Mammalian cells and methods for engineering the same

A method, comprising:

• a. producing a plurality of adeno-associated viral (AAV) vectors from a library of mammalian cells, wherein the library of mammalian cells comprises a plurality of mammalian cells, wherein each mammalian cell in the plurality of mammalian cells individually comprises:
• (i) a nucleic acid sequence comprising a barcode, two functional AAV ITR sequences and a pair of cis-acting integration sequences, wherein the barcode is positioned between the AAV ITR sequences which are flanked by the cis-acting integration sequences, and wherein the nucleic acid sequence is integrated into the genome of the mammalian cell based on the cis-acting integration sequences, so that AAV vectors produced by the mammalian cell include the barcode;
• (ii) one or more library variants that result in one or more perturbations, wherein at least one library variant comprises a guide RNA (gRNA), and each mammalian cell of the plurality includes a different one or more library variants;
• (iii) an RNA-guided nuclease, and
• (iv) one or more nucleic acid sequences essential for production of AAV vectors,
• wherein the barcode in each mammalian cell is unique to that mammalian cell relative to other mammalian cells in the plurality and identifies the one or more library variants;
• and
• b. detecting the barcodes of the plurality of AAV vectors, so that the particular mammalian cell that produced a particular AAV vector is identified, and the one or more library variants in that mammalian cell is also identified.