Method for comprehensive identification of cell lineage specific genes
First Claim
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1. A method for identifying genes expressed during differentiation of a cell comprising the steps of:
- a) integrating into a site in the genome of a host cell, a cell lineage targeting vector comprising, a pair of recombinase recognition sites flanking one or more polyadenylation sites, a first selectable marker placed downstream of or between the two recombinase recognition sites, a reporter gene placed downstream of the recombinase recognition sites, and a cell lineage specific gene promoter placed upstream of the recombinase recognition sites or a cell specific lineage gene placed downstream of the recombinase recognition sites, b) amplifying cells generated from the host cell;
c) integrating into the genome of a plurality of the amplified cells, a gene-trap vector comprising a splice acceptor, a type IIS restriction endonuclease cleavage site, a recombinase, one or more polyadenylation sites, a second selectable marker and a splice donor;
d) allowing the cells to differentiate;
e) isolating cells in which the reporter gene is expressed indicating expression of the cell lineage specific gene;
f) identifying trapped genes in the isolated cells.
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Abstract
This invention provides a method for identification and characterization of genes expressed during differentiation of cells. Cell lineage specific genes are identified in embryonic stem cells lines by unique vectors constructed to permit rapid characterization of expressed genes.
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Citations
21 Claims
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1. A method for identifying genes expressed during differentiation of a cell comprising the steps of:
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a) integrating into a site in the genome of a host cell, a cell lineage targeting vector comprising, a pair of recombinase recognition sites flanking one or more polyadenylation sites, a first selectable marker placed downstream of or between the two recombinase recognition sites, a reporter gene placed downstream of the recombinase recognition sites, and a cell lineage specific gene promoter placed upstream of the recombinase recognition sites or a cell specific lineage gene placed downstream of the recombinase recognition sites, b) amplifying cells generated from the host cell;
c) integrating into the genome of a plurality of the amplified cells, a gene-trap vector comprising a splice acceptor, a type IIS restriction endonuclease cleavage site, a recombinase, one or more polyadenylation sites, a second selectable marker and a splice donor;
d) allowing the cells to differentiate;
e) isolating cells in which the reporter gene is expressed indicating expression of the cell lineage specific gene;
f) identifying trapped genes in the isolated cells. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method for identifying genes expressed during differentiation of a cell comprising the steps of:
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a) integrating into a site in the genome of a host cell, a cell lineage targeting vector comprising a pair of recombinase recognition sites flanking one or more polyadenylation sites, a first selectable marker, a reporter gene, and a cell lineage specific gene promoter or a cell lineage specific gene, wherein recombinase based excision allows the expression of the reporter gene;
b) amplifying cells generated from the host cell;
c) integrating into a plurality of the amplified cells, a gene-trap vector comprising a splice acceptor, a type IIS restriction endonuclease cleavage site, a recombinase, a second selectable marker, and either a splice donor or a polyadenylation site, wherein integration of the gene-trap vector into an endogenous gene allows the recombinase to be produced and also incorporates a type IIS endonuclease site into the endogenous gene. c) allowing the host cells to differentiate;
d) isolating cells in which the reporter gene is expressed indicating expression of the cell lineage specific gene;
e) digesting DNA from the isolated cells to form fragments comprising portions of trapped genes;
f) concatenating and sequencing the fragments comprising portions of trapped genes. - View Dependent Claims (13, 14)
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15. A method for identifying genes expressed during differentiation of a cell comprising the steps of:
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a) integrating into a site in the host cell of a genome, a cell lineage targeting vector comprising a pair of recombinase recognition sites flanking one or more polyadenylation sites, a first selectable marker, a reporter gene, and a cell lineage specific gene promoter or a cell lineage specific gene, wherein recombinase based excision allows the expression of the reporter gene;
b) amplifying cells generated from the host cell in a) c) integrating into a plurality of the amplified cells, a gene-trap vector comprising a splice acceptor, a type IIS restriction endonuclease cleavage site, a recombinase, a second selectable marker, and either a splice donor or a polyadenylation site, wherein integration of the gene-trap vector into an endogenous gene allows the recombinase to be produced and also incorporates a type IIS endonuclease site into the endogenous gene. c) allowing the host cells to differentiate;
d) isolating cells in which the reporter gene is expressed indicating expression of the cell lineage specific gene;
e) preparing mRNA from cells in which the reporter gene is expressed in d);
f) synthesizing a first and second cDNA strands from the mRNA;
g) digesting with type IIS restriction endonucleases to produce Assay Tags wherein each Assay Tag comprises a portion of a trapped gene and a portion of the gene-trap vector;
h) concatenating the Assay Tags;
i) amplifying and sequencing the concatamers to identify the sequence of the portion of the trapped gene. - View Dependent Claims (16, 17, 18, 19, 20, 21)
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Specification