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ProteomicsRAPIDASH: Tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues, cancer cells, and macrophages - label-free MS RAPIDASH of L36-FLAG and S17-FLAG E14 mESCs
Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translation. Nevertheless, a lack of technologies to enrich RAPs across sample types has prevented systematic analysis of RAP identities, dynamics, and functions. W...
ORGANISM(S): Mus musculus (Mouse) 
2024-09-12 | PXD054300 | Pride
Acquity uplc m-class system Embryonic stem cell Orbitrap elite Ribo-flag immunoprecipitation Ribosome Ribosome-associated proteins Mouse 
TranscriptomicsIntegrative AUF1 PAR-CLIP analysis uncovers AUF1 roles in translation and genome integrity (PAR-CLIP)
We report that AUF1 modulates global mRNA stability and translation, in turn promoting the maintenance of DNA integrity. Please see individual series. In short, for AUF1 PAR-CLIP, the four isoforms of AUF1 (p37, p40, p42, and p45) tagged with a Flag epitope were expressed in HEK293 cells. For total ...
ORGANISM(S): Homo sapiens 
2014-11-05 | E-GEOD-52971 | biostudies-arrayexpress
TranscriptomicsMapping of Rec12 oligonucleotides in Schizosaccharomyces pombe
Meiotic recombination facilitates accurate pairing and faithful segregation of homologous chromosomes by forming physical connections (crossovers) between homologs. Developmentally programmed DNA double-strand breaks (DSBs) generated by Spo11 protein (Rec12 in fission yeast) initiate meiotic recombi...
ORGANISM(S): Schizosaccharomyces pombe 
2013-08-20 | E-GEOD-49977 | biostudies-arrayexpress
TranscriptomicsPolynucleotide phosphorylase can interact with small noncoding RNAs in both stabilizing and degradative modes
In all bacterial species examined thusfar, small regulatory RNAs (sRNAs) contribute to intricate patterns of genetic regulation. Many of the actions of these nucleic acids are mediated by chaperones such as the Hfq protein, and genetic screens have identified the exoribonuclease polynucleotide phosp...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2016-01-13 | E-GEOD-69856 | biostudies-arrayexpress
TranscriptomicsRIP-seq to identify transcripts interacting with pluripotency factors in mouse embryonic stem cells
Sox2 is a master transcriptional regulator of embryonic development. Having found that Sox2 interacts with RNA-binding proteins, we designed an experiment to discover RNAs associated with Sox2 and other pluripotency factors. Briefly, we used RNA immunoprecipitation followed by high-throughput sequen...
ORGANISM(S): Mus musculus 
2019-02-11 | E-MTAB-7640 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation and RNA-seq analysis in purified quiescent yeast cells to identify the genomic RNA polymerase II and histone H3 methylation occupancy profiles and the quiescent cell transcriptome.
A defining characteristic of quiescent cells is their low level of gene activity compared to growing cells. Using a yeast model for cellular quiescence, we compared the genome-wide profiles of multiple histone modifications between growing and quiescent cells, and correlated these profiles with the...
ORGANISM(S): Saccharomyces cerevisiae 
2016-09-01 | E-GEOD-72650 | biostudies-arrayexpress
TranscriptomicsRibo-seq of iPSC-derived neurons with TDP-43 knockdown
TDP-43 is a key splicing regulator. Here, we perform ribosome profiling on iPSC-derived neurons to examine how translation is affected by TDP-43 knockdown.
ORGANISM(S): Homo sapiens 
2022-02-28 | E-MTAB-10235 | biostudies-arrayexpress
TranscriptomicsCytoplasmic Rbfox1 regulates the neuronal expression of synaptic and autism-related genes
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Mus musculus 
2015-12-10 | E-GEOD-71917 | biostudies-arrayexpress
TranscriptomicsTarget discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Homo sapiens 
2015-07-06 | E-GEOD-69586 | biostudies-arrayexpress
TranscriptomicsYeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Schizosaccharomyces pombe 
2014-07-01 | E-GEOD-46506 | biostudies-arrayexpress
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