RNA 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 (C1QTNF1-AS1 oligonucleotides 1, 3 and 5), efficiently retrieve C1QTNF1-AS1 and extracted proteins from these samples were compared using label-free (LFQ) Quantitative proteomics. C1QTNF1-AS1 oligonucleotides 2 and 4 were excluded from the analysis as they did not retrieve C1QTNF1-AS1.