Live-seq for live cell transcriptome profiling

Single-cell RNA-seq (scRNA-seq) has greatly advanced the characterization of cellular heterogeneity in physiological and pathological conditions. However, since cells are lysed and can thus only be profiled once, it is currently impossible to perform downstream functional assays on the same cells and to obtain a direct scRNA-seq-based read-out of transcriptional dynamics. Here, we present Live-seq, a novel single cell transcriptomic biopsy approach based on fluidic force microscopy that differs from other scRNA-seq methods because the cells can be kept alive for further analysis. We demonstrate that live-seq allows the identification of both cell types and states. In addition, when coupled to an inverted optical microscope, it uniquely enables linking single cell transcriptomes to downstream functional properties through real-time imaging. There are 1012 samples in total, with 296 Live-seq samples, 564 scRNA-seq samples and 162 scRNA-seq samples those were previously subjected to Live-seq extraction (scRNA_post_Liveseq). All this information is included in the "extract protocol" column of the metadata sheet. Both the Live-seq and scRNA-seq samples contains four different cell types/treatments, which include ASPC, IBA cell, RAW264.7 cell with and without LPS treatment (40 ng/ul). Note that Raw264.7_G9 is a Raw264.7 subline expressing mCherry under the control of Tnf promoter and EGFP-Rela fusion protein. For scRNA_post_Liveseq, the cells were harvest 0h, 1 hour or 4 hours post Live-seq extraction. This information is included in the “source name” and “treatment protocol” column of the metadata sheet. The title of each sample is named by this manner: "extraction protocol"."source name". "treatment protocol"."characteristics: Batch"."(a unique sample number)". For a few Live-seq samples, double extraction on the same cells were applied. A unique ID was generated in the “characteristics: double_extraction_pairs” column for the same cells, while “double_extraction_order” indicates the first or the second extraction.