Molecular fingerprints for bone marrow cells, acute lymphoblastic leukemia [scRNA-seq]

The overall goal of this study was to characterize bone marrow cells based on their transcriptome, surface protein expression and BCR-VDJ-profile for accurate identification of clinically relevant cell states. This submission includes B-cell acute lymphoblastic (pre-)leukemia samples from mice. This project has received funding from ERA perMed JTC2018 under the title „Genomics-based tools for personalized treatment to reduce chemotherapy burden in paediatric cancer” (Acronym “GEPARD”) Overall design: CITE-seq (scRNA-seq) and scVDJ-seq samples were generated from murine bone marrow cells using the 10X Genomics Chromium platform and protocols. Bone marrow cells (different B cell populations) were collected and sorted from wildtype and PAX5 heterozygous mice. Cells were stained with specific hashtag antibodies to label mice or B cell populations. Single cell suspensions were loaded and processed for sequencing.