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ProteomicsIdentification of proteins and miRNAs that specifically bind an mRNA in vivo
Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protei...
ORGANISM(S): Caenorhabditis elegans 
2019-08-12 | PXD013720 | Pride
Q exactive hf-x Caenorhabditis elegans Rna pulldown Q exactive plus 
TranscriptomicsPaternal RNA contributions in the C. elegans zygote
Development of the early embryo is thought to be mainly driven by maternal gene products and post-transcriptional gene regulation. Here, we used metabolic labeling to show that RNA can be transferred by sperm into the embryo. To identify genes with paternal expression in the embryo, we performed cro...
ORGANISM(S): Caenorhabditis elegans 
2014-06-04 | E-GEOD-57351 | biostudies-arrayexpress
TranscriptomicsDetection of circRNA in Drosophila Fly heads and S2 cells using RNA-seq with or without RNaseR tretment
We determined circRNA abundance in fly Heads and S2 cells by generating and analyzing high-throughput RNA-sequencing libraries prepared from rRNA-depleted RNA. In order to determine whether the observed sequencing reads are due to bona fide circRNAs, we pre-treated the RNA with RNAse-R before the rR...
ORGANISM(S): Drosophila melanogaster 
2014-10-14 | E-GEOD-55872 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of miRNA expression among various mouse hematopoietic cell types and hippocampal tissue
Compare miRNA expression among various hematopoietic cell types and hippocampal tissue
ORGANISM(S): Mus musculus 
2005-12-01 | E-MEXP-372 | biostudies-arrayexpress
TranscriptomicsIdentification and characterization of circular RNAs as a new class of putative biomarkers in human blood
Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here,...
ORGANISM(S): Homo sapiens 
2015-10-26 | E-GEOD-73570 | biostudies-arrayexpress
TranscriptomicsConservation of mRNA and protein expression during development of C. elegans
Spatiotemporal control of gene expression is crucial for development and subject to evolutionary changes. Although proteins are the final product of most genes, the developmental proteome of an animal has not yet been comprehensively defined, and the correlation between RNA and protein abundance dur...
ORGANISM(S): Caenorhabditis elegans 
2014-01-23 | E-GEOD-53359 | biostudies-arrayexpress
Transcriptomicssmall RNA profiling in human cell line following Dicer silencing
microRNAs (miRNAs) are a large class of small non-coding RNAs which post-transcriptionally regulate the expression of a large fraction of all animal genes and are important in a wide range of biological processes. Recent advances in high-throughput sequencing allow miRNA detection at unprecedented s...
ORGANISM(S): Homo sapiens 
2011-09-12 | E-GEOD-31069 | biostudies-arrayexpress
TranscriptomicsTranscriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL PAR-CLIP)
Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivi...
ORGANISM(S): Caenorhabditis elegans 
2014-11-20 | E-GEOD-55325 | biostudies-arrayexpress
TranscriptomicsTranscriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK RNA-Seq)
Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivi...
ORGANISM(S): Homo sapiens 
2014-11-20 | E-GEOD-55326 | biostudies-arrayexpress
TranscriptomicsTranscriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK PAR-CLIP)
Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivi...
ORGANISM(S): Homo sapiens 
2014-11-20 | E-GEOD-55324 | biostudies-arrayexpress
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