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TranscriptomicsTranscription profiling of human cell lines
The three-dimensional (3D) folding of the chromosomal fibre in the human interphase nucleus is an important, but poorly understood aspect of gene regulation. Especially basic principles of 3D chromatin and chromosome organisation are still elusive. In this paper, we quantitatively analyse the 3D str...
ORGANISM(S): Homo sapiens 
2008-06-15 | E-GEOD-6890 | biostudies-arrayexpress
ProteomicsDrosophila melanogaster exp 132
PeptideRank is an approach that uses a rank-based algorithm for peptide detectability prediction from shotgun proteomics data. The best performance is achieved when it is trained on organism-specific shotgun proteomics datasets. The Drosophila shotgun proteomics data presented here have been used am...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-06-04 | PXD000730 | Pride
Nuclear and cytoplasmic fraction Kc167 cells Drosophila melanogaster 
ProteomicsDrosophila melanogaster exp 135
PeptideRank is an approach that uses a rank-based algorithm for peptide detectability prediction from shotgun proteomics data. The best performance is achieved when it is trained on organism-specific shotgun proteomics datasets. The Drosophila shotgun proteomics data presented here have been used am...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2019-06-04 | PXD000726 | Pride
Nuclear and cytoplasmic fraction Kc167 cells Oge Drosophila melanogaster 
ProteomicsThe small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti
The Alphaproteobacterium Sinorhizobium meliloti lives in soil and is capable of fixing molecular nitrogen in symbiosis with legume plants. In this work, the small proteome of S. meliloti strain 2011 was studied to uncover translation of both annotated and novel small open reading frame (sORF)-encode...
ORGANISM(S): Sinorhizobium meliloti 2011 
2023-03-13 | PXD034931 | Pride
Rhizobia Proteomics Proteogenomics Sorf Small proteins Ribosome profiling 
ProteomicsA proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships
Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal foodborne disease. Many different Listeria strains and serotypes exist, buthowever a proteogenomic resource that which would allow to bridges the gap in ourthe molecular understanding of th...
ORGANISM(S): Listeria Monocytogenes 
2021-01-26 | PXD014294 | panorama
ProteomicsA proteogenomic resource enabling integrated analysis of Listeria genotype-proteotype-phenotype relationships
Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, the third most common foodborne disease. Many different Listeria strains and seroptypes exist, however a proteogenomic resource which would provide a basis for bridging the gap in the molecular understanding b...
ORGANISM(S): Listeria Monocytogenes Egd-e (ncbitaxon:169963) Listeria Monocytogenes Str. Scott A (ncbitaxon:1027396) 
2019-06-01 | MSV000083881 | MassIVE
ProteomicsSimultaneous targeted and discovery-driven clinical proteotyping using hybrid-PRM/DIA
Background MS-based proteotyping has been widely used for biomarker discovery. However, the clinical/translational proteotyping community requires strategies that not only enable the discovery of novel biomarker candidates but also increase the likelihood of establishing these protein-based biomarke...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000092996 | MassIVE
ProteomicsEx vivo drug response heterogeneity reveals personalized therapeutic strategies for patients with multiple myeloma
Multiple myeloma (MM) is a plasma cell malignancy defined by complex genetics and extensive patient heterogeneity. Despite a growing arsenal of approved therapies, MM remains incurable and in need of guidelines to identify effective personalized treatments. Here, we survey the ex vivo drug and immun...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-03-06 | MSV000088992 | MassIVE
ProteomicsHigh-throughput identification of repurposable neuroactive drugs with potent anti-glioblastoma activity
Glioblastoma, the most aggressive primary brain cancer, has dismal prognosis, yet systemic treatment is limited to DNA-alkylating chemotherapies. New therapeutic strategies may emerge from exploring neurodevelopmental and neurophysiological vulnerabilities of glioblastoma. To this end, we here syste...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
MSV000090357 | MassIVE
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