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Transposon sequencing
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Ebook "Functional genomics and evolution of photosynthetic systems" aims toward a genome-level understanding of the structure, function, and evolution of photosynthetic systems and the advantages accrued from the availability of phyletically diverse sets of gene sequences for the major components of the photosynthetic apparatus.
426p
tachieuhoa
28-01-2024
3
2
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(BQ) Ebook Plant Reverse Genetics: Methods and Protocols – Part 1 presents the following content: Chapter 1 : analysis of high-throughput sequencing data; chapter 2: identification of plant micrornas using expressed sequence tag analysis; chapter 3: microarray data analysis; chapter 4: setting up reverse transcription quantitative-pcr experiments; chapter 5: virus-induced gene silencing in nicotiana benthamiana and other plant species; chapter 6: agroinoculation and agroinfiltration: simple tools for complex gene function analyses; chapter 7: full-length cdna overexpressor gene hunting syst...
134p
runordie7
30-08-2022
7
2
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Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next-generation sequencing. However, PCR amplification can introduce significant quantitative error.
17p
vigalileogalilei
27-02-2022
12
1
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Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures.
20p
viaristotle
29-01-2022
10
0
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There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based single-cell whole-genome sequencing (scWGS) method named SMOOTH-seq (single-molecule real-time sequencing of long fragments amplified through transposon insertion).
19p
viarchimedes
26-01-2022
14
0
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The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can survive and grow in blood during an infection have not yet been characterized. Here, we identify genes that contribute to growth of E. faecium in human serum through transcriptome profiling (RNA-seq) and a highthroughput transposon mutant library sequencing approach (Tn-seq).
12p
vilarryellison
29-10-2021
10
1
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Transposon-mediated, non-viral gene delivery is a powerful tool for generating stable cell lines and transgenic animals. However, as multi-copy insertion is the preferred integration pattern, there is the potential for uncontrolled changes in endogenous gene expression and detrimental effects in cells or animals. Our group has previously reported on the generation of several transgenic cattle by using microinjection of the Sleeping Beauty (SB) and PiggyBac (PB) transposons and seeks to explore the long-term effects of this technology on cattle.
12p
vibeauty
23-10-2021
7
0
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Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature invertedrepeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities.
16p
vibeauty
23-10-2021
12
1
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The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare.
12p
visilicon2711
20-08-2021
12
2
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Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are currently underway.
14p
visilicon2711
20-08-2021
11
1
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Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy.
17p
viansan2711
30-07-2021
19
1
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In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes.
11p
vijeeni2711
24-07-2021
15
0
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Knowledge of which genes are essential to the survival of an organism is critical to understanding the function of genes, and for the identification of potential drug targets for antimicrobial treatment. Previous statistical methods for assessing essentiality based on sequencing of tranposon libraries have usually limited their assessment to strict ‘essential’ or ‘non-essential’ categories.
12p
viwyoming2711
16-12-2020
16
1
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Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, making it difficult to identify locations of its insertions by alignment programs for NGS.
9p
vikentucky2711
26-11-2020
11
0
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Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional mutant populations.
8p
vikentucky2711
24-11-2020
17
1
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Tn-Seq is a high throughput technique for analysis of transposon mutant libraries to determine conditional essentiality of a gene under an experimental condition. A special feature of the Tn-seq data is that multiple mutants in a gene provides independent evidence to prioritize that gene as being essential.
11p
viflorida2711
30-10-2020
10
2
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The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest.
10p
viflorida2711
30-10-2020
12
2
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Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described for identifying conditionally essential genes whose tolerance for insertions varies between two conditions.
15p
vicolorado2711
23-10-2020
16
1
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Brassica includes many successfully cultivated crop species of polyploid origin, either by ancestral genome triplication or by hybridization between two diploid progenitors, displaying complex repetitive sequences and transposons.
13p
viminato2711
22-05-2020
14
0
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Transposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the wheat genome remains largely unclear.
11p
viharuno2711
21-04-2020
12
1
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