Study of an allelic series using transcriptomic phenotypes
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ABSTRACT:
PROVIDER: PRJNA420450 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression profiling holds great promise for genetics because of its ability to measure thousands of genes quantitatively. Although transcriptomes have recently been used to perform epistasis analyses for pathway reconstruction, there has not been a systematic effort to understand how expression profiles will vary among distinct mutants of the same gene. Here, we study an allelic series in C. elegans consisting of one wild type and two mutant alleles of mdt-12, a highly pleiotropic gene whose gene product is a subunit of Mediator complex, which is essential for transcriptional regulation in eukaryotes. We developed a false hit analysis to identify which populations of genes commonly differentially expressed with respect to the wild type are likely the result of statistical artifact. We concluded that expression perturbations caused by these alleles split into four distinct modules called phenotypic classes. To understand the dominance relationship between the two mutant alleles, we developed a dominance analysis for transcriptional data. Dominance analysis of these phenotypic classes support a model where mdt-12 has multiple functional units that function independently to target the Mediator complex to specific genetic loci.
2020-01-01 | GSE107523 | GEO
Project description:Allelic dilution series series of C57BL6/J:CAST/EiJ RNA using Smart-seq3
| PRJEB46197 | ENA
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
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
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
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
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
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
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
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