Transcriptome-wide characterization of genetic perturbations

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 3, 2024

Abstract Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these are often noisy due to cost and technical constraints, limiting power detect true effects with conventional differential expression analyses. Here, we introduce TRanscriptome-wide Analysis Differential Expression (TRADE), a statistical framework which estimates transcriptome-wide distribution from gene-level measurements. Within TRADE, derive multiple novel, interpretable metrics, including “transcriptome-wide impact”, an estimator overall transcriptional effect perturbation is stable across sampling depths. We analyze new published large-scale datasets show that many not statistically significant, but detectable in aggregate TRADE. In genome-scale screen, find typical gene affects estimated 45 genes, whereas essential over 500 genes. An advantage our approach its ability compare contexts dosages despite differences power. use this identify cell-type dependent examples where responses only larger magnitude, also qualitatively different, function dosage. Lastly, expand analysis case/control comparison for neuropsychiatric conditions, finding correlations greater than diagnoses. TRADE lays analytic foundation systematic atlases, well experiments more broadly.

Язык: Английский

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Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 27, 2024

SUMMARY Single-cell CRISPR screens link genetic perturbations to transcriptional states, but high-throughput methods connecting these induced changes their regulatory foundations are limited. Here we introduce Multiome Perturb-seq, extending single-cell simultaneously measure perturbation-induced in gene expression and chromatin accessibility. We apply Perturb-seq a CRISPRi screen of 13 remodelers human RPE-1 cells, achieving efficient assignment sgRNA identities single nuclei via an improved method for capturing barcode transcripts from nuclear RNA. organize accessibility measurements into coherent programs describing the integrated effects on cell state, finding that ARID1A SUZ12 knockdowns induce enriched developmental features. Pseudotime analysis connects expression, highlighting value multimodal profiling. Overall, our provides scalable simply implemented system dissect logic underpinning state.

Язык: Английский

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Saturation profiling of drug-resistant genetic variants using prime editing

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 12, 2024

Язык: Английский

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Precision mutational scanning: your multipass to the future of genetics

Nature Methods, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 19, 2024

Язык: Английский

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NIS-Seq enables cell-type-agnostic optical perturbation screening

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 19, 2024

Язык: Английский

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Advances in optical pooled screening to map spatial complexity

Nature Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 7, 2024

Язык: Английский

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