The mammalian genome is folded into complex structures giving rise to multiple layers of compaction, while still accommodating dynamic and complicated tasks such as replication, transcription, and DNA repair. It is now widely accepted that the 3-dimensional (3D) genome organization plays an important role in both establishing and maintaining stable gene expression patterns, which impacts the development of cell-type identities. The development of chromosome conformation capture (3C) technology has been crucial in the endeavor to understand the organization of the 3D genome, and various structures such as A/B compartments and topological associated domains (TAD’s), have been described in detail. Recently, development of Micro-C technology has enabled generation of high-resolution contact maps to study small-scale chromatin conatcts such as enhancer-promoter interactions, hence, solving the resolution limitations of other developed 3C technologies. However, it is still an ongoing challenge to elucidate the regulatory relationship between cell-type specific enhancer-promoter interactions and the corresponding differences in the transcriptional programs observed in diverse cell types of a complex heterogeneous tissue such as the mammalian cerebral cortex. By utilizing the high-resolution capacity of Micro-C, we aim to overcome the challenge of tissue heterogeneity by developing a method combining Micro-C with Fluorescence Associated Nuclei Sorting, called Micro-C-FANS. The development of Micro-C-FANS will aid the efforts to understand how the 3D organization is accompanying the establishment of cell-type specific transcriptional programs, and how different cell-type identities are maintained, both in adult cortical tissue in vivo as well as during mammalian cortical development in vitro.