Abstract: The current methods and compositions of the disclosure provide a platform for detecting the transcriptomic, genomic, or proteomic profile in relation to particular characteristics of a single cell, such as the location of a cell within a tissus. Accordingly, aspects of the disclosure relate to a method for barcoding eukaryotic cell nuclei comprising: transferring oligonucleotides into the nuclei of cells and performing single-cell analysis to identify the sequence of the barcode; wherein the oligonucleotides comprise a barcode region and a target region.