CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide-RNA expression to transcriptome responses in thousands of individual cells. Our method for CRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.

Resident macrophages support embryonic development and tissue homeostasis and repair. The mechanisms that control their differentiation remain unclear. We report here that Erythro-Myeloid Progenitors generate pre-macrophages (pMacs) that simultaneously colonize the whole embryo from embryonic day (E)9.5 in a chemokine-receptor dependent manner. The core macrophage program initiated in pMacs is rapidly diversified as expression of transcriptional regulators becomes tissue-specific in early macrophages. This process appears essential for macrophage specification and maintenance, as inactivation of Id3 impairs the development of liver macrophages and results in selective Kupffer cell deficiency in adults. We propose that macrophage differentiation is an integral part of organogenesis as colonization of organ anlagen by pMacs is followed by their specification into tissue macrophages, hereby generating the macrophage diversity observed in postnatal tissues.

and PCT/EP2016/057355 applied for by Spatial Transcriptomics AB (10x Genomics) covering the described technology. M.R. is employed by Illumina Inc. A.R. is a founder and equity holder of Celsius Therapeutics and an SAB member of Syros Pharmaceuticals and Thermo Fisher Scientific.Reporting summary: Further information on research design is available in the Life Sciences Reporting Summary linked to this article. Data availability:The raw mouse data have been deposited to NCBI's GEO archive GSE130682. Raw files for the breast cancer sample are available through an MTA with Åke Borg