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Titrating gene expression with allelic series of CRISPR guide RNAs

ABSTRACT: Titrating gene expression with allelic series of CRISPR guide RNAs

PROVIDER: PRJNA545894 | ENA |

REPOSITORIES: ENA

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Titrating gene expression with allelic series of CRISPR guide RNAs

Project description:Cellular phenotypes arise from the degrees to which different genes are expressed, yet the ability to monitor these phenotypes is limited by a lack of tools to precisely control gene expression. We describe the development of allelic series of systematically compromised sgRNAs to titrate expression of human genes with CRISPR interference. Using large-scale measurements of compromised sgRNA activities, we both identify empirically validated intermediate-activity sgRNAs and derive the factors governing sgRNA activity using deep learning, enabling construction of a compact sgRNA library to titrate expression of ~2,400 essential genes and a genome-wide in silico library. Staging cells along a continuum of essential gene expression levels using sgRNA series combined with rich single-cell RNA-seq readout reveals expression threshold-specific responses and gene-specific expression-to-phenotype relationships. Our work provides a general tool to control gene expression with applications ranging from tuning of biochemical pathways to identification of suppressors for diseases of dysregulated gene expression.

2019-11-18 | GSE132080 | GEO

Proteome analysis of huntingtin knock-in allelic series - Heart

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, heart samples from the complete allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2018-09-03 | PXD010958 | Pride

Proteome analysis of huntingtin knock-in allelic series - Muscle

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, gastrocnemius samples from the complete remaining allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2018-09-03 | PXD010957 | Pride

Proteome analysis of huntingtin knock-in allelic series - Striatum

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, striatum samples from the complete remaining allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2017-05-26 | PXD006302 | Pride

Proteome analysis of huntingtin knock-in allelic series - Cerebellum

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, cerebellum samples from the complete remaining allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2017-03-23 | PXD005526 | Pride

Proteome analysis of huntingtin knock-in allelic series - Hippocampus

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, hippocampus samples from the complete remaining allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2017-03-23 | PXD005538 | Pride

Proteome analysis of huntingtin knock-in allelic series - Cortex

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, cortex samples from the complete remaining allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2017-03-23 | PXD005485 | Pride

Proteome analysis of huntingtin knock-in allelic series - Liver

Project description:The objective of this project is to study the proteome in different tissues of huntingtin knock-in allelic series in mice. In the current part of the study, liver samples from the complete remaining allelic series collected at 2, 6, and 10 months were analyzed. To this end, comprehensive quantitative, label-free proteome analysis was performed using Evotec’s quantitative Deep Proteome Profiling technology.

2017-03-22 | PXD005641 | Pride

Study of an allelic series using transcriptomic phenotypes

Project description:Study of an allelic series using transcriptomic phenotypes

| PRJNA420450 | ENA

Chemically synthesized guide RNAs can direct CRISPR-CasRx cleavage of circRNAs with high efficiency and specificity

Project description:In this study, we demonstrate that CRISPR/RfxCas13d (CasRx)-mediated circRNA depletion is, for the circRNAs studied, more efficient than Argonaute 2-dependent short hairpin RNA (agoshRNA)-mediated depletion and with fewer off-target effects on the linear host RNAs. We also designed and optimally used synthetic guide RNAs (syn-gRNAs) in combination with CasRx to efficienctly deplete circRNA ciRS-7. None of the knockdown strategies tested (pre-gRNA, gRNA, syn-gRNA and agoshRNA) showed any significant off-target effects at the transcriptomics level. Differential expression analysis was performed for each KD setup versus non-targeting control (three biological replicates of each). In conclusion, CasRx-mediated circRNA knockdown using both vector-based and syn-gRNA strategies is a useful tool for future studies on circRNA functions.

2023-04-30 | GSE189963 | GEO

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