Image-seq

Image-seq integrates in situ and in vivo imaging with single-cell RNA sequencing (scRNA-seq) to generate spatially and temporally resolved transcriptional profiles of viable cells for mapping cellular organization and microenvironment-specific heterogeneity.

Key Features:

• Spatial and Temporal Resolution: Combines in situ and in vivo imaging with scRNA-seq to provide spatial and temporal transcriptional data from cells isolated based on precise tissue location.
• Preservation of Cellular Integrity: Isolates viable, intact cells from intact tissues while maintaining structural integrity to support downstream single-cell and multi-omics analyses.
• Advanced Sequencing Techniques: Uses high-throughput droplet-based sequencing and SMARTseq-v4 library preparation for high-sensitivity single-cell RNA sequencing.

Scientific Applications:

• Bone marrow and leukemia biology: Enables study of cellular heterogeneity and interactions within bone marrow microenvironments relevant to leukemia research.
• Acute myeloid leukemia (AML) biomarker discovery: Supported identification of DPP4 as highly upregulated during early AML progression, highlighting a more proliferative subpopulation confined to specific bone marrow niches.
• Mapping microenvironment-specific heterogeneity: Facilitates investigation of cellular heterogeneity and dynamics within defined tissue microenvironments.

Methodology:

Imaging-guided isolation of cells from intact tissues to retain spatial information; library preparation using droplet-based sequencing and SMARTseq-v4 for high-sensitivity RNA sequencing; compatibility with downstream multi-omics enabled by isolation of viable cells.