Genome-edited tomato sequencing
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ABSTRACT:
PROVIDER: PRJEB83984 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tomato CRISPR-Edited Microbiome Associated Raw sequence reads
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Project description:We report the first use of genome-edited human kidney organoids, combined with single-cell transcriptomics, to study APOL1 risk variants at the native genomic locus in different nephron cell types. This approach captures interferon-mediated induction of APOL1 gene expression and cellular dedifferentiation with a secondary insult“second hit” of endoplasmic reticulum stress.
2020-01-24 | GSE135663 | GEO
Project description:We have found that MtFTb genes play a role in the response to LD conditions, both under vernalized and non-vernalized conditions. To explore the regulatory gene network downstream of FTb genes on a global scale, we performed RNA sequencing of the gene-edited Mtftb1/b2 vs WT plants. For this, we grew wild-type and gene-edited Mtftb1/2 plants under two different conditions: vernalised long days (VLD), where the plants were vernalized for 14 days and then grown for two weeks under LD photoperiod, with the aim of capture changes in expression profiles in the period in which the plant becomes physiologically committed to flower; the second condition was non-vernalised long days (NVLD), where non-vernalized plants were grown for 60 days, a crucial time point when wild-type plants typically undergo the transition to flowering. This approach allowed us to investigate the gene expression changes in the FTb1/2 mutant independent of vernalization effects.
2024-08-01 | E-MTAB-13536 | biostudies-arrayexpress
Project description:We report here NGS RNA-seqencing datasets with wild-type (Chiifu) and GI-edited Chinese cabbage (named gi/CRISPR) grown under optimal temperature (22℃) or treated with high-temperature (37°C for 1 h). Through these RNA-seq analyses, we found differential expression of genes involved in elongated growth between Chiifu and gi/CRISPR plants.
2022-08-30 | GSE211884 | GEO
Project description:Oocytes, the irreplaceable gametes for generating a new organism, are matured in the ovary of living female animals. It is unknown whether any genetic manipulations can be applied to oocytes inside the living ovaries. As a proof-of-concept, we here demonstrate genetic amendments of zebrafish immature oocytes within the ovary. Oocyte microinjection in situ (OMIS) stimulates tissue repair responses, but some of microinjected immature oocytes are matured, ovulated and fertilizable. By OMIS-mediated Cas9 approach, ntla and gata5 loci of oocytes arrested at prophase I of meiosis are successfully edited before fertilization. Through OMIS, high efficiency of biallelic mutations in single or multiple loci using Cas9/gRNAs allows immediate manifestation of mutant phenotypes in F0 embryos and multiple transgenes can co-express the reporters in F0 embryos with patterns similar to germline transgenic embryos. Our approach opens a door to efficient modification of the genome and provides a possibility to repair defective oocytes in situ.
2018-08-31 | GSE111677 | GEO
Project description:SNV microarray data from eleven family members in a family with high rates of cardiomyopathy Source name refers to patient position in pedigree from "Genome-edited cardiac models reveal combinatorial genetic interactions in human cardiomyopathy" by Deacon et al
2018-10-27 | GSE121844 | GEO
Project description:Gene-edited Mtsoc1 triple mutant Medicago plants do not flower
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Project description:Acute lymphoblastic leukemia harboring the fusion genes involving the MEF2D transcription factor (MEF2D-ALL) is associated with poor clinical outcomes. To explore binding sites in the genome in MEF2D-ALL, we genome-edited a MEF2D-ALL cell line Kasumi-7 so that the fusion is tagged with HA at the carboxyl-terminal and co-expressed with GFP. We used this cell line for ChIP-seq using anti-HA antibody. Pair-end reads for Input and HA ChIP DNA are provided.
2020-06-30 | E-MTAB-8466 | biostudies-arrayexpress
Project description:Background: Beta-thalassemia is among the commonest monogenic disorders, posing a major global health challenge. Editing of genetic modifiers of β-thalassemia, such as BCL11A erythroid enhancer and HBG promoters, enhances fetal hemoglobin (HbF) expression and confers major therapeutic potential. Double-strand-break (DSB)-independent genome editing tools, such as base editors, are potentially safer and better suited for multiplexed application than traditional DSB-dependent CRISPR/Cas technology. However, harmful inadvertent on- and off-target events remain a concern and must be excluded before clinical application, including chromosomal rearrangements, which are invisible to standard detection technologies. Results: Using primary patient-derived CD34+ cells from three donors, we investigated simplex and duplex BE-based disruption of the BCL11A erythroid enhancer and the BCL11A binding site (-115bp) on the HBG promoter for DNA-level events and functional studies at the RNA, protein, and morphological level. Analyses included direct comparison to DSB-based editing, as the current clinically applied standard, and analysis of DNA recombination events by CAST-seq to allow wider inferences for relative safety of DSB-, BE- and duplex BE-based editing. Our study reveals the effectiveness of duplex base editing, with robust γ-globin and HbF induction and significantly improved functional correction over simplex editing. Moreover, duplex editing resulted in low incidence of simple and complex genomic alterations in both therapeutically relevant target loci. Conclusions: Here we display simultaneous duplex base editing by targeting both BCL11A erythroid enhancer and HBG promoter for functional correction and genome integrity. Our study highlights the efficacy, safety, and therapeutic potential of the present duplex BE approach
2025-12-22 | GSE307482 | GEO
Project description:Wild-type (WT) miR-378a-3p or edited miR-378a-3p were expressed in SB2 KD-ADAR1 cells to identify the genes regulated by edited miR-378a-3p vs WT miR-378a-3p. PARVA was one of the genes identified to be regulated by edited miR-378a-3p. We demonstrate that this regulation of PARVA is lost in highly metastatic melanoma cells. Microarray analysis was used to evaluate the robustness and reproducibility of the method used to generate the ex vivo tumor tissue model and confirm its ability to recapitulate the essential features of the original tumor.
2018-02-22 | GSE107088 | GEO