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MetabolomicsElucidation of the epitranscriptomic RNA modification landscape of chikungunya virus

The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. ...

2024-06-11 | MTBLS8697 | MetaboLights
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
TranscriptomicsSingle-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms
Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we established an expe...
ORGANISM(S): Homo sapiens 
2021-06-16 | E-MTAB-7334 | biostudies-arrayexpress
TranscriptomicsAnalysis and design of RNA sequencing experiments for identifying mRNA isoform regulation
Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expr...
ORGANISM(S): Homo sapiens 
2010-11-07 | E-GEOD-23694 | biostudies-arrayexpress
TranscriptomicsIsoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq
To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (C...
ORGANISM(S): Mus musculus 
2012-01-17 | E-GEOD-33343 | biostudies-arrayexpress
TranscriptomicsSingle-cell RNA counting at allele- and isoform-resolution using Smart-seq3
Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencin...
ORGANISM(S): mixed sample 
2020-04-14 | E-MTAB-8735 | biostudies-arrayexpress
MetabolomicsTargeted metabolomic analysis in hepatic extracts, serum, and urine of female mice gavaged with TCDD every 4 days for 28 days
TCDD is an environmental contaminant that elicits a number of hepatic effects including fat accumulation, inflammation, and fibrosis that can progress to hepatocellular carcinoma. RNA-Seq and targeted metabolomics were integrated with complementary dioxin response element (DRE) location and aryl hyd...
2017-02-02 | MTBLS225 | MetaboLights
ProteomicsEMpire: Deep isoform level integration of the transcriptome, translatome, and proteome
In this study, we make used of mRNA-seq and its ability to reliably quantify isoforms, integrating this data with ribosome profiling and LC-MS/MS, to assign ribosome footprints and peptides at the isoform level. We leverage the principle that most cell types, and even tissues, predominantly express...
ORGANISM(S): Homo sapiens (Human) 
2018-08-21 | PXD008693 | Pride
Proteomics Mrna-seq Protien isoforms Lc-ms/ms 
TranscriptomicsAlternative Isoform Regulation in Human Tissue Transcriptomes
Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of...
ORGANISM(S): Homo sapiens 
2008-09-30 | E-GEOD-12946 | biostudies-arrayexpress
ProteomicsDynamics and consequences of widespread transcript isoform changes during neuronal differentiation
Static gene expression programs have been extensively characterized in stem cells and mature human cells. However, the dynamics of RNA isoform change upon cell-state transitions during cell differentiation, and the determinants and functional consequences have largely remained unclear. Here, we used...
ORGANISM(S): Homo sapiens (Human) 
2024-04-11 | PXD046084 | Pride
Cell differentiation Neurogenesis Multi-omics Rna isoform Nanopore sequencing 
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