In normal and malignant development, rare heterogeneous populations of stem and progenitor cells sustain tissues and tumours, respectively. The ability to trace the ontogeny of diverse cell types as they arise from these functionally distinct clonal populations is of fundamental importance to biology. We previously developed an expressed single-cell lineage tracing technology termed single-cell profiling and lineage tracing (SPLINTR) that enables the accurate ascription of clonal relationships onto high-resolution cell type specific transcriptional maps and applied this system to identify the transcriptional determinants of clonal dominance in normal and malignant haematopoiesis.
While SPLINTR provides a powerful strategy to identify and transcriptionally profile rare clones of interest, we are currently unable to retrospectively isolate clones from heterogenous populations of cells for further molecular and functional characterisation. Moreover, the current SPLINTR design shows limited barcode capture in multimodal sequencing assays including single cell ATAC sequencing. We report here the design and validation of a single-cell profiling and lineage tracing with conditional extraction of live linages (SPLINTR-CELL) system. SPLINTR-CELL expands the original SPLINTR functionality to encompass programmable clone retrieval using CRISPR activation, compatibility with additional multi-omics approaches including scATAC/scCUT&TAG and a versatile array of fluorescent protein markers. We are using SPLINTR-CELL to further our molecular understanding how clonal memory maintains populations of stem cells in normal and malignant haematopoietic development.