Loïc Binan

Investigating spatial gene circuits and gene–phenotype mechanisms with Perturb-FISH

Loïc Binan

ca (code pays fourni par la source)

Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits

Loïc Binan, Aiping Jiang, Serwah A. Danquah, Vera Valakh et autres

Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging …

us (code pays fourni par la source)

Perturb-FISHv3 v1

Loïc Binan, Sami Farhi, Brian Cleary

This is the 07-21-2024 update version to this protocol protocol describes how the Sami Farhi lab, https://www.broadinstitute.org/bios/sami-farhi, carries out Perturb-FISH and was provided by Loïc Binan, https://sites.broadinstitute.org/opp/people/lo%C3%AFc-binan. See the author's paper for a wider context of this protocol: https://doi.org/10.1101/2023.11.30.569494 Note: This protocol …

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Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits

Loïc Binan, Serwah A. Danquah, Vera Valakh, Brooke Simonton et autres

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 …

us (code pays fourni par la source)

Scalable genetic screening for regulatory circuits using compressed Perturb-seq

Douglas W. Yao, Loïc Binan, Jon Bezney, Brooke Simonton et autres

Pooled CRISPR screens with single-cell RNA sequencing readout (Perturb-seq) have emerged as a key technique in functional genomics, but they are limited in scale by cost and combinatorial complexity. In this study, we modified the design of Perturb-seq by incorporating algorithms applied …

us (code pays fourni par la source)

Migration speed of captured breast cancer subpopulations correlates with metastatic fitness

Nicolas Desjardins‐Lecavalier, Matthew G. Annis, Alexander Nowakowski, Alexander Kiepas et autres

The genetic alterations contributing to migration proficiency, a phenotypic hallmark of metastatic cells required for colonizing distant organs, remain poorly defined. Here, we used single-cell magneto-optical capture (scMOCa) to isolate fast cells from heterogeneous human breast cancer cell populations, based on their …

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Optimization-based decoding of Imaging Spatial Transcriptomics data

John Bryan, Loïc Binan, Cai McCann, Yonina C. Eldar et autres

MOTIVATION: Imaging Spatial Transcriptomics techniques characterize gene expression in cells in their native context by imaging barcoded probes for mRNA with single molecule resolution. However, the need to acquire many rounds of high-magnification imaging data limits the throughput and impact of existing …

us, il (code pays fourni par la source)

Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells

Martin H. Berryer, Matthew Tegtmeyer, Loïc Binan, Vera Valakh et autres

Emerging evidence of species divergent features of astrocytes coupled with the relative inaccessibility of human brain tissue underscore the utility of human pluripotent stem cell (hPSC) technologies for the generation and study of human astrocytes. However, existing approaches for hPSC-astrocyte generation are …

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Cell migration capacity alone can be hereditary and predict metastatic burden

Nicolas Desjardins‐Lecavalier, Matthew G. Annis, Alexander Nowakowski, Alexander Kiepas et autres

ca (code pays fourni par la source)

Compressed Perturb-seq: highly efficient screens for regulatory circuits using random composite perturbations

Douglas W. Yao, Loïc Binan, Jon Bezney, Brooke Simonton et autres

Pooled CRISPR screens with single-cell RNA-seq readout (Perturb-seq) have emerged as a key technique in functional genomics, but are limited in scale by cost and combinatorial complexity. Here, we reimagine Perturb-seq's design through the lens of algorithms applied to random, low-dimensional observations. …

us (code pays fourni par la source)

Optimization-Based Decoding of Imaging Spatial Transcriptomics Data

John Bryan, Loïc Binan, Cai McCann, Yonina C. Eldar et autres

Motivation Imaging Spatial Transcriptomics (iST) techniques characterize gene expression in cells in their native context by imaging barcoded probes for mRNA with single molecule resolution. However, the need to acquire many rounds of high-magnification imaging data limits the throughput and impact of …

us, il (code pays fourni par la source)

Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells

Martin H. Berryer, Matthew Tegtmeyer, Loïc Binan, Vera Valakh et autres

ABSTRACT Astrocytes play essential roles in normal brain function, with dysfunction implicated in diverse developmental and degenerative disease processes. Emerging evidence of profound species divergent features of astrocytes coupled with the relative inaccessibility of human brain tissue underscore the utility of human …

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