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TranscriptomicsConvergent Sense/Antisense Transcription At Intragenic Super-Enhancers Targets AID-initiated Genomic Instability
Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via transcription-dependent cytidine deamination of single stranded DNA targets. While largely specific for immunglob...
ORGANISM(S): Homo sapiens 
2014-12-04 | E-GEOD-62296 | biostudies-arrayexpress
ProteomicsAntisense affinity selection of the lncRNA NTRAS in HeLa lysate
Biochemical characterization of the hypoxia-induced long non coding RNA NTRAS. NTRAS was found to regulate cell cycle progression, in vitro sprouting angiogenesis, and the paracellular permeability in human umbilical vein endothelial cells (HUVECs). Using desthiobiotinylated 2’O-Me-RNA probes, we pu...
ORGANISM(S): Homo sapiens (Human) 
2022-04-25 | PXD030620 | Pride
Rna-protein-interaction Antisense affinity selection Lncrna 
UnknownIdentification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages.
Not available
S-EPMC4357732 | biostudies-literature
ProteomicsShadow ORFs illuminated: long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionises our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in Pseudomon...
ORGANISM(S): Pseudomonas Aeruginosa 
2021-02-08 | PXD024029 | panorama
ProteomicsIdentification of protein interaction partners of the lncRNA CALA
The stimuli-responsive lncRNA CALA impacts endothelial cell function as silencing impairs angiogenic capacity in vitro. To uncover the molecular mechanism of CALA, we here combined antisense affinity selection of CALA-RNPs with mass spectrometry to identify the protein interactome of CALA. We theref...
ORGANISM(S): Homo sapiens (Human) 
2022-07-04 | PXD033516 | Pride
Rna/protein interaction 
TranscriptomicsNon-coding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells
Non-coding sense and antisense germline transcription within the immunoglobulin heavy chain locus precedes V(D)J recombination and has been proposed to be associated with Igh locus accessibility, although its precise role remains elusive. However, no global analysis of germline transcription through...
ORGANISM(S): Mus musculus 
2012-10-18 | E-GEOD-40984 | biostudies-arrayexpress
TranscriptomicsTrf4p in vivo crosslinking and ribonucleoprotein-immunopurification-chip analysis (X-RIP-Chip)
In vivo cross-linking and ribonucleoprotein-immunopurification experiments followed by microarray analysis of bound RNAs (X-RIP-chip). Cells expressing recombinant tandem-affinity purification (TAP)-tagged Trf4 protein were cross-linked with formaldehyde, and Trf4-containing ribonucleoprotein comple...
ORGANISM(S): Saccharomyces cerevisiae 
2010-06-24 | E-GEOD-16105 | biostudies-arrayexpress
GenomicsJpx RNA regulates CTCF anchor site selection and formation of chromosome loops
Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops
PRJNA602661 | ENA
ProteomicsInhibition of the RNA exosome by chemically stabilized long antisense oligonucleotides
The protein interactions of ADAR-recruiting oligonucleotides inside the cellular environment was identified using the isASO-ID protocol and SILAC-MS/MS. We identified two exoribonucleases to bind differently to the oligonucleotides with respect to their 3’-terminal 2’-ribose modifications leading to...
ORGANISM(S): Homo sapiens (Human) 
2026-09-30 | PXD079777 | Pride
Antisense oligonucleotide Basu Proximity biotinylation Biotin ligase Silac Rna quality control In situ biotinylation Rna exosome 
TranscriptomicsRNA expression profiles in CD34+ and in stromal cells of patients with refractory anemia with ringed sideroblasts
Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcri...
ORGANISM(S): Homo sapiens 
2010-06-22 | E-GEOD-18911 | biostudies-arrayexpress
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