TE-Array-- A high throughput tool to study transposon transcription
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA228116 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:TE-Array is a custom Agilent microarray that probes for transposable elements in both sense and antisense orientations in humans and mice. TE-Array was used to study expression levels of transposable elements (TE) in a panel of normal mouse tissues. TE-Array comprises of 4 different custom Agilent 4X44K designs. These 4 different designs have probes for human sense orientation, human antisense orientation, mouse sense orientation and mouse antisense orientation transposable elements. These array designs were used to study the transposon abundance profile in 7 different mouse tissue samples, 2 mouse cell lines and 1 transposon transfected versus untransfected human cell line.
2013-11-16 | E-GEOD-52412 | biostudies-arrayexpress
Project description:TE-Array is a custom Agilent microarray that probes for transposable elements in both sense and antisense orientations in humans and mice. TE-Array was used to study expression levels of transposable elements (TE) in a panel of normal mouse tissues.
2013-11-16 | GSE52412 | GEO
Project description: Not available
| S-EPMC3878892 | biostudies-literature
Project description:Somatic transposon mutagenesis in mice is an efficient strategy to investigate the genetic mechanisms of tumorigenesis. The identification of tumor driving transposon insertions traditionally requires the generation of large tumor cohorts to obtain information about common insertion sites. Tumor driving insertions are also characterized by their clonal expansion in tumor tissue, a phenomenon that is facilitated by the slow and evolving transformation process of transposon mutagenesis. We describe here an improved approach for the detection of tumor driving insertions that assesses the clonal expansion of insertions by quantifying the relative proportion of sequence reads obtained in individual tumors. To this end, we have developed a protocol for insertion site sequencing that utilizes acoustic shearing of tumor DNA and Illumina sequencing. We analyzed various solid tumors generated by PiggyBac mutagenesis and for each tumor >10^6 reads corresponding to >10^4 insertion sites were obtained. In each tumor, 9 to 25 insertions stood out by their enriched sequence read frequencies when compared to frequencies obtained from tail DNA controls. These enriched insertions are potential clonally expanded tumor driving insertions, and thus identify candidate cancer genes. The candidate cancer genes of our study comprised many established cancer genes, but also novel candidate genes such as Mastermind-like1 (Mamld1) and Diacylglycerolkinase delta (Dgkd). We show that clonal expansion analysis by high-throughput sequencing is a robust approach for the identification of candidate cancer genes in insertional mutagenesis screens on the level of individual tumors. Solid tumors in mice were generated by somatic transposon mutagenesis with a PiggyBac transposon system. Insertion sites of transposons in 11 tumors and 6 non-cancerous tail controls were determined by Illumina high-throughput sequencing. Insertions were determined both on 5' and 3' sides of the transposon (PB5 and PB3, respectively). Quantitative analysis of read numbers revealed enrichment of certain insertions in tumors, but not in controls, and these enriched insertions identify candidate cancer genes.
2013-08-28 | E-GEOD-46210 | biostudies-arrayexpress
Project description:We have developed a microarray intended for use in finding all transposons in a region of interest. By selectively amplifying and hybridizing transposon flanking DNA to our array, we can localize all transposons in the region present on our TIP-chip, a dense tiling array. We have tested our technology in yeast and have been successful. Keywords: transposon insertion profiling, genomic DNA, yeast
2007-01-01 | GSE5646 | GEO
Project description:Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. Using our tool, we demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancers, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis, and we translated this technology to the crop soybean. We have engineered a ‘junk’ TE into a useful and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
2024-05-03 | GSE227103 | GEO
Project description:Sporosarcina sp. Te-1 Genome sequencing
| PRJNA713852 | ENA
Project description:Genome editing tools with high precision are key to develop improved crops but current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone. Transposable elements (TEs) evolved to insert their DNA seamlessly into genomes, albeit in a quasi-random pattern. We developed a genome engineering tool that controls the TE insertion site and subsequently the delivery of any cargo attached to this TE. Using our tool, we demonstrated sequence-specific targeted delivery (guided by the CRISPR gRNA) of enhancers, an open reading frame and gene expression cassette into the genome of the model plant Arabidopsis, and we translated this technology to the crop soybean. We have engineered a ‘junk’ TE into a useful and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
2024-05-03 | GSE227104 | GEO
Project description:CRISPR/Cas systems have gained prominence as powerful tools for genome engineering. Recent investigations into the crucial role of transposable elements (TEs) have stimulated research interest in manipulating TEs to elucidate their functions. Nevertheless, designing single guide RNAs (sgRNAs) that are both specific and efficient for TE manipulation presents a formidable challenge, considering the repetitive nature and high copy numbers of TEs. Although various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer explicitly for TE manipulation has yet to be established. To bridge this gap, we presented CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn. CRISPR-TE could identify all potential sgRNAs for TEs and offers a comprehensive solution for efficient TE targeting at both the single duplicate and subfamily levels. We also demonstrated that young TEs can be targeted with higher coverage at the subfamily level. Finally, we validated the overexpression of SVAD, a human-specific TE, using dCas9-VP64 activator incorporated with three sgRNAs designed by our tool. Collectively, our findings suggest that CRISPR-TE may serve as a versatile framework for designing sgRNAs aimed at TE targeting.
2024-03-24 | GSE228266 | GEO
Project description:Streptococcus pneumoniae is a major cause of serious infections such as pneumonia and meningitis in both children and adults worldwide. Here, we describe the development of a high-throughput genome-wide technique, Genomic Array Footprinting (GAF), for the identification of genes essential for this bacterium at various stages during infection. GAF enables negative screens by means of a combination of transposon mutagenesis and microarray technology for the detection of transposon insertion sites. We tested several methods for the identification of transposon insertion sites and found that amplification of DNA adjacent to the insertion site by PCR resulted in non-reproducible results, even when combined with an adapter. However, restriction of genomic DNA followed directly by in vitro transcription circumvented these problems. Analysis of parallel reactions generated with this method on a large mariner transposon library, showed that it was highly reproducible and correctly identified essential genes. Comparison of a mariner library to one generated with the in vivo transposition plasmid pGh:ISS1, showed that both have an equal degree of saturation, but that 9% of the genome is preferentially mutated by either one. The usefulness of GAF was demonstrated in a screen for genes essential for survival of zinc stress. This identified a gene encoding a putative cation efflux transporter, and its deletion resulted in an inability to grow under high zinc conditions. In conclusion, we developed a fast, versatile, specific, and high-throughput method for the identification of conditionally essential genes in S. pneumoniae. Keywords: GAF Identification of transposon insertion sites
2007-06-26 | GSE6913 | GEO