Elucidation of NEAT1 protein-binding partners was conducted using a human proteome microarray as detailed in Jeong et al.16 and analyzed using GENEPIX PRO 5.0 (Molecular Devices, CA, USA) that was used to scan the chip images. For every spot, signal intensity was defined as foreground median intensity divided by its local background median intensity. Two rounds of normalization were applied. First, within-chip normalization was used to adjust the median signal intensity of each block to 1. Second, whole chip normalization was applied to standardize this set of signal intensities to a mean of 0 and standard deviation of 1, with the resulting normalized signal intensity called the z-score. Arrays contained two identical probes corresponding to each protein and were repeated three times. To be considered as a positive interaction, probes corresponding to a protein were required to have an average z-score of ≥2 (P < 0.0015) over the array experiments conducted, which resulted in 92 positive hits. Median z-score for the six conducted replicates is presented in Fig. 1a as a kernel density plot. NEAT1 probes were synthesized as follows:
