Protocol for analyzing lncRNA-gene interactions in human fetal spinal cord development using single-cell and Stereo RNA sequencing

Investigating changes in long noncoding RNA (lncRNA) and gene pairs across regions of the human fetal spinal cord offers crucial insights into human development. We present a protocol for analyzing lncRNA-gene pairs using 10× Visium Stereo RNA sequencing (Stereo-seq) and 10× Genomics single-cell RNA sequencing (scRNA-seq) data. We describe steps for collecting spinal cord tissues from gestational weeks 8 to 12, processing samples, and conducting sequencing analyses to explore cis and trans lncRNA regulatory interactions. For complete details on the use and execution of this protocol, please refer to Miao et al.¹.