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42 results for “insertion site”
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>
Text-fig. 3. Schematic position of the human modifications (cut marks, impact marks, ochre traces, inserted bones) recognised on the canid remains from Předmostí, indicated on a wolf skeleton; the frequencies of the modifications are not shown. Modified after © 2003 ArcheoZoo.org / Michel Coutureau (Inrap). in Consumption Of Canid Meat At The Gravettian Předmostí Site, The Czech Republic
Text-fig. 3. Schematic position of the human modifications (cut marks, impact marks, ochre traces, inserted bones) recognised on the canid remains from Předmostí, indicated on a wolf skeleton; the frequencies of the modifications are not shown. Modified after © 2003 ArcheoZoo.org / Michel Coutureau (Inrap).
Comprehensive characterisation of the genomic insertion site of a transgene in highly repetitive, centromeric region of Anopheles mosquitoes
<p>The availability of the genomic sequence of the malaria mosquito <em>Anopheles</em> <em>gambiae</em> has sparked in recent years the development of transgenic technologies with the potential to be used as novel tools for vector control. These technologies rely on genome editing that confers features able to affect vector capacity. This can be achieved by either reducing the mosquito population or by making mosquitoes refractory to the parasite infection. Although sophisticated molecular techniques such as those based on AttB/AttP site-specific recombination and CRISPR/Cas9 systems can lead to the integration of transgenes in specific sites of the genome, methods that allow semi-random integration are still in use due to their high efficiency; PiggyBac transposon-mediated integrations fall in this category. Characterization of the insertion site of transgenes in transgenic strains generated via PiggyBac integration can be hampered when the transgene is inserted in regions of the genome rich in repetitive sequences. Here we describe a number of techniques that were used to identify the genomic location of the transgene in a repetitive region in the <em>Anopheles gambiae</em> strain Ag(PMB)1 which was initially reported on Chromosome 3R 36D. Whilst Inverse PCR used in previous analysis was unable to distinguish between multiple genomic locations as potential insertion sites of the transgene, here we demonstrate that the use of FISH identifies clearly the integration of the transgene in a poorly annotated centromeric region of Chromosome 2R 19D. This study emphasises the need for accuracy in sequencing data for the genome of organisms of medical importance such as <em>Anopheles </em>mosquitoes. An effort to further improve reference genomes is of paramount importance to support and facilitate vector control interventions based on genome editing.</p>
Text-fig. 4. Rib fragment inserted in the nasal cavity of canid skull fragment (10). in Consumption Of Canid Meat At The Gravettian Předmostí Site, The Czech Republic
Text-fig. 4. Rib fragment inserted in the nasal cavity of canid skull fragment (10).
Injection of Local Anesthetic to Trocar Insertion Sites After Laparoscopy
ClinicalTrials.gov study NCT01688596. IPD Sharing: NO. Countries: 1. Publications: 10.
Insertion sites sizes (FR) and phalangeal size (PTA)
<p>Data to replicate the results of the paper "Insertion sites in manual proximal phalanges of African apes and modern humans. Looking for behavioral traces in phalanges"</p> <p> </p> <p>The database includes the insertion sites sizes (mm<sup>2</sup>) for the A2 pulley in a sample of gorilla, chimpanzee and human hands. These areas in anthropology are called "flexor ridges" (FR). They were measured in 3D models of manual proximal phalanges 2-5 (PP2-PP5) It also includes the area (mm<sup>2</sup>) of the corresponding phalanges (PTA), the length of the first metacarpal of the corresponding hand (MC1_length) and the sex of the individuals, when known. </p> <p> </p> <p>Please cite: Bucchi, A., Luengo, J., Del Bove, A & Lorenzo, C. (2020) Lorenzo. Insertion sites in manual proximal phalanges of African apes and modern humans. American Journal of Physical Anthropology 173(3), 556-567. doi: 10.1002/ajpa.24127.</p>
The Influence of Nursing Technique Applied at the Central Venous Catheter Insertion Site Upon the Incidence of Infection
ClinicalTrials.gov study NCT03875352. IPD Sharing: NO. Countries: 1. Publications: 5.
Unilateral TAP Block vs Trocar Insertion Sites Infiltration Anesthesia in Laparoscopic Cholecystectomy
ClinicalTrials.gov study NCT03543202. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Identifying Local Signs at the Catheter Insertion Site With Artificial Intelligence
ClinicalTrials.gov study NCT05440396. IPD Sharing: NO. Countries: 1. Publications: 6.
Long Peripheral Intravenous Catheter Insertion Site and Catheter-related Complications in Antimicrobial Therapy
ClinicalTrials.gov study NCT06455228. IPD Sharing: NO. Countries: 1. Publications: 1.
Effect-site Concentration of Propofol for I-gel Insertion During Anesthesia Induction With a Single-dose Dexmedetomidine
ClinicalTrials.gov study NCT02268656. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Central Venous Catheter Insertion Site and Colonization in Pediatric Cardiac Surgery
ClinicalTrials.gov study NCT03282292. IPD Sharing: YES. Countries: 1. Publications: 10.
Variability of Infant LP Insertion Site Based On Procedural Experience
ClinicalTrials.gov study NCT02949869. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
A Comparison of Peripheral Nerve Catheter Securement Techniques at the Insertion Site in Healthy Volunteers
ClinicalTrials.gov study NCT03375190. IPD Sharing: NO. Countries: 1. Publications: 1.
Evaluation of Tissue Glue on PICC and Midline Catheters Insertion Sites
ClinicalTrials.gov study NCT04900740. IPD Sharing: NO. Countries: 1. Publications: 8.
Data from: High-throughput genotyping of green algal mutants reveals random distribution of mutagenic insertion sites and endonucleolytic cleavage of transforming DNA
A high-throughput genetic screening platform in a single-celled photosynthetic eukaryote would be a transformative addition to the plant biology toolbox. Here, we present ChlaMmeSeq (Chlamydomonas MmeI-based insertion site Sequencing), a tool for simultaneous mapping of tens of thousands of mutagenic insertion sites in the eukaryotic unicellular green alga Chlamydomonas reinhardtii. We first validated ChlaMmeSeq by in-depth characterization of individual insertion sites. We then applied ChlaMmeSeq to a mutant pool and mapped 11,478 insertions, covering 39% of annotated protein coding genes. We observe that insertions are distributed in a manner largely indistinguishable from random, indicating that mutants in nearly all genes can be obtained efficiently. The data reveal that sequence-specific endonucleolytic activities cleave the transforming DNA and allow us to propose a simple model to explain the origin of the poorly understood exogenous sequences that sometimes surround insertion sites. ChlaMmeSeq is quantitatively reproducible, enabling its use for pooled enrichment screens and for the generation of indexed mutant libraries. Additionally, ChlaMmeSeq allows genotyping of hits from Chlamydomonas screens on an unprecedented scale, opening the door to comprehensive identification of genes with roles in photosynthesis, algal lipid metabolism, the algal carbon-concentrating mechanism, phototaxis, the biogenesis and function of cilia, and other processes for which C. reinhardtii is a leading model system.
Data from: High-throughput genotyping of green algal mutants reveals random distribution of mutagenic insertion sites and endonucleolytic cleavage of transforming DNA
Open the record for dataset details and reuse information.
Targeted site integration in plants using a transposon system [insertion-seq]
GEO Series GSE227104. Glycine max; Arabidopsis thaliana. 11 samples. Type: Other.
Genome-wide identification of genes critical for in vivo fitness of porcine extraintestinal pathogenic Escherichia coli by using transposon-directed insertion site sequencing
GEO Series GSE197084. Escherichia coli PCN033. 12 samples. Type: Other.
Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites
GEO Series GSE178440. Homo sapiens. 73 samples. Type: Other.
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