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ProteomicsRNA antisense oligonucleotide pulldown coupled with mass spectrometry (MS) to identify C1QTNF1-AS1 protein interactors
We used C1QTNF1-AS1 antisense oligonucleotide pulldown coupled with MS to identify protein interactors of lncRNA C1QTNF1-AS1 in human HCT116 cells. Five antisense oligonucleotides against C1QTNF1-AS1 and luciferase (negative control) were used for the pulldown. Three independent oligonucleotides (C...
ORGANISM(S): Homo sapiens (Human) 
2026-03-12 | PXD059546 | Pride
Antisense oligo pulldown  rna interactome  lc-ms/ms  label-free quantification 
ProteomicsIER3-AS1 interacting proteins by AP-MS
Characterisation IER3-AS1 interacting proteins using chromatin oligo-affinity precipitation (ChOP) followed by mass spectrometry. The HeLa cell lysates was incubated with biotinylated antisense oligonucleotides (ASO), targeting an experimental target antisense long noncoding RNA IER3-AS1 or a contr...
ORGANISM(S): Homo sapiens (Human) 
2022-10-15 | PXD035704 | Pride
Chromatin oligo-affinity precipitation Orbitrap Lncrna Long noncoding rna Ier3-as1 Hnrnpk Lc-ms/ms 
GenomicsSimple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator (Pulldown)
PRJNA723893 | ENA
ProteomicsIdentification of RNA-binding protein interactors of duck lncrna (lnc455) using Multiple Oligo-assisted RNA Pulldown with Hybridization followed by Mass Spectrometry (MORPH-MS)
This project used MORPH-MS to identify proteins that interact with a duck lncRNA called lnc455, which is linked to antiviral responses. While lnc455 was predicted to enhance RIG-I/MAVS signaling, its effects appeared to be indirect. Using MORPH-MS, we mapped the lncRNA’s binding partners and uncover...
ORGANISM(S): Gallus gallus (Chicken) 
2026-04-27 | PXD067094 | Pride
Morph-ms Type i ifn Duck Lncrna 
ProteomicsMaTAR25 RNA Antisense Pulldown and Mass Spectrometry
It has been suggested that lncRNAs can interact with transcriptional regulators/co-factors to form ribonucleoprotein (RNP) complexes to regulate the expression of downstream genes in the cell nucleus. To identify potential interacting proteins of MaTAR25, we used two different paired sets of biotin-...
ORGANISM(S): Mus musculus (Mouse) 
2020-12-23 | PXD017398 | Pride
Breast cancer Mouse Protein interaction Lncrna Biotin-oligos Matar25 
ProteomicsIdentification of interacting proteins with U4 snRNA with and without USP39
RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However, the regulatory mechanisms connecting these processes remain poorly understood. Here, we show that impaired spliceosome assembly caused by USP39 deficiency ...
ORGANISM(S): Homo sapiens (Human) 
2024-09-25 | PXD050688 | Pride
Human U4 snrna Spliceosome Usp39 As oligo pulldown 
TranscriptomicsRNA-seq of definitive endoderm differentiation of human embryonic stem cells in early G1 phase of the cell cycle
The experiment was designed to investigate transcriptional dynamics during definitive endoderm differentiation of human embryonic stem cells (hESCs) in early G1 phase of the cell cycle. For this, the FUCCI system was used to sort hESCs in Early G1 (EG1). Samples were taken at 0h (hESCs), 12h, 24h, 3...
ORGANISM(S): Homo sapiens 
2020-09-07 | E-MTAB-9194 | biostudies-arrayexpress
TranscriptomicsHuman RNase L Tunes Gene Expression by Selectively Destabilizing the MicroRNA-Regulated Transcriptome
Purpose: The goal of this study was to map the pathway of mRNA decay by human RNase L Methods: Total RNA was extracted (RNeasy kit, Qiagen). RNA integrity was verified by an RNA 6000 Nano Chip, using BioAnalyzer and 2100 Expert software (Agilent Technologies). The mRNA was enriched by oligo-dT pulld...
ORGANISM(S): Homo sapiens 
2015-12-21 | GSE75530 | GEO
TranscriptomicsNovel RNA-binding activity of MYF5 enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis
Skeletal muscle contains long multinucleated and contractile structures known as muscle fibers, which arise from the fusion of myoblasts into nucleated myotubes during myogenesis. The myogenic regulatory factor (MRF) MYF5 is the earliest to be expressed during myogenesis and functions as a transcri...
ORGANISM(S): Mus musculus 
2016-08-08 | E-GEOD-73704 | biostudies-arrayexpress
TranscriptomicsGlobal Analysis of Glucocorticoid Receptor-Associated Transcripts and Identification of a Target RNA Motif
Posttranscriptional regulation is emerging as a key factor in glucocorticoid (GC)-mediated gene regulation. We investigated the role of the human glucocorticoid receptor (GR) as an RNA-binding protein and its effect on mRNA turnover in human airway epithelial cells. Cell treatment with the potent ...
ORGANISM(S): Homo sapiens 
2011-06-24 | E-GEOD-24748 | biostudies-arrayexpress
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