RT @NatureBiotech: @eric_lubeck @TakaKud0 @ProCogia Advances in optical pooled screening to map spatial complexity #NBTNV .

Also check out recent wonderfully complementary approaches PerturbView by @eric_lubeck and Aviv Regev, and NIS-seq by @schmidburgk.

We’re looking for postdocs to leverage CRISPRmap to do pooled spatial genomics perturbation studies in vivo. Open to experimental and computational scientists. Please reach out at jg4106@columbia.edu!.

Our study wouldn't have been possible without the wonderful collaboration of @CicciaAlberto, @DrEdmondChan, @elhamazizi, @SnoeckLab.and @landau_lab, and support by @NIHDirector New innovator award support from @NIH_CommonFund and @theNCI. #NIHHighRisk.

We performed a variant analysis study in a breast cancer context, and show efficient in situ barcode detection in hESCs, iPSCs and derived motor neurons, and in cancer cells in the tumor microenvironment.

Excited to share: "Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap", just published in @NatureBiotech. Spearheaded by @Jiacheng_Gu_, and powered by everyone in the @GaublommeL at @Columbia_Bio and collaborators.

RT @NatureBiotech: Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap .

We’re looking for postdocs to leverage CRISPRmap in pooled spatial genomic perturbation studies. Open to experimental and computational candidates. Looking forward to discuss the opportunities! Please reach out at jg4106@columbia.edu!.

First author @Jiacheng_Gu_ didn't have to adjust the CRISPRmap protocol reported on biorxiv for barcode readout in these cell types.

Update: for those interested in optical pooled screening in stem/pluripotent cells and neurons, we tested CRISPRmap in hESCs, iPSCs and iPSC derived neurons, and observed good barcode recovery. Shout out to the Wichterle lab and @SnoeckLab for their help in these cell contexts.

We’re looking for postdocs to leverage CRISPRmap to do pooled spatial genomics perturbation studies in vivo. Open for experimental and computational folks. Looking forward to discuss the opportunities! Please reach out at jg4106@columbia.edu! Retweets appreciated!.

Also check out a recent wonderfully complementary approach by @eric_lubeck and Aviv Regev!

Try CRISPRmap for your own research goals! Reagent costs associated with barcode readout are quite low (~$80 per million cells), readout dyes can be matched to your existing microscopy setup, and we're happy to provide some initial reagents for you to get started.

Multi-omic spatial analysis of how CRISPR-perturbed cells respond to various environmental cues in the tissue context offers the potential to significantly expand our understanding of tissue biology in both health and disease.

Approximately a million cells were profiled, providing a comprehensive phenotypic assessment of the functional consequences of the studied variants. CRISPRmap enabled us to pinpoint likely-pathogenic patient-derived mutations that were previously classified as VUS.

We also conducted a multi-omic base-editing screen in a breast cancer cell line on core DNA damage repair genes studying how nucleotide variants influence DNA damage signaling following treatment with ionizing radiation or DNA damaging agents commonly used for cancer therapy

Briefly, we developed a next-gen optical pooled screening approach that enables FISH-based readout of perturbation-identifying barcodes, and apply it in tumor tissue in combination with multiplexed immunofluorescence.

An effort made possible by @NIHDirector New innovator award support from @NIH_CommonFund and @theNCI. #NIHHighRisk.

Excited to share: "CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue". We applied our novel approach in wonderful collaborations with @CicciaAlberto, @DrEdmondChan, @elhamazizi, and @landau_lab.

Gaublomme and Azizi labs at Columbia are looking to jointly hire a computational postdoc. Any referral of talented people that might be interested would be greatly appreciated!.