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GenomicsTranslation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames. To address this question, we performed ribosome profiling of 32 medullob...
EGAS00001007426 | EGA
GenomicsAccurate annotation of human protein-coding small open reading frames
Accurate annotation of human protein-coding small open reading frames
PRJNA515538 | ENA
TranscriptomicsCynomolgus monkey testicular cDNAs for discovery of novel human genes
BACKGROUND: In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. RESULT: The full-insert sequ...
ORGANISM(S): Homo sapiens 
2010-06-05 | E-GEOD-513 | biostudies-arrayexpress
TranscriptomicsK562 polyA RNA-Seq
RNA-Seq reads and TopHat (Trapnell et al. Bioinformatics 2009) alignments of K562 cell-line transcriptome. These were used to validate the expression of short peptides idenitified by Mass-Spectrometry in K562 cells. K562 polyA+ RNA (Batch 1) and total RNA (batch 2) was purchased from Ambion. We use...
ORGANISM(S): Homo sapiens 
2012-11-14 | E-GEOD-34740 | biostudies-arrayexpress
TranscriptomicsHigh resolution view of bacteriophage lambda gene expression by ribosome profiling
Bacteriophage lambda is one of the most extensively studied organisms, and has been a primary model for understanding basic modes of genetic regulation. Here we examine the progress of lambda gene expression during phage development by ribosome profiling, and thereby provide a very high resolution ...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2013-07-01 | E-GEOD-47509 | biostudies-arrayexpress
TranscriptomicsGenome-wide measurement of RNA folding energies
RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in ...
ORGANISM(S): Saccharomyces cerevisiae 
2012-09-09 | E-GEOD-39680 | biostudies-arrayexpress
TranscriptomicsWidespread Occurrence of m6A in bacterial mRNA
N6-methyladenosine (m6A) is one of the most abundant modifications in eukaryotic RNA. Recent mapping of m6A methylomes in mammals, yeast, and plants as well as characterization of m6A methyltransferases, demethylases, and binding proteins have revealed regulatory functions of this dynamic RNA modifi...
ORGANISM(S): Pseudomonas aeruginosa PAO1 
2015-07-08 | E-GEOD-65347 | biostudies-arrayexpress
UnknownHundreds of putatively functional small open reading frames in Drosophila.
Not available
S-EPMC3334604 | biostudies-literature
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 
TranscriptomicsAccurate annotation of human protein-coding small open reading frames
Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three huma...
ORGANISM(S): Homo sapiens 
2019-07-03 | GSE125218 | GEO
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