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GenomicsClonal expansion analysis of transposon insertions by high-throughput sequencing identifies candidate cancer genes in a PiggyBac mutagenesis screen
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 dri...
ORGANISM(S): Mus musculus 
2013-08-28 | E-GEOD-46210 | biostudies-arrayexpress
TranscriptomicsMIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing
This SuperSeries is composed of the following subset Series: GSE32180: MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [microarray] GSE32184: MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [deep sequencing] Refer to...
ORGANISM(S): Mus musculus 
2011-11-30 | E-GEOD-32183 | biostudies-arrayexpress
GenomicsSynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes
This sample was prepared with a modified version of the Tn4001 transposon commonly used in Mycoplasmas. This transposon is described to work more efficiently in Mycoplasma agalactiae and, by extension, in other Mycoplasma species. This sample was prepared transforming this bacteria with a newly desi...
ORGANISM(S): Mycoplasma agalactiae 
2019-11-15 | E-MTAB-7425 | biostudies-arrayexpress
TranscriptomicsMIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [deep sequencing]
Here we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcr...
ORGANISM(S): Mus musculus 
2011-11-30 | E-GEOD-32184 | biostudies-arrayexpress
TranscriptomicsAn epigenetic role for maternally inherited piRNAs in transposon silencing
In plants and mammals, small RNAs indirectly mediate epigenetic inheritance by specifying cytosine methylation. Here, we find that small RNAs themselves serve as vectors for epigenetic information. Crosses between Drosophila strains that differ in the presence of a particular transposon can pr...
ORGANISM(S): Drosophila melanogaster 
2008-11-28 | E-GEOD-13081 | biostudies-arrayexpress
TranscriptomicsTransposon-based construction of strand-specific RNA-seq libraries
We have developed two methods for efficiently consructing RNA-seq libraries using transposition. Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specifi...
ORGANISM(S): Homo sapiens 
2011-10-10 | E-GEOD-32307 | biostudies-arrayexpress
TranscriptomicsRNA clamping by Vasa assembles a piRNA Amplifier complex on transposon transcripts
Germline-specific Piwi-interacting RNAs (piRNAs) protect the genome against selfish genetic elements and are essential for fertility in animals. piRNAs targeting active transposons are amplified by a feed-forward loop known as the Ping-pong cycle, which links endonucleolytic slicing of target RNA...
ORGANISM(S): Bombyx mori 
2014-06-04 | E-GEOD-57420 | biostudies-arrayexpress
ProteomicsTransposon sequencing uncovers an essential regulatory function of phosphoribulokinase for methylotrophy
Methylotrophy is the ability of organisms to grow at the expense of reduced one-carbon compounds such as methanol or methane. Here, we used transposon sequencing combining hyper-saturated transposon mutagenesis with high-throughput sequencing to define the essential methylotrophy genome of Methyloba...
ORGANISM(S): Methylobacterium extorquens PA1 
2017-07-11 | PXD006834 | Pride
Methylobacterium extorquens pa1 Lc-ms/ms Label-free quantification 
TranscriptomicsTransposon insertion sequencing (Tn-Seq) to identify fitness determinants during nitrogen starvation, carbon starvation, and transitions between them in Pseudomonas aeruginosa
We performed Tn-Seq to identify genetic fitness determinants for starvation survival in Pseudomonas aeruginosa. A pooled mutant library of approximately 180,000 randomly inserted transposon mutants was grown into stationary phase in rich medium (lysogeny broth) and an aliquot of this mutant pool was...
ORGANISM(S): Pseudomonas aeruginosa 
2026-03-04 | E-MTAB-15727 | biostudies-arrayexpress
TranscriptomicsDe novo piRNA cluster formation in the Drosophila germline triggered by transgenes containing a transcribed transposon fragment
PIWI interacting RNAs (piRNAs) provide defense against transposable element (TE) expansion in the germline of metazoans. piRNAs are processed from the transcripts encoded by specialized heterochromatic clusters enriched in damaged copies of transposons. How these regions are recognized as a source o...
ORGANISM(S): Drosophila melanogaster 
2013-04-25 | E-GEOD-41780 | biostudies-arrayexpress
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