genetic perturbations. Samples were prepared using wildtype HAP1 cells and HAP-derived cell lines that included CRISPR/Cas9-induced gene knockout in tyrosine kinases. Cells were cultured in reduced serum conditions for 16h, then stimulated with a polypeptide or small molecule for 6 hours. Cells were harvested and extracted RNA was subjected to RNA-seq library preparation in 96-well plates using the QuantSeq protocol. Sequencing was performed on an Illumina HiSeq 2000 system following a T-fill reaction, with 48 samples multiplexed on each lane.