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TranscriptomicsAnalysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns
Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest compo...
ORGANISM(S): Saccharum officinarum 
2012-04-16 | E-GEOD-35143 | biostudies-arrayexpress
TranscriptomicsTranscript profiling in LTR mutants
STN7-dependent phosphorylation of an as yet unknown thylakoid protein triggers the signaling events associated with the long-term acclimatory response (LTR). The LTR-associated signaling events regulate the expression of photosynthesis-related genes on the post-transcriptional level (nucleus), as i...
ORGANISM(S): Arabidopsis thaliana 
2009-06-01 | E-GEOD-15939 | biostudies-arrayexpress
GenomicsRetrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells
In this study, we analyzed the DNA methylation levels of 4799 IAP LTRs in three murine cell types: AB2.2 ES cells, somatic cells and a neuroblastoma cell line Neuro2A. According to the results, half of the IAP LTR retrotransposons show constant methylation patterns between the three cell types where...
ORGANISM(S): Mus musculus 
2015-06-15 | E-GEOD-60007 | biostudies-arrayexpress
GenomicsTrichoderma viride strain:LTR-2
Trichoderma viride LTR-2 Whole Genome sequencing
PRJNA266090 | ENA
TranscriptomicsSpt6 Levels are Modulated by PAAF1 and 26S Proteasome to Regulate the HIV-1 LTR and a Subset of Cellular Genes involved in Cancer.
Effect of PAAF1 and Spt6 knock-down on gene expression. Total RNAs were extracted from HeLa-LTR-Luc cells in which PAAF1 or Spt6 had been knock down by a specific siRNA or HeLa-LTR-Luc cells that had been transfected with a control siRNA (“si Neg”). Differentially expressed genes in PAAF1 knock-down...
ORGANISM(S): Homo sapiens 
2012-05-28 | E-GEOD-32033 | biostudies-arrayexpress
TranscriptomicsTranscription factor profiling of T cells containing stably integrated or transiently transfected HTLV-1 LTR.
Transcription factor profiling of T cells containing stably integrated or transiently transfected HTLV-1 LTR. Nuclear extract from one million stably or transiently transfected Jurkat (CD4 T cell) cell line was extracted and labeled with TransSignal Probe mix (Panomics) and then hybridized to the ar...
ORGANISM(S): Homo sapiens 
2011-11-12 | E-GEOD-33628 | biostudies-arrayexpress
TranscriptomicsmiRNA profiling of Jurkat with stably integrated HTLV1-LTR in the presence of HTLV-1 Tax
RNA interference (RNAi) is a natural cellular mechanism to silence gene expression and is predominantly mediated by microRNAs (miRNAs) that target messenger RNA. Viruses can manipulate the cellular processes necessary for their replication by targeting the host RNAi machinery. This study explores th...
ORGANISM(S): Homo sapiens 
2012-08-08 | E-GEOD-39986 | biostudies-arrayexpress
GenomicsLong noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [ChIRP-Seq]
Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [ChIRP-Seq]
PRJNA360462 | ENA
TranscriptomicsTranscript profiling in LTR mutants
STN7-dependent phosphorylation of an as yet unknown thylakoid protein triggers the signaling events associated with the long-term acclimatory response (LTR). The LTR-associated signaling events regulate the expression of photosynthesis-related genes on the post-transcriptional level (nucleus), as in...
ORGANISM(S): Arabidopsis thaliana 
2009-06-01 | GSE15939 | GEO
GenomicsLTR-retrotransposon control by tRNA-derived small RNA
LTR-retrotransposon control by tRNA-derived small RNA
PRJNA324286 | ENA
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