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TranscriptomicsWidespread Co-translational RNA Decay Reveals Ribosome Dynamics
It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5′–3′ transcript degradation follows the last translating ribosome, producing...
ORGANISM(S): Schizosaccharomyces pombe 
2015-06-04 | E-GEOD-63120 | biostudies-arrayexpress
TranscriptomicsSaccharomyces cerevisiae Transcript Isoform mapping
Extensive transcriptional heterogeneity revealed by isoform profiling Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5' capped mRNA transcription start site and the 3' polyadenylation site in different conditions: WT cell...
ORGANISM(S): Saccharomyces cerevisiae 
2013-05-06 | E-GEOD-39128 | biostudies-arrayexpress
ProteomicsMislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3
Severe forms of dilated cardiomyopathy (DCM) are associated with point mutations in the alternative splicing regulator RBM20 that are frequently located in the arginine/serine-rich domain (RS-domain). Such mutations can cause defective splicing and cytoplasmic mislocalization, which leads to the for...
ORGANISM(S): Homo sapiens (Human) 
2023-06-19 | PXD038790 | Pride
Human Heart Splicing Dilated cardiomyopathy 
TranscriptomicsGenome-wide study of nuclear poly(A) binding protein Nab2p depletion
Polyadenylation of mRNA is a key step in eu- karyotic gene expression. However, despite the ma- jor impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S....
ORGANISM(S): Saccharomyces cerevisiae 
2015-08-13 | E-GEOD-65001 | biostudies-arrayexpress
GenomicsGenome-wide Ste12-binding site mapping in MATa segregants of YJM789 x S96 cross
In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverge...
ORGANISM(S): Saccharomyces cerevisiae 
2010-02-18 | E-GEOD-19635 | biostudies-arrayexpress
TranscriptomicsSaccharomyces cerevisiae 3' poly(A) site mapping
The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented ef...
ORGANISM(S): Saccharomyces cerevisiae 
2013-01-10 | E-GEOD-40110 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA Seq of hematopoietic stem and progenitor cells
This dataset is part of a study that investigated how the hematopoietic system coordinates the rapid and efficient regeneration of the megakaryocytic lineage during stress scenarios. We found that the phenotypic hematopoietic stem cell (HSC) compartment contains stem-like megakaryocyte-committed pro...
ORGANISM(S): Mus musculus 
2015-08-31 | E-GEOD-64002 | biostudies-arrayexpress
GenomicsHeLa Cell Genome Sequencing Studies

This study contains all authorized whole genome sequence data of the HeLa cell line from datasets currently in dbGaP. These data have been approved for health, medical, and/or biomedical research purposes. Access to these data can be granted for one year. Accessible data will include the studies ...

phs000640.v1.p1 | EGA
OtherInsights into RNA biology from an atlas of mammalian mRNA-binding proteins.
Data from ProteomeXchange, PXD ID: PXD002880. Experiment: KS_A4_3, file: folder summary. Published as part of Cell. 2012 Jun 8;149(6):1393-406 . From the Abstract: {{i}} RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV cro...
ORGANISM(S): Homo_sapiens_viruses, Human_female 
GPM11210041750 | GPMDB
Resource Reanalysis 
OtherInflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors.
Data from ProteomeXchange, PXD ID: PXD001500. Experiment: IFNAR_KO_Prog_78a, file: 120503_JH_IFNAR_KO_Prog_78a_10.mzml. Published as part of Cell Stem Cell. 2015 Aug 19. pii: S1934-5909(15)00306-9 . From the Abstract: {{i}} ... Here, we report that the phenotypic hematopoietic stem cell (HSC) compa...
ORGANISM(S): Mus_musculus_viruses, Mouse 
GPM32310023393 | GPMDB
Resource Reanalysis 
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