Microassay for serial analysis of gene expression and applications thereof
First Claim
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1. A method of obtaining a library of tags capable of defining a specific state of a biological sample, comprising:
- (1) extracting mRNA from the biological sample by contacting the biological sample with an oligo(dT) covalently bound to paramagnetic beads, (2) generating a double-strand cDNA library from the extracted mRNA according to a process comprising;
(a) synthesizing the 1st strand of the cDNA by reverse transcription of the mRNA template into a 1st complementary single-strand cDNA, using a reverse transcriptase lacking Rnase H activity, and (b) synthesising the 2nd strand of the cDNA by nick translation of the mRNA in the mRNA-cDNA hybrid form by an E. coli DNA polymerase, (3) cleaving the cDNAs with an anchoring enzyme, wherein the anchoring enzyme is a restriction endonuclease having a 4-bp recognition site, (4) separating the cleaved cDNAs in two aliquots, (5) linking the cDNA contained in each of the two aliquots with two different oligonucleotide linkers comprising a type IIS recognition site, (6) digesting the products obtained in (5) with a type IIS restriction enzyme, to obtain two different tags, (7) blunt-ending the tags with a DNA polymerase, and mixing the tags ligated with the different linkers, (8) ligating the tags obtained in (7) with a DNA ligase, to form ditags, and (9) determining the nucleotide sequence of at least one tag of the ditags, to detect gene expression.
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Abstract
A method of obtaining a library of tags able to define a specific state of a biological sample, such as a tissue or a cell culture. The present method provides an important advantage over other methods used to analyze gene expression in that libraries may be generated from tiny amounts of cells, e.g., from 30,000-100,000 cells.
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Citations
30 Claims
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1. A method of obtaining a library of tags capable of defining a specific state of a biological sample, comprising:
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(1) extracting mRNA from the biological sample by contacting the biological sample with an oligo(dT) covalently bound to paramagnetic beads, (2) generating a double-strand cDNA library from the extracted mRNA according to a process comprising;
(a) synthesizing the 1st strand of the cDNA by reverse transcription of the mRNA template into a 1st complementary single-strand cDNA, using a reverse transcriptase lacking Rnase H activity, and (b) synthesising the 2nd strand of the cDNA by nick translation of the mRNA in the mRNA-cDNA hybrid form by an E. coli DNA polymerase, (3) cleaving the cDNAs with an anchoring enzyme, wherein the anchoring enzyme is a restriction endonuclease having a 4-bp recognition site, (4) separating the cleaved cDNAs in two aliquots, (5) linking the cDNA contained in each of the two aliquots with two different oligonucleotide linkers comprising a type IIS recognition site, (6) digesting the products obtained in (5) with a type IIS restriction enzyme, to obtain two different tags, (7) blunt-ending the tags with a DNA polymerase, and mixing the tags ligated with the different linkers, (8) ligating the tags obtained in (7) with a DNA ligase, to form ditags, and (9) determining the nucleotide sequence of at least one tag of the ditags, to detect gene expression. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 20, 22)
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11. A method of obtaining a library of tags able to define a specific state of a biological sample, comprising:
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(1) extracting mRNA from the biological sample by contacting the biological sample with an oligo(dT) covalently bound to paramagnetic beads, (2) generating a double-strand cDNA library from the extracted mRNA according to a process comprising;
(a) synthesizing the 1st strand of the cDNA by reverse transcription of the mRNA template into a 1st complementary single-strand cDNA, using a reverse transcriptase lacking Rnase H activity, and (b) synthesising the 2nd strand of the cDNA by nick translation of the mRNA in the mRNA-cDNA hybrid form by an E coli DNA polymerase, (3) cleaving the cDNAs with the restriction endonuclease Sau3A I as an anchoring enzyme, (4) separating the cleaved cDNAs in two aliquots, (5) ligating the cDNA contained in each of the two aliquots via the Sau3A I restriction site to a linker consisting of one double-strand cDNA molecule having one of the following formulas;
GATCGTCCC-X1 or GATCGTCCC-X2, wherein X1 and X2, which comprise 30-37 nucleotides and are different, include a 20-25 bp PCR priming site having a Tm of 55°
C.-65°
C., andwherein GATCGTCCC correspond to a Sau3A I restriction site joined to a BsmF I restriction site, (6) digesting the products from (5) with the tagging enzyme BsmF I and releasing linkers with anchored short piece of cDNA corresponding to a transcript-specific tag, the digestion generating BsmF I tags specific of the initial mRNA, (7) blunt-ending the BsmF I tags with a DNA polymerase and mixing the tags ligated with the different linkers, (8) ligating the tags obtained in (7) to form ditags with a DNA ligase, (9) amplifying the ditags obtained in (8) with primers comprising 20-25 bp and having a Tm of 55°
-65°
C.,(10) isolating the ditags having between 20 and 28 bp from the amplification products obtained in (9) by digesting the amplification products with the anchoring enzyme Sau3A I and separating the digested products by gel electrophoresis, (11) ligating the ditags obtained in (10) to form concatemers, purifying the concatemers, and separating the concatemers having more than 300 bp, (12) cloning and sequencing the concatemers, and (13) analyzing the different obtained tags. - View Dependent Claims (18, 19, 21, 23, 24, 25)
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26. A kit useful for detection of a gene expression profile, comprising:
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(a) at least one container which contains an oligonucleotide linker consisting of one double-strand cDNA molecule having one of the following formulas;
GATCGTCCC-X1 or GATCGTCCC-X2, wherein X1 and X2, which comprise 30-37 nucleotides and are different, include a 20-25 bp PCR priming site having a Tm of 55°
C.-65°
C., andwherein GATCGTCCC correspond to a Sau3A I restriction site joined to a BsmF I restriction site, and (b) at least one container which contains primers comprising 20-25 bp and having a Tm of 55°
65°
C. - View Dependent Claims (27, 28, 29, 30)
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Specification