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TranscriptomicsNascent-seq indicates widespread cotranscriptional RNA editing in Drosophila
The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high-throughput sequencing. There ...
ORGANISM(S): Drosophila melanogaster 
2012-05-31 | E-GEOD-37232 | biostudies-arrayexpress
TranscriptomicsNascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [StrandSpe_NascentSeq]
Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control...
ORGANISM(S): Mus musculus 
2012-11-10 | E-GEOD-36873 | biostudies-arrayexpress
GenomicsCLK:BMAL1 is a pioneer-like transcription factor [MNase-Seq]
The mammalian circadian clock relies on the master genes CLOCK (CLK) and BMAL1 and drives rhythmic gene expression to regulate biological functions under circadian control. We recently uncovered a surprising disconnect between the rhythmic binding of CLK:BMAL1 on DNA and the transcription of its tar...
ORGANISM(S): Mus musculus 
2014-01-06 | E-GEOD-47142 | biostudies-arrayexpress
GenomicsCLK:BMAL1 is a pioneer-like transcription factor [CLK_ChIP]
The mammalian circadian clock relies on the master genes CLOCK (CLK) and BMAL1 and drives rhythmic gene expression to regulate biological functions under circadian control. We recently uncovered a surprising disconnect between the rhythmic binding of CLK:BMAL1 on DNA and the transcription of its tar...
ORGANISM(S): Mus musculus 
2014-01-06 | E-GEOD-47144 | biostudies-arrayexpress
TranscriptomicsNascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [Nascent-Seq]
Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control...
ORGANISM(S): Mus musculus 
2012-11-10 | E-GEOD-36872 | biostudies-arrayexpress
GenomicsCLK:BMAL1 is a pioneer-like transcription factor [H2AZ-ChIP]
The mammalian circadian clock relies on the master genes CLOCK (CLK) and BMAL1 and drives rhythmic gene expression to regulate biological functions under circadian control. We recently uncovered a surprising disconnect between the rhythmic binding of CLK:BMAL1 on DNA and the transcription of its tar...
ORGANISM(S): Mus musculus 
2014-01-06 | E-GEOD-47143 | biostudies-arrayexpress
TranscriptomicsNascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [RNA-Seq]
Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control...
ORGANISM(S): Mus musculus 
2012-11-10 | E-GEOD-36871 | biostudies-arrayexpress
GenomicsNascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [ChIP-seq]
Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expression. A substantial fraction of the transcriptome undergoes oscillations in many organisms and tissues, which governs the many biochemical, physiological and behavioral functions under circadian control...
ORGANISM(S): Mus musculus 
2012-11-10 | E-GEOD-36874 | biostudies-arrayexpress
TranscriptomicsNascent-Seq Indicates Widespread Cotranscriptional pre-mRNA Splicing in Drosophila
To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced nascent RNA transcripts from Drosophila S2 cells as well as from Drosophila heads. 87% of introns assayed manifest more than 50% cotranscriptional splicing. The remaining 13% are cotranscriptionally spliced poorly,...
ORGANISM(S): Drosophila melanogaster 
2011-12-01 | E-GEOD-32950 | biostudies-arrayexpress
TranscriptomicsThe Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs [miRNA-seq].
Using high throughput sequencing of Drosophila head RNA, a small set of miRNAs that undergo robust circadian oscillations in levels were discovered. We concentrated on a cluster of six miRNAs, mir-959-964, all of which peak at about ZT12 or lights-off. The data indicate that the cluster pri-miRNA is...
ORGANISM(S): Drosophila melanogaster 
2012-11-02 | E-GEOD-40943 | biostudies-arrayexpress
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