TE-Array-- A high throughput tool to study transposon transcription
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ABSTRACT:
PROVIDER: PRJNA228116 | ENA |
REPOSITORIES: ENA
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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:Although transposable element (TE) derived DNA accounts for more than half of mammalian genomes and initiates a significant proportion of RNA transcripts, high throughput methods are rarely leveraged specifically to detect expression from interspersed repeats.To characterize the contribution of transposons to mammalian transcriptomes, we developed a custom microarray platform with probes covering known human and mouse transposons in both sense and antisense orientations. We termed this platform the "TE-array" and profiled TE repeat expression in a panel of normal mouse tissues. Validation with nanoString® and RNAseq technologies demonstrated that TE-array is an effective method. Our data show that TE transcription occurs preferentially from the sense strand and is regulated in highly tissue-specific patterns.Our results are consistent with the hypothesis that transposon RNAs frequently originate within genomic TE units and do not primarily accumulate as a consequence of random 'read-through' from gene promoters. Moreover, we find TE expression is highly dependent on the tissue context. This suggests that TE expression may be related to tissue-specific chromatin states or cellular phenotypes. We anticipate that TE-array will provide a scalable method to characterize transposable element RNAs.
| S-EPMC3878892 | biostudies-literature
Project description:We identified known and unknown transposon elements in the cells from healthy donors, FXD patients, and ALL patients by long-read RNA-sequencing. Using these identified TEs, we analyzed the expression of TE-derived genes by shot-read (illumina) RNA-sequencing. We found that expression of some specific TE-derived genes were changed in FXD compared to those in healthy donors. These findings suggested the involvement of modified expressions of TE-derived genes in the pathogenesis of FXD.
2024-10-30 | GSE264090 | GEO
Project description:We identified known and unknown transposon elements in the cells from healthy donors, FXD patients, and ALL patients by long-read RNA-sequencing. Using these identified TEs, we analyzed the expression of TE-derived genes by shot-read (illumina) RNA-sequencing. We found that expression of some specific TE-derived genes were changed in FXD compared to those in healthy donors. These findings suggested the involvement of modified expressions of TE-derived genes in the pathogenesis of FXD.
2024-10-30 | GSE264089 | GEO
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:A new high-density oligonucleotide array of the human transcriptome (GG-H array) has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing, as well as detection of coding SNPs and non-coding transcripts. The GG-H array was validated using samples from multiple independent preparations of human liver and muscle, and compared with results obtained from mRNA sequencing analysis. The GG-H array is highly reproducible in estimating gene and exon abundance, and is sensitive in detecting expression changes and alternative splicing. This array has been implemented in a multi-center clinical program and has generated high quality, reproducible data. When current cost, as well as sample and time requirements for sequencing are considered in the context of a required throughput of hundreds of samples per week for a clinical trial, the array provides a high-throughput and cost effective platform for clinical genomic studies.
2011-01-27 | GSE26072 | 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 | GSE227104 | GEO