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20
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ShareScore release 0.9.0
Dataset results
20 results for “T-DNA”
T-DNAreader: fast and precise identification of T-DNA insertion sites using RNA-seq data
<p><em><span>Agrobacterium</span></em><span>-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into the host genome and multiple T-DNAs can integrate in a single transformation event, necessitating the development of efficient, reliable tools to identify the T-DNA insertion sites (TISs). Here, we developed T-DNAreader to identify TISs from RNA-sequencing (RNA-seq) data with high precision, sensitivity, and speed, outperforming existing tools. T-DNAreader detected previously unknown TISs in characterized mutant plants. Overall, T-DNAreader enables the simple identification of TISs within transcribed regions and standardizes the characterization of T-DNA-containing transgenic plants.</span></p>
Dataset: T-DNA characterization of genetically modified 3-R-gene late blight resistant potato events with a novel procedure utilizing the Samplix Xdrop® Enrichment Technology
<p>Before commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, Polymerase Chain Reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole genomic sequencing coverage that meets regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234 and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.</p>
Targeted sequencing of T-DNA borders in OCP1xOGC transgenic lines of Camelina
<p>Background: Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.</p> <p>Results: We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via <em>Agrobacterium</em>. We present an example using the allohexaploid oil-seed plant <em>Camelina sativa</em> to determine insertion site location of two transgenes.</p> <p>Conclusion: This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.</p>
Dataset: T-DNA characterization of genetically modified 3-R-gene late blight resistant potato events with a novel procedure utilizing the Samplix Xdrop® Enrichment Technology
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Targeted sequencing of T-DNA borders in OCP1xOGC transgenic lines of Camelina
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Data from: Evaluating population genomic candidate genes underlying flowering time in Arabidopsis thaliana using T-DNA insertion lines
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RNA-seq of Arabidopsis thaliana seedlings with T-DNA insertions in TCP14
GEO Series GSE90083. Arabidopsis thaliana. 9 samples. Type: Expression profiling by high throughput sequencing.
Dyw2-DYW2_OTP100: Identification of the transcriptome defects (nuclear and organelles) of the T-DNA KO mutants of DYW2 and OTP100
GEO Series GSE100298. Arabidopsis thaliana. 12 samples. Type: Expression profiling by high throughput sequencing.
Analysis of gene expression from fbn5-1 T-DNA insertion mutant of Arabidopsis
GEO Series GSE68275. Arabidopsis thaliana. 8 samples. Type: Expression profiling by array.
Arabidopsis thaliana open flowers: Wild type vs. sdg4 mutant (SALK T-DNA line_128444)
GEO Series GSE9543. Arabidopsis thaliana. 2 samples. Type: Expression profiling by array.
Expression data from the T-DNA insertion line atpip1;2-1
GEO Series GSE62167. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- T-DNA mutants (2)
GEO Series GSE46937. Histoplasma capsulatum. 18 samples. Type: Expression profiling by array.
A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen -- T-DNA mutants (1)
GEO Series GSE46936. Histoplasma capsulatum. 16 samples. Type: Expression profiling by array.
Expression data of Arabidopsis thaliana wild-type plants and quadruple nas T-DNA insertion mutants grown under different Fe supply conditions
GEO Series GSE24348. Arabidopsis thaliana. 24 samples. Type: Expression profiling by array.
Whole-genome resequencing of T-DNA insertion lines
GEO Series GSE102126. Arabidopsis thaliana. 9 samples. Type: Other.
The position and complex genomic architecture of plant T-DNA insertions revealed by 4C
GEO Series GSE147542. Arabidopsis thaliana. 118 samples. Type: Other.
Arabidopsis thaliana ecotype Col-0 versus T-DNA mutant sir1-1
GEO Series GSE20670. Arabidopsis thaliana. 6 samples. Type: Expression profiling by array.
Transcription profiling of wild type Basmati 370 and its T-DNA insertional mutant OsAPC6.
GEO Series GSE31200. Oryza sativa; Oryza sativa Indica Group. 4 samples. Type: Expression profiling by array.
Transcription profiling of Basmati T-DNA insertional mutant lines
GEO Series GSE31248. Oryza sativa; Oryza sativa Indica Group. 6 samples. Type: Expression profiling by array.
myb52-2 t-dna -Transcriptome analysis of atmyb52 mutant vs wild-type
GEO Series GSE43647. Arabidopsis thaliana. 4 samples. Type: Expression profiling by array.
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