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MetabolomicsThe patatin-like protein PlpD forms novel structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane

Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote c...

2025-12-08 | MTBLS9803 | MetaboLights
TranscriptomicsNuclear scaffold and matrix attachment of HeLa chromatin
The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nucl...
ORGANISM(S): Homo sapiens 
2010-05-22 | E-GEOD-13774 | biostudies-arrayexpress
TranscriptomicsNuclear scaffold and matrix attachment of Aortic Adventitial Fibroblast (AoAF) chromatin
The nuclear scaffold/matrix provides an anchor for higher order genome structure that has both structural and functional implications. Different extraction protocols, i.e., utilizing either 25 mM LIS or 2 M NaCl, isolate somewhat different protein constituents of either the nuclear scaffold or nucl...
ORGANISM(S): Homo sapiens 
2009-03-10 | E-GEOD-13792 | biostudies-arrayexpress
MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
TranscriptomicsIn Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts
Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown a...
ORGANISM(S): Arabidopsis thaliana 
2014-02-03 | E-GEOD-45549 | biostudies-arrayexpress
TranscriptomicsGene expression profiling of retinoblastoma Y79 cell line grown with scaffold compared to cells without scaffold
Retinoblastoma Y79 cell line was grown on 3D scaffolds and compared its gene expression profile with Y79 cells grown without scaffold. Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
ORGANISM(S): Homo sapiens 
2010-10-01 | E-GEOD-24453 | biostudies-arrayexpress
ModelsWang2022 - Scaffolding protein functional sites using deep learning
Deep learning approaches for scaffolding such functional sites without needing to prespecify the fold or secondary structure of the scaffold. The first approach, “constrained hallucination,” optimizes sequences such that their predicted structures contain the desired functional site. The second appr...
2023-05-10 | BIOMD0000001071 | BioModels
Machine Learning Model FAIR-AIML 
ProteomicsMitotic chromosome scaffold
Quantitative proteomics analysis of mitotic chromosome scaffold based on SILAC
ORGANISM(S): Gallus Gallus 
2018-10-07 | PXD007269 | JPOST Repository
Proteomicsmitotic chromosome scaffold SMC2ON vs OFF
Quantitative proteomics analysis of mitotic chromosome scaffold based on SILAC
ORGANISM(S): Gallus Gallus 
2018-10-07 | PXD008429 | JPOST Repository
GenomicsThe Protein Complex Ragulator is the Substrate-specific Scaffold for mTORC1 to Regulate Transcription Factor EB
The Protein Complex Ragulator is the Substrate-specific Scaffold for mTORC1 to Regulate Transcription Factor EB
PRJNA719171 | ENA
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