Methods of genetic analysis of
View Patent ↗The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of E. coli genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. In one embodiment the nucleic acid sequences provided are present as an array of probes that may be used to measure gene expression of at least 20,000 E. coli genes and at least 500 intragenic regions. As such, the invention relates to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.
1. An array comprising a plurality of nucleic acid probes, wherein the plurality of nucleic acid probes of the array comprises each of the sequences listed in SEQ ID Nos. 1-224,976, and wherein each probe in the plurality of nucleic acid probes consists of one of the sequences listed in SEQ ID Nos. 1-224,976.
2. The array of claim 1 further comprising at least one probe that is the perfect complement of one of the sequences listed in SEQ ID Nos. 1-224,976.
3. The array of claim 1 wherein said plurality of nucleic acid probes is attached to a solid support.
4. The array of claim 1 wherein each probe is attached to the array in a different localized area that is determinable.
5. The array of claim 1 wherein the array comprises a plurality of beads wherein the probes are attached to the beads and the probes on a bead consist of one of the sequences listed in SEQ ID Nos. 1-224,976.
6. The array of claim 1 wherein the array consists of a single contiguous solid support.
7. A method of monitoring gene expression levels in a biological sample comprising E. coli nucleic acid, comprising:
isolating nucleic acid derived from the sample;
labeling the nucleic acid;
hybridizing the labeled nucleic acid to an array comprising a plurality of nucleic acid probes, wherein the plurality of nucleic acid probes of the array comprises each of the sequences listed in SEQ ID Nos. 1-224,976 and, wherein each probe in the plurality of nucleic acid probes consists of one of the sequences listed in SEQ ID Nos. 1-224,976; and
detecting a hybridization pattern, wherein the intensity of signal resulting from hybridization to probes on the array is used to monitor gene expression levels.
8. The method of claim 7 wherein said monitoring gene expression levels comprises comparing gene expression levels of nucleic acids derived from two or more different samples and further comprises the step of:
comparing said hybridization patterns between said nucleic acids derived from said two or more different samples.
9. The method of claim 7 wherein the labeled nucleic acid hybridized to the array consists essentially of DNA.
10. The method of claim 7 wherein the labeled nucleic acid hybridized to the array consists essentially of RNA that is complementary to the target mRNA.
11. The method of claim 7 wherein the labeled nucleic acid hybridized to the array consists essentially of RNA that is in the sense orientation relative to the target mRNA.
12. The method of claim 7 wherein the labeled nucleic acid is hybridized to the array in a single reaction.
13. A method of monitoring gene expression in a bacterial sample, comprising:
isolating nucleic acid derived from the bacterial sample;
labeling the nucleic acid with a detectable label;
hybridizing the labeled nucleic acid to an array comprising a plurality of nucleic acid probes, wherein the plurality of nucleic acid probes of the array comprises each of the sequences listed in SEQ ID Nos. 1-224,976, and wherein each probe in the plurality of nucleic acid probes consists of one of the sequences listed in SEQ ID Nos. 1-224,976; and
detecting a hybridization pattern; and analyzing the hybridization pattern to determine a relative expression level of at least 100 genes.
14. A method of identifying a bacterial sample as being from a strain selected from the group of strains consisting of K12, O 157:H7-EDL933, O 157:H7 Sakai or CFT073 comprising:
obtaining a labeled nucleic acid sample derived from the bacterial sample;
hybridizing the labeled nucleic acid sample to an array comprising a plurality of nucleic acid probes, wherein the plurality of nucleic acid probes of the array comprises each of the sequences listed in SEQ ID Nos. 1-224,976, and wherein each probe in the plurality of nucleic acid probes consists of one of the sequences listed in SEQ ID Nos. 1-224,976; and
identifying the bacterial sample as being E. coli strain K12 if the sample hybridizes to probes to E. coli strain K12 ; E. coli strain O 157:H7-EDL933 if the sample hybridizes to probes to E coli strain O 157:H7-EDL933 ; E. coli strain O 157:H7 Sakai if the sample hybridizes to probes to E. coli strain O 157:H7 Sakai, and E. coli strain CFT073 if the sample hybridizes to probes to E. coli strain CFT073.