Identifying LINC00899 binding sites in HeLa cells with CHART-seq

LncRNAs represent a major transcriptional output of the human genome, but the function of many of these elements is unknown. For chromatin-localized lncRNAs, identification of genomic binding sites of these lncRNAs provides one opportunity to characterize their function. In this experiment, we have used capture hybridization analysis of RNA targets with high-throughput sequencing (CHART-seq) to identify the binding sites of the lncRNA LINC00899 in HeLa cells. LINC00899 is of interest as its depletion results in mitotic delay, suggesting a role in mitotic progression. This experiment contains 5 replicate batches where each batch contains a sample with antisense capture oligonucleotides (COs) to hybridize to ad pull down the lncRNA transcript; an input control for the antisense pulldown; a control sample with sense COs, which should not hybridize to and pull down the lncRNA transcript; and an input control for the sense pulldown. All samples in the same batch were generated at the same time, and each pulldown (antisense or sense) was performed on chromatin obtained from independent cell cultures. All samples were subjected to high-throughput paired-end sequencing across two lanes.