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ProteomicsMulti-protease approach for the improved identification and molecular characterization of small proteins and short open reading frame-encoded peptides
The identification of proteins below 70 amino acids in bottom-up proteomics is still a challenging task due to the limited number of peptides generated by proteolytic digestion. This includes the short open reading frame-encoded peptides (SEP), which are a subset of the small proteins that were not ...
ORGANISM(S): Methanosarcina mazei Go1 
2021-04-01 | PXD023921 | Pride
Lc-msms Peptidomics Sorf Sep 
ProteomicsExploring the hidden world of Methanosarcina mazei: Unravelling the secrets of its small proteome and its nitrogen-dependent regulation
The mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1, is crucial for climate and environmental research due to its ability to produce methane from H2 plus CO2, acetate, and methylamines. Here, we established the first Ribo-seq protocol for M. mazei strain Gö1 under two...
ORGANISM(S): Methanosarcina mazei Go1 
2024-08-02 | PXD045039 | Pride
Archaea  methanoarchaea  ribosome profiling  ribo-seq  small proteome  sorf  nitrogen  dual function srna 
ProteomicsMultidimensional separation schemes enhance the identification and molecular characterization of low molecular weight proteomes and short open reading frame encoded peptides in top-down proteomics
In the present work we developed a sample preparation approach for the combined bottom-up and top-down proteomics analysis of small open reading frame encoded proteins (SEP). Key improvements were made by the application of solid phase extraction (SPE) supported enrichment of LMW proteins, followed ...
ORGANISM(S): Methanosarcina mazei Go1 
2021-11-02 | PXD019792 | Pride
Microprotein Sep 
ProteomicsSmall ORF16 modulates the Mtr complex activity in Methanosarcina mazei depending on the molecular hydrogen availability
Small open reading frame (small ORF)-encoded proteins, with less than 100 amino acids in length, have attracted increasing attention over the past decade after being largely overlooked due to limitations in classical bioinformatics and biochemical methodologies. For the mesophilic archaeal model sys...
ORGANISM(S): Methanosarcina mazei Go1 
2026-09-07 | PXD064332 | Pride
Tetrahydrosarcinapterin s-methyltransferase (mtr) Small orf encoded proteins Methanosarcina mazei Lc msms 
UnknownRituximab maintenance therapy after autologous stem-cell transplantation in patients with relapsed CD20(+) diffuse large B-cell lymphoma: final analysis of the collaborative trial in relapsed aggressive lymphoma.
Not available
S-EPMC3646314 | biostudies-literature
TranscriptomicsLong noncoding RNA expression during human B-cell development
Long noncoding RNAs (lncRNAs) have emerged as important regulators of diverse cellular processes, but their roles in the developing immune system are poorly understood. In this study, we analysed lncRNA expression during human B-cell development by array-based expression profiling of eleven distinct...
ORGANISM(S): Homo sapiens 
2016-02-09 | E-GEOD-69033 | biostudies-arrayexpress
TranscriptomicsThe footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus
We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distri...
ORGANISM(S): Arabidopsis thaliana x Arabidopsis halleri 
2016-06-01 | E-GEOD-80462 | biostudies-arrayexpress
UnknownMitotic control of kinetochore-associated dynein and spindle orientation by human Spindly
Not available
S-JCBD-200812167 | bioimages
UnknownLRP8-mediated selenocysteine uptake is a targetable vulnerability in MYCN-amplified neuroblastoma.
Not available
S-SCDT-10_15252-EMMM_202318014 | biostudies-other
ModelsModeling the relevance of immune and metabolic cues in the macrophage/fibroblast interplay during fibrosis applied to kidney transplantation
In this model, we integrate in vitro observations of macrophage/fibroblasts in coculture with hypoxia and inflammatory signals. We obtain conditions under which the wound healing process progresses normally or becomes fibrotic.
2022-09-27 | MODEL2209160001 | BioModels
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