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ProteomicsDeeply mining a universe of peptides Encoded by Long Noncoding RNAs
Long non-coding RNAs (lncRNAs) are generally defined as RNA transcripts longer than 200 nucleotides that are not translated into proteins. Recently, many small open reading frames (smORFs) embedded in lncRNA scripts have been verified to be able to encode functional polypeptides (namely lncRNA-SEPs ...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2023-05-06 | PXD016981 | Pride
Lncrna Mass spectrometry Smorf Enrichment Seps 
ProteomicsLong noncoding RNA (lncRNA), smORF encoded polypeptides (SEPs), NONCODE database, enrichment, mass spectrometry
Many small open reading frames (smORFs) embedded in lncRNA transcripts have been shown to encode biologically functional polypeptides (smORFs-encoded polypeptides, SEPs) in different organisms. Despite significant advances in genomics, bioinformatics and proteomics that largely enabled the discovery...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-06-15 | PXD019486 | Pride
Noncode database Mass spectrometry Long noncoding rna (lncrna) Enrichment Smorf encoded polypeptides (seps) 
ProteomicsIdentification of proteins from the secretory / excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus
A. foliaceus secretory / excretory products (SEPs) were collected from 560 active adult parasites and identified and characterised using LC-ESI-MS/MS analysis.
ORGANISM(S): Argulus foliaceus 
2020-02-28 | PXD016226 | Pride
Argulus 
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
ProteomicsDetection of SEPs by MS (Second Round)
Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is ...
ORGANISM(S): Escherichia coli 
2019-10-14 | PXD010490 | Pride
Seps Mycoplasma bovis Escherichia colo 
ProteomicsDetection of SEPs by MS (Second Round)
Identifying smORFs and SEPs is technically and computationally challenging. Experimentally, techniques as ribosome profiling (Ribo-Seq and mass spectroscopy (MS) are used. Ribo-Seq sequences the mRNA and does not provide the translated frame, thus identifying proteins encoded by overlapping ORFs is ...
ORGANISM(S): Staphylococcus aureus 
2019-10-14 | PXD011038 | Pride
Seps Staphylococcus aureus Pseudomonas aeruginosa 
ProteomicsImproved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides
Computational, genomic, and proteomic approaches have been used to discover nonannotated proteincoding small open reading frames (smORFs). Some novel smORFs have crucial biological roles in cells and organisms, which motivates the search for additional smORFs. Proteomic smORF discovery methods are a...
ORGANISM(S): Homo sapiens (Human) 
2017-10-17 | PXD005643 | Pride
Smorf-encoded polypeptides (seps) Lc-ms 
ProteomicsIdentification of phosphorylated SEPs in Hep3B cells by LC/MS/MS
We identified phosphorylated SEPs in Hep3B cells. ACN precipitation, thermo precipitation and HCl precipitation were used to enrich SEPs. Three materials (nmTiO2, umTiO2, IMAC) were used to enrich phosphorylated peptides.
ORGANISM(S): Homo Sapiens 
PXD047431 |
UnknownBenefits of the Subdural Evacuating Port System (SEPS) Procedure Over Traditional Craniotomy for Subdural Hematoma Evacuation.
Not available
S-EPMC7495698 | biostudies-literature
ProteomicsThe identification and analysis of sORF and SEPs in Deinococcus radiodurans
The identification and analysis of sORF and SEPs in Deinococcus radiodurans
ORGANISM(S): Deinococcus Radiodurans R1 
2022-09-23 | PXD033880 |
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