# US 2019/0169604 A1 · Methods and compositions related to barcode assisted ancestral specific expression (baase) > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0169604 A1 - Document ID: US20190169604A1 - Status: Published application - Kind: A1 - Application number: 16/324,627 - Filed: 2017-08-11 - Published: 2019-06-06 - Earliest claimed: 2016-08-12 - Assignees: Board of Regents, The University of Texas System - Applicants: Board of Regents, the University of Texas System - Inventors: Amy BROCK; Aziz AL'KHAFAJI - Web page: https://patentgrep.com/patent/US20190169604A1 ## CPC - C12N 15/102: {Mutagenizing nucleic acids} - C12N 15/1065: {Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags} - C12N 9/22: Ribonucleases {[RNase]; Deoxyribonucleases [DNase]} - C12N 15/10: Processes for the isolation, preparation or purification of DNA or RNA (chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34) - C12N 15/11: DNA or RNA fragments; Modified forms thereof (DNA or RNA not used in recombinant technology, C07H21/00); {Non-coding nucleic acids having a biological activity} - C12N 15/111: {General methods applicable to biologically active non-coding nucleic acids} - C12N 15/63: Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression - C12N 2310/20: involving clustered regularly interspaced short palindromic repeats [CRISPR] - C12N 2740/16043: viral genome or elements thereof as genetic vector - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) ## Abstract Disclosed herein are methods and platforms related to modulating expression of a gene of interest within a select population of cells comprising: providing a population of cells; providing a vehicle, plasmid, vector or recombinant virus, or equivalent thereof, capable of stably expressing a guide nucleic acid comprising randomized barcodes, thereby producing a population of barcoded cells; allowing said barcoded cell to divide, thereby forming a barcoded progeny of cells; saving an aliquot of cells; identifying the barcode in a lineage of interest from the barcoded progeny of cells; reconstituting the aliquot of saved cells, and transforming the reconstituted aliquot of cells with a transcriptional element comprising a transcriptional effector, the barcode of the lineage of interest, and a gene of interest; utilizing the transcriptional effector to modify expression of the gene of interest within the lineage of interest. ## Claims ### Claim 1 A method of modulating expression of a gene of interest within a select population of cells comprising: a. providing a population of cells; b. providing a vehicle, plasmid, vector or recombinant virus, or equivalent thereof, capable of stably expressing a guide nucleic acid comprising randomized barcodes, thereby producing a population of barcoded cells; c. allowing said barcoded cell to divide, thereby forming a barcoded progeny of cells; d. saving an aliquot of cells after step b) or step c); e. identifying the barcode in a lineage of interest from the barcoded progeny of cells; f. reconstituting the aliquot of cells from step c) and transforming the reconstituted aliquot of cells to a transcriptional element comprising a transcriptional effector, the barcode of the lineage of interest, and a gene of interest; g. utilizing the transcriptional effector to modulate expression of the gene of interest within the lineage of interest. ### Claim 2 (depends on 2) The method of claim 2, wherein the transcriptional effector is dCas9-VPR. ### Claim 3 (depends on 1) The method of claim 1, wherein the gene of interest is a reporter. ### Claim 4 (depends on 1) The method of claim 1, wherein cells are selected via cell sorting. ### Claim 5 (depends on 4) The method of claim 4, wherein cell sorting is done using single cell sorting, fluorescent activated cell sorting (FACS), physical cell manipulation, laser capture, or magnetic cell sorting. ### Claim 6 (depends on 1) The method of claim 1, wherein the barcode is created with a DNA construct. ### Claim 7 (depends on 6) The method of claim 6, wherein the DNA construct comprises a randomized barcoded crRNA segment upstream of a tracrRNA under control of a promoter. ### Claim 8 (depends on 1) The method of claim 1, wherein, prior to identifying the barcode in a lineage of interest, the cells are exposed to a candidate agent. ### Claim 9 (depends on 8) The method of claim 8, wherein the barcode in a lineage of interest is identified as being of interest based on an activity of the candidate agent. ### Claim 10 (depends on 9) The method of claim 9, wherein the activity is modulation of a given activity of the cell. ### Claim 11 (depends on 10) The method of claim 10, wherein the modulation is upregulation of a certain gene or genes. ### Claim 12 (depends on 11) The method of claim 11, wherein the modulation of downregulation of a certain gene or genes. ### Claim 13 (depends on 10) The method of claim 10, wherein the candidate agent causes apoptosis. ### Claim 14 (depends on 10) The method of claim 10, wherein the candidate agent causes cell multiplication. ### Claim 15 (depends on 10) The method of claim 10, wherein a plurality of barcoded cells are each treated with a different candidate agent. ### Claim 16 (depends on 10) The method of claim 10, wherein said candidate agent is selected from one or more of: a protein, a small molecule, an organic molecule, a carbohydrate, a polysaccharide, a polynucleotide, a polypeptide, and a lipid. ### Claim 17 (depends on 1) The method of claim 1, wherein the genome of the selected cells can be sequenced. ### Claim 18 (depends on 1) The method of claim 1, wherein after step g), cells in the lineage of interest can be identified and selected. ### Claim 19 (depends on 1) The method of claim 1, wherein the transcriptional element is a plasmid. ### Claim 20 (depends on 1) The method of claim 1, wherein the barcode of the lineage of interest is upstream the gene of interest. ### Claim 21 (depends on 1) The method of claim 1, wherein the guide nucleic acid is gRNA. ### Claim at position 22 22-63. (canceled)