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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
TranscriptomicsGenome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was tr...
ORGANISM(S): Homo sapiens 
2012-08-08 | E-GEOD-39561 | biostudies-arrayexpress
TranscriptomicsTranscriptome of Aspergillus oryzae following ER stress
The Aspergillus oryzae, an important filamentous fungus used in food fermentation and enzyme industry, has been revealed to own prominent features in its genomic compositions by genome sequencing and various other tools. However, the functional complexity of the A. oryzae transcriptome has not yet b...
ORGANISM(S): Aspergillus oryzae 
2010-02-02 | E-GEOD-18851 | biostudies-arrayexpress
GenomicsRNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs
RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs
PRJNA414611 | ENA
TranscriptomicsRibosome profiling of HeLa cells infected with Enterovirus coxsackiepol (strain CVA-13/Flores)
Ribosome profiling of enterovirus infected cells was used to investigate expression of the virus polyprotein and upstream open reading frames. Samples were either pretreated with initiation inhibitor lactimidomycin (LTM) to cause ribosomes to accumulate at initiation sites, or were flash frozen with...
ORGANISM(S): Homo sapiens 
2025-11-26 | E-MTAB-14994 | biostudies-arrayexpress
ProteomicsUnveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling
The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open read...
ORGANISM(S): Homo sapiens (Human) 
2025-01-15 | PXD043984 | Pride
Hiv-1 Ribosome profiling Immunopeptidome 
GenomicsProteogenomic discovery of novel open reading frames with HLA immune presentation on human beta cells
Proteogenomic discovery of novel open reading frames with HLA immune presentation on human beta cells
PRJNA1082757 | ENA
TranscriptomicsDecoding human cytomegalovirus using ribosome profiling
The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like other complex viruses, our understanding of its protein coding potential is far from complete. Here, we use ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow t...
ORGANISM(S): Human Herpesvirus 5 
2012-10-17 | E-GEOD-41605 | biostudies-arrayexpress
GenomicsUnveiling novel conserved HIV-1 open reading frames encoding T-cell antigens using ribosome profiling.
Unveiling novel conserved HIV-1 open reading frames encoding T-cell antigens using ribosome profiling.
PRJNA1001014 | ENA
ProteomicsAn optimized proteomics approach reveals novel alternative proteins in mouse liver development
Alternative open reading frames (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry (MS) as the only direct way of identificati...
ORGANISM(S): Mus musculus (Mouse) 
2022-12-23 | PXD033940 | Pride
Liver development. Mass spectrometry Fractionation Alternative open reading frames (altorfs) Alternative proteins (altprots) Enrichment 
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