Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1246654 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32987806.fastq.gz | Fastqsanger.gz | |||
| SRR32987806_1.fastq.gz | Fastqsanger.gz | |||
| SRR32987806_2.fastq.gz | Fastqsanger.gz | |||
| SRR32987807.fastq.gz | Fastqsanger.gz | |||
| SRR32987807_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 54 |
Similar Datasets
Project description:The CRISPR-Cas9 system enables efficient sequence-specific mutagenesis for creating germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-guideRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we established in vitro-assembled, fluorescent Cas9-sgRNA RNPs in stabilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. Sequence analysis of targeted loci in individual embryos reveals highly efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis reveals preliminary loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show efficient targeting of functional non-coding elements in gene-regulatory regions using saturating mutagenesis towards uncovering functional control elements in transgenic reporters and endogenous genes. Our results suggest that in vitro assembled, fluorescent Cas9-sgRNA RNPs provide a rapid reverse-genetics tool for direct and scalable loss-of-function studies beyond zebrafish applications.
2016-05-01 | E-MTAB-4143 | biostudies-arrayexpress
Project description:In this study, we aimed at determining RNA interactors of L1TD1 RNPs. To achieve this, DNMT1 KO and DNMT1 L1TD1 DKO HAP1 cells were generated by Crispr/Cas9 gene editing tool and L1TD1 RIP was performed by using these cell lines. Our study reveals a comprehensive analysis of differentially enriched transcripts in L1TD1 containing RNPs.
2025-01-01 | GSE254459 | GEO
Project description:Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C
2011-06-29 | GSE27132 | GEO
Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
2021-04-30 | GSE100541 | GEO
Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
2016-09-16 | GSE83893 | GEO
Project description:The goal of this study was to compare differentially expressed transcripts in onion bulbs induced when inoculated with Salmonella using transcriptome profiling (RNA-seq) .Transcriptomic analysis of onion bulb tissue (Variety Don Victor) in response to Salmonella was performed 24 hours and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) in onion. Within 24 hours of inoculation, 4259 genes were upregulated while 3393 genes were downregulated. After 7 days, 8213 and 6417 genes were up and down-regulated, respectively, as shown below. (FDR<0.05 and Abs (log 2(Y/X) >0)
2025-02-28 | GSE260624 | GEO
Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses.
2012-01-15 | GSE28159 | GEO
Project description:This study aimed to compare differentially expressed transcripts in Salmonella recovered from the inoculated onion bulbs using transcriptome profiling (RNA-seq). The Salmonella strains of Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation. Transcriptomic analysis of Salmonella was performed 1 day (24 hours) and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) . 925 and 736 genes were upregulated within 24 hours and seven days after inoculation, while the number of downregulated genes in the same timeframe was 690 and 826, respectively (FDR<0.05 and Abs (log 2(Y/X) >0).
2025-02-28 | GSE260691 | GEO
Project description:To obtain a Notch-depleted base cell line into which we could integrate specific ligands or receptors for quantitative analysis of Notch signaling interactions, we conducted 2 rounds of transfection with RNPs (ribonucleoproteins) consisting of gRNAs targeting Notch2 and Jagged1 complexed with Cas9 protein. After antibiotic selection and screening of monoclonal colonies, we obtained the C2C12-Nkd clone, which showed loss of Notch2 protein and Jag1 transcript.
2023-06-02 | GSE233573 | GEO