This dataset includes RNA sequencing (RNA-seq) data from the HNT-34 AML (acute myeloid leukemia) cell line after knockout of the SLAMF6 gene by CRISPR/Cas9 (SLAMF6-KO) or mock-knockout with a construct targeting the firefly luciferase gene (SLAMF6-WT). Libraries were produced using the Illumina stranded mRNA prep kit and sequenced on an Illumina Novaseq 6000 system (Illumina). The dataset is available as raw sequencing reads (fastq.bz2) or as merged transcripts per million (TPM) data for all cases generated using Salmon (salmon.merged.gene_tpm.tsv.gz).