Tumor microenvironment rewiring after arsenic trioxide therapy in acute promyelocytic leukemia revealed by single-cell RNA sequencing

Bone marrow samples were obtained from n=15 patients were diagnosed with APL and n=6 patients have received ATO therapy. To obtain gene expression matrices for BM cells from APL samples, we aligned the FASTQ files to the human GRCh38 reference (2020-A version) using the count module of the Cell Ranger pipeline (10X Genomics, default settings, version 6.1.2). For T-cell receptor (TCR) and B-cell receptor (BCR) alignment, FASTQ files were mapped to the human vdj-GRCh38 reference (2020-A version) using the vdj module of the Cell Ranger pipeline (10X Genomics, default settings, version 6.1.2).