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"funding_reference_identifier": "https://ror.org/01cwqze88", "funding_reference_identifier_type": "ROR", "award_number": "1-R01-MH128366-01", "award_title": "Unraveling the Genetic Programs Engaged in ASD Neurons Through Coupled Transcriptomic and Phenotypic Readouts"}, {"fundername": "National Institutes of Health", "funding_reference_identifier": "https://ror.org/01cwqze88", "funding_reference_identifier_type": "ROR", "award_number": "1-RF1-MH121289-01", "award_title": "Scaling up spatial RNA profiling with compressed sensing"}], "Publication": [{"id": "301", "relatedidentifier": "https://dx.doi.org/10.17504/protocols.io.6qpvr356bvmk/v1", "relatedidentifiertype": "DOI", "pmcid": "", "relationtype": "IsDocumentedBy", "citation": "Perturb-FISH Protocol", "sheet_id": "830", "data_set_id": "None"}, {"id": "300", "relatedidentifier": "https://doi.org/10.1101/2023.11.30.569494", "relatedidentifiertype": "DOI", "pmcid": "", "relationtype": "IsCitedBy", "citation": "Lo\u03cac Binan, Serwah Danquah, Vera Valakh, Brooke Simonton, Jon Bezney, Ralda Nehme, Brian Cleary, Samouil L Farhi. 2023 Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits bioRxiv 2023.11.30.569494; doi: https://doi.org/10.1101/2023.11.30.569494", "sheet_id": "830", "data_set_id": "None"}], "Instrument": [{"microscopetype": "Epifluorescent", "microscopemanufacturerandmodel": "Vizgen MERSCOPE Alpha", "objectivename": "NIkon plan Apo", "objectiveimmersion": "Oil", "objectivena": "1.4", "objectivemagnification": "60x", "detectortype": "sCMOS camera with 2048 x 2048 pixel sensor", "detectormodel": "Hamatsu orcaflash 4.0", "illuminationtypes": "5 lasers", "illuminationwavelength": "405, 475, 545, 635 and 750 nm", "detectionwavelength": "776nm,671nm,572nm,525nm,422nm", "sampletemperature": "25C"}], "Specimen": [{"localid": "UCSFi001-A", "species": "Human", "ncbitaxonomy": "NCBI:txid9606", "age": "30.0", "ageunit": "year", "sex": "Male", "genotype": "CRISPRi targeting of 127 autism spectrum disorder (ASD) risk genes via dCas9-KRAB and MERFISH measurement of their effects on 254 genes with published links to ASD", "organlocalid": "astrocyte", "organname": "brain", "samplelocalid": "UCSFi001-A", "atlas": "", "locations": "", "linkage": []}], "Dataset": [{"bildirectory": "/bil/data/0c/bd/0cbd479c521afff9", "title": "Perturb-FISH simultaneous CRISPR screening and spatial transcriptomics in astrocytes", "socialmedia": "New Perturb-FISH method involves simultaneous CRISPR screening and spatial transcriptomics in astrocytes", "subject": "CRISPR, MERFISH, macrophages, NFkB pathway, astrocyte, autism spectrum disorder", "subjectscheme": "", "rights": "Creative Commons Attribution 4.0 International (CC BY 4.0)", "rightsuri": "https://creativecommons.org/licenses/by/4.0", "rightsidentifier": "CC-BY-4.0", "dataset_image": "", "generalmodality": "spatial transcriptomics", "technique": "MERFISH", "other": "Perurb-FISH, CRISPR, Calcium Imaging", "abstract": "Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. 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