Dissecting immune circuits by linking CRISPR pooled screens with single cell RNA-seq [SET1]

In multicellular organisms, dedicated regulatory circuits control cell-type diversity and response. The crosstalk and redundancies within these circuits and substantial cellular heterogeneity pose a major research challenge. We present CRISP-seq, an integrated method for massively parallel single-cell RNA-seq and CRISPR pooled screens. We show that profiling the perturbation and transcriptome in the same cell, enables to elucidate, the function of multiple factors and their interactions. In this benchmarking study, we applied this technology to probe regulatory circuits of innate immunity. By sampling tens of thousands of perturbed cells in vitro and in mice, we identified interactions and redundancies between developmental and signaling-dependent factors controlling the commitment toward different cell lineages or the inflammatory and antiviral pathways. CRISP-seq thereby emerges as a broadly applicable, comprehensive, and unbiased approach for elucidating mammalian regulatory circuits. Overall design: Transcriptional and CRISPR profiles from single myeloid cells, infected with lentiviral vectors carrying different gRNAs, were generated by deep sequencing of tens of thousands of single cells, sequenced in several batches in an Illumina Nextseq 500. Experiment was paired-end, but read2 was used to read cell and molecule barcodes only. Additional details about experimental design (associating each single cell with its amplification batch and index sorting readout) available as Series supplementary file.

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Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I