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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
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
ModelsBoehm2014 - isoform-specific dimerization of pSTAT5A and pSTAT5B
Boehm2014 - isoform-specific dimerization of pSTAT5A and pSTAT5B To study STAT5 activation, the authors build a dynamic model of pSTAT5 isoform dimerization. Combinatorial binding of pSTAT5A and pSTAT5B is analysed using model hypotheses and concurrent experiments. Model parameters are derived from ...
2024-09-02 | BIOMD0000000591 | BioModels
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
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
TranscriptomicsIdentification of Common Genetic Variants that Account for Transcript Isoform Variation between Human Populations
In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribu...
ORGANISM(S): Homo sapiens 
2010-08-19 | E-GEOD-9703 | biostudies-arrayexpress
ProteomicsSEPepQuant enhances the detection of possible isoform regulations in shotgun proteomics
Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is challenging due to the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in norma...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD044809 | Pride
Protein isoform Shotgun proteomics Quantification 
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
ProteomicsAn alternative cytoplasmic SFPQ isoform with divergent phase separation potential is upregulated in ALS
Splicing factor proline- and glutamine-rich (SFPQ) is an RNA-binding protein that broadly regulates RNA metabolism. Although its nuclear roles are well-studied, evidence of SFPQ’s cytoplasmic functionality is emerging. Altered expression and nuclear-to-cytoplasmic mislocalisation of SFPQ is a hallma...
ORGANISM(S): Homo sapiens (Human) 
2025-09-01 | PXD051918 | Pride
Cytoplasmic sfpq isoform Als 
TranscriptomicsEffects of CEBPA isoform expression on NB4 cells
Here we investigated the effects of CEBPA transcription factor expression on myeloid NB4 cells. The sequence of rat CEBPA was C-terminally fused to a promiscuous biotin ligase tag (BirA*) and NB4 cell lines were engineered to express the fusion protein under the control of a doxycycline inducible p...
ORGANISM(S): Homo sapiens 
2021-06-26 | E-MTAB-9947 | biostudies-arrayexpress
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