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TranscriptomicsUV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli
UV-crosslinking and high througput sequencing of cDNAs (CRAC) was used to map the binding sites Hfq in enterohaemorhaggic E. coli (EHEC). Hfq was tagged with a His-FLAG dual affintiy tag and UV crosslinked after growth in the MEM-HEPES media essentailly as per Granneman et al (2009) PNAS. We additio...
ORGANISM(S): Escherichia coli O157:H7 str. Sakai 
2014-05-22 | E-GEOD-46118 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of A375 cells treated with tetracycline-based crosslinking probes, with and without competition by parent tetracyclines, to show specific binding of the tetracycline analogs Col-3 and doxycycline on rRNA substructures of the human ribosome
Upon finding that the tetracyclines COL-3 and doxycycline target unique rRNA substructures of the 80S ribosome (E-MTAB-7147), we confirmed these putative ribosomal binding sites by showing that tetracycline-based crosslinking probes are specifically competed from these rRNA structures by their paren...
ORGANISM(S): Homo sapiens 
2018-08-31 | E-MTAB-7161 | biostudies-arrayexpress
GenomicsUPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking
UPA-Seq: Prediction of functional lncRNAs using the sensitivities to UV-crosslinking
PRJNA472627 | ENA
ProteomicsMapping protein-DNA interactions by UV femtosecond laser crosslinking and mass spectrometry analysis
Transcription factors (TFs) regulate target genes by specific interaction with DNA sequences. Detecting and understanding these interactions on molecular level is of fundamental interest in both biological and clinical context. Crosslinking mass spectrometry is a powerful tool to assist structure pr...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Sus scrofa domesticus (domestic pig) 
2020-06-22 | PXD014898 | Pride
Femtosecond laser Uv Transcription factor Protein-dna crosslinking Mass spectrometry 
ProteomicsEarly Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC
In this study, NAC was UV-crosslinked using the photo-crosslinking amino acid p-benzoyl-L-phenylalanine (pBPA) in order to determine specific interaction sites of the alphaNAC N-terminus in the native protein structure. Furthermore, quantitative chemical crosslinking coupled to mass spectrometry (q-...
ORGANISM(S): Homo sapiens (Human) Caenorhabditis elegans 
2019-07-25 | PXD011995 | Pride
Nac Structural mass spectrometry Uv-crosslinking Q-xl-ms 
ProteomicsNative alpha synuclein crosslinking
Alpha synuclein in it's native state in solution was crosslinked using a variety of short-range crosslinking reagents. Crosslinks detected by mass spectrometry were then used as constraints in a discrete molecular dynamics simulation of the synuclein protein, and a structural ensemble of the protein...
ORGANISM(S): Homo sapiens (Human) 
2019-02-28 | PXD011645 | Pride
Alpha synuclein Crosslinking Modelling 
GenomicsUV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli
UV-crosslinking and high throughput sequencing of cDNAs (CRAC) of the RNA chaperone Hfq in enterohaemorhaggic E. coli
PRJNA197291 | ENA
ProteomicsFly RBPome - Early embryogenesis is characterized by the maternal to zygotic transition (MTZ), in which maternally deposited messenger RNAs are translated and subsequently degraded while zygotic transcription begins
Early embryogenesis is characterized by the maternal to zygotic transition (MTZ), in which maternally deposited messenger RNAs are translated and subsequently degraded while zygotic transcription begins. Posttranscriptional gene regulation by RNA-binding proteins (RBPs) is a dominant force controlli...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2016-04-26 | PXD002992 | Pride
Fly 
ProteomicsDithiothreitol (DTT) acts as a specific, UV-inducible cross-linker in elucidation of protein-RNA interactions
In the present paper, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. To prove this three model systems, a) a small synthetic peptide from smB'/B protein incubated with U1snRNA oligonucleotide, b) in vitro reconstituted 15.5K protein with U4 snRNA oligonucleotide and c) nativ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae (Baker's yeast) 
2015-10-13 | PXD002656 | Pride
Dtt 
UnknownChemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.
Not available
S-EPMC12359043 | biostudies-literature
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