This dataset contains the prediction results reported in the paper “ELE: Estimating tissue-specific lncRNA gene essentiality using graph neural networks”. The files include model-predicted essential lncRNA genes and non-essential lncRNA genes from three human tissues and three mouse tissues, as well as common essential lncRNA genes shared across the three tissues within each species. The dataset is provided to support transparency and reproducibility of the reported results. File format: Microsoft Excel (.xlsx). Related article: ELE: Estimating tissue-specific lncRNA gene essentiality using graph neural networks