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ProteomicsThe proteins binding with locust pre-miR-276
In order to investigate the proteins interacting with precusor of miR-276 (pre-miR-276), the RNA-pull down followed by mass spectrometry (MS) were performed in locust terminal oocyte extracts. The RNA oligos labeled with biotin at the 3’ end for pre-miR-276 (62 nt) and pre-miR-67 (69 nt) of C. elega...
ORGANISM(S): Locusta Migratoria 
PXD041810 |
OtherssDNA-seq mapping of DNA secondary structures in mouse ES cells
DNA N6-methyladenine (N6-mA) is an emerging epigenetic mark in the mammalian genome. Levels of N6-mA undergo drastic fluctuation during early embryogenesis, indicative of active regulation. Here we demonstrate that the 2-oxoglurarate oxygenase ALKBH1 functions as a nuclear eraser of N6-mA in unpairi...
ORGANISM(S): Mus musculus 
2020-06-29 | GSE126077 | GEO
Transcriptomicscontrol-ethanol liver RNA
cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity ...
ORGANISM(S): Homo sapiens 
2004-12-22 | GSE2099 | GEO
UnknownToehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin.
Not available
S-EPMC5711847 | biostudies-literature
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 
TranscriptomicsTranscription profiling of pig liver after ethanol treatment vs. control
cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity ...
ORGANISM(S): Homo sapiens 
2008-06-11 | E-GEOD-2099 | biostudies-arrayexpress
ProteomicsSpecialized replication mechanisms maintain genome stability at human centromeres
Reveal a specific set of proteins important to maintain centromere integrity, through quantitative PICh (Proteomics of Isolated Chromatin). Centromeric chromatin was pulled down through RNA probes annealing specifically to a 300bp-long conserved centromeric sequence.
ORGANISM(S): Homo sapiens (Human) 
2024-02-14 | PXD047847 | Pride
Replication stress Proteomics Genome instability Centromere Dna damage Dna replication 
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 
ProteomicsDissecting genotype-specific effects of disease-associated genetic variants
Background For many complex diseases, including Parkinson’s disease, regulatory elements located in intergenic regions have been putatively associated with disease risk and development. However, the biological mechanisms linking these intergenic loci to disease pathogenesis remain largely unknown. F...
ORGANISM(S): Homo sapiens (Human) 
2026-04-07 | PXD065108 | Pride
Specific alterations Snv 5mc Ipsc Crispr Snp Gene expression 3d structure Gene editing Genetic variation Epigenetic 
ProteomicsmiR-122-dependent binding of TNRC6 to HCV RNA
The liver-specific microRNA, miR-122, is an essential host factor for replication of hepatitis C virus (HCV), an important infectious cause of chronic liver disease and hepatocellular carcinoma. miR-122 stabilizes the positive-strand HCV RNA genome and promotes viral RNA synthesis by binding two clo...
ORGANISM(S): Homo sapiens (Human) 
2019-04-24 | PXD013054 | Pride
Ap-ms Risc complex Protein translation Rna stability Microrna 
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