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TranscriptomicsThe Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection
Termination of RNAPII transcription is associated with RNA 3’ end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in S. cerevisiae do not rely on RNA cleavage for termination, but instead ter...
ORGANISM(S): Schizosaccharomyces pombe 
2016-07-22 | E-GEOD-82326 | biostudies-arrayexpress
TranscriptomicsSnapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution
Ribosome assembly in eukaryotes involves the activity of hundreds of assembly factors that direct the hierarchical assembly of ribosomal proteins and numerous ribosomal RNA folding steps. However, detailed insights into the function of assembly factors and ribosomal RNA folding events are lacking. T...
ORGANISM(S): Saccharomyces cerevisiae 
2014-11-14 | E-GEOD-52878 | biostudies-arrayexpress
TranscriptomicsSpliceosome-Mediated-Decay (SMD) regulates expression of non-intronic genes in budding yeast
Purpose: The goals of this study were to determine whether the spliceosome interacts with non-intronic mRNAs Methods: RNAseq was performed on RNA that immunoprecipitated with the yeast SMD1 protein. Tandem-affinity-purified RNAs were extracted and RNAseq libraries were generated using the EpiCentre...
ORGANISM(S): Saccharomyces cerevisiae 
2013-10-11 | E-GEOD-49966 | biostudies-arrayexpress
TranscriptomicsRegulation of mRNA Levels by Suicidal Introns that Induce Nuclear Decay
In eukaryotic cells, inefficient splicing is surprisingly common and leads to degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here we uncover a mechanism by which intronic transcripts are targeted for nuclear degradation in fission yeast. Su...
ORGANISM(S): Schizosaccharomyces pombe 
2015-11-19 | E-GEOD-73144 | biostudies-arrayexpress
ProteomicsRNase III CLASH uncovers sRNA regulatory networks coupling metabolism to production of cytolytic toxins in methicillin resistant Staphylococcus aureus
Methicillin resistant Staphylococcus aureus (MRSA) is an infectious pathogen that poses a significant threat to human health. MRSA is renowned for its ability to adapt to and even thrive in hostile environment within its host. By expressing a battery of virulence factors and toxins, MRSA is able to ...
ORGANISM(S): Staphylococcus aureus 
2022-06-16 | PXD025122 | Pride
Toxin Srna Staphylococcus aureus 
TranscriptomicsTranscriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae
Purpose: The exosome plays major roles in RNA processing and surveillance but the in vivo target range and substrate acquisition mechanisms remain unclear. We applied an in vivo cross-linking technique coupled with deep sequencing (CRAC) that captures transcriptome-wide interactions between individu...
ORGANISM(S): Saccharomyces cerevisiae 
2012-09-25 | E-GEOD-40046 | biostudies-arrayexpress
ProteomicsGlobal mapping of RNA-binding proteins in multi-drug resistant Staphylococcus aureus using 2C_1
S. aureus strain JKD6009 RNase III-HTF and USA300 RNase III-HTF were used in our study to capture the RNA-binding proteome in Staphylococcus aureus. Both strains were inoculated in TSB (Tryptone soya broth, Oxioid CM0129) and overnight cultured in 37°C, 200 rpm shaker. Strain JKD6009 RNase III-HTF w...
ORGANISM(S): Staphylococcus aureus 
2022-05-31 | PXD023368 | Pride
Silica purification Uv cross-linking Rbdome Protein-rna interactions Rna-binding proteins Rbpome Staphylococcus aureus 
ProteomicsGlobal mapping of RNA-binding proteins in multi-drug resistant Staphylococcus aureus using 2C_2
S. aureus strain JKD6009 RNase III-HTF and USA300 RNase III-HTF were used in our study to capture the RNA-binding proteome in Staphylococcus aureus. Both strains were inoculated in TSB (Tryptone soya broth, Oxioid CM0129) and overnight cultured in 37°C, 200 rpm shaker. Strain JKD6009 RNase III-HTF w...
ORGANISM(S): Staphylococcus aureus 
2022-05-31 | PXD023427 | Pride
Silica purification Uv cross-linking Rbdome Protein-rna interactions Rna-binding proteins Rbpome Staphylococcus aureus 
ProteomicsGlobal mapping of RNA-binding proteins in multi-drug resistant Staphylococcus aureus using 2C_3
S. aureus strain JKD6009 RNase III-HTF and USA300 RNase III-HTF were used in our study to capture the RNA-binding proteome in Staphylococcus aureus. Both strains were inoculated in TSB (Tryptone soya broth, Oxioid CM0129) and overnight cultured in 37°C, 200 rpm shaker. Strain JKD6009 RNase III-HTF w...
ORGANISM(S): Staphylococcus aureus 
2022-05-31 | PXD023408 | Pride
Silica purification Uv cross-linking Rbdome Protein-rna interactions Rna-binding proteins Rbpome Staphylococcus aureus 
TranscriptomicsUV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli
UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additio...
ORGANISM(S): Escherichia coli O157:H7 str. Sakai 
2014-05-22 | E-GEOD-46118 | biostudies-arrayexpress
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