Abstract: The present disclosure provides methods, systems and compositions for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix.

Abstract: A method of altering cells with a pooled library of bar-coded nucleic acids is provided including combining a group of cells with the pooled library of bar coded nucleic acids under conditions which promote uptake of one or more barcoded nucleic acids from the pooled library into the cells, analyzing an individual cell for phenotype, sequencing the individual cell to identify the one or more barcoded nucleic acids from the pooled library, and correlating the phenotype for the individual cell with the one or more barcoded nucleic acids from the pooled library.