Population:
The population under study consists of patients diagnosed with mantle cell lymphoma. The results of the analysis will refer to this specific group of individuals.
Description of sampling:
Sample processing for scRNA-seq samples: Mononuclear cells were isolated from bone marrow samples by standard density centrifugation using Lymphoprep (Axis-Shield) following the manufacturer’s instructions. Intestinal, tonsillar, and lymphoid tissues were processed into single-cell suspensions using mechanical dissociation and then filtered through 70 μm containers. Single cells were cryopreserved in fetal bovine serum (FBS) supplemented with 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen before use.
Cell sorting for scRNAseq samples: The cells used for flow cytometry were thawed in RPMI 1640 cell medium (Gibco). The cells were blocked with human FcR Blocking Reagent (Miltenyi Biotec) for 10 min and subsequently stained with anti-CD19 BV421 and anti-CD235a FITC in FACS buffer (PBS with 2% FBS) for 20 min on ice. Immediately before sorting, the cells were briefly incubated with propidium iodide staining solution. For the MCL samples, live CD235a- cells, CD235a-CD19+ cells, and CD235a-CD19- cells were sorted in FACS buffer using a BD FACSAria Fusion Sorter (BD Biosciences). Live CD235a- cells were used for single-cell sequencing, while live CD235a- CD19+ and CD235a- CD19- cells were used to extract DNA for tumor and germline WGS, respectively. For the control sample, live CD19- cells and live CD19+ cells were sorted separately and then mixed at a 3:7 ratio for single-cell sequencing.
scRNA-seq sequencing and data analysis: Using the Chromium Next GEM Single-Cell 5′ Reagent Kit v2 (10x Genomics), the cells were loaded onto separate lanes of the Next GEM Chromium Controller (10x Genomics) for encapsulation (target recovery of 10,000 cells for each sample). Single-cell gene expression (GEX) libraries were constructed following the manufacturer’s protocols.
WGS sequencing: For fresh-frozen tissue samples, genomic DNA from tumors and matched blood samples was extracted separately by using a DNeasy Tissue and Blood Kit (Qiagen). For the single-cell suspension MCL samples, FACS (CD19+/CD19-) or an EasySep human B-cell enrichment kit was used to separate B cells and non-B cells to represent the tumor samples and nontumor (germline) controls, respectively. Genomic DNA from the sorted cells was extracted using the DNeasy Tissue and Blood Kit.
Number of individuals/objects:
Data format/data structure:
