Methods for encoding non-biological information on microarrays

• US 20050049796A1
• Filed: 04/02/2004
• Published: 03/03/2005
• Est. Priority Date: 09/03/2003
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Webb, Peter G., Fredrick, Joseph P., Tso, Jacqueline M.
• Application Number:
  US10/817,115
• Publication Number:
  US 20050049796A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00542 Alphanumeric characters
• CPC Class Codes: B01J 2219/00545 Colours
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

Methods and compositions for encoding and decoding array information on an array are provided. The methods involve contacting an array containing one or more array information features with a sample containing target that binds to at least one of the one or more array information features to produce at least one signal that provides information about the array.

Claims

1. A computer-readable medium comprising:

information for decoding encoded array information obtained from an array comprising one or more array information features.

2. The computer readable medium of claim 1, wherein said array is an array of nucleic acids.

3. The computer-readable medium of claim 1, wherein said information comprises a table that contains:

a list of feature identifiers; and

a list of probe identifiers corresponding to said feature identifiers.

4. The computer-readable medium of claim 3, wherein said table indicates that certain features of said array are array information features.

5. The computer readable medium of claim 3, wherein said table indicates which features correspond to which bit of a code.

6. The computer-readable medium of claim 1, wherein said information indicates an executable program for decoding said encoded array information.

7. The computer-readable medium of claim 1, wherein said information is a file that has a unique identifier that corresponds to a unique identifier of an array.

8. The computer-readable medium of claim 1, wherein said array information features encode binary coded information, and said file contains information for decoding said binary coded information.

9. The computer-readable medium of claim 7, wherein said binary coded information is encoded using a binary coded decimal (BCD) or binary ASCII code.

10. The computer-readable medium of claim 1, wherein said decoded array information indicates a particular array of a multi-array substrate.

11. A method for obtaining information about an array, comprising:

reading an array comprising one or more array information features to provide encoded information for said array; and

decoding said encoded information using a computer readable medium of claim 1 to provide information about said array.

12. The method of claim 11, wherein said information about said array indicates identifies said array as particular array of a multi-array substrate.

13. The method of claim 11, wherein said array is a nucleic acid array.

14. The method of claim 11, wherein said scanning provides a data file comprising feature identifiers and numerical assessments of the brightness of said array information features.

15. The method of claim 11, wherein said decoding comprises

identifying an executable program using said file, and

executing said program,

to decode said encoded information and provide information about said array.

16. The method of claim 15, wherein said executable program is obtained from a remote location.

20. A method of assaying a sample, said method comprising:

(a) contacting said sample with an array comprising one or more array information features,

(b) reading said array with an array scanner to obtain data, and

(c) decoding said data using a computer readable medium of claim 1 to provide information for said array.

21. The method of claim 20, wherein said information for said array indicates that the data was derived from a particular array of a multi-array substrate.

22. The method according to claim 20, wherein said array is a nucleic acid array.

23. A method comprising transmitting a result obtained from a method of claim 20 from a first location to a second location.

24. The method of claim 23, where said second location is a remote location.

25. A method comprising receiving data representing said data obtained by the method of claim 20.

26. A kit for use with an array scanner, said kit comprising:

(a) a computer-readable medium according to claim 1;

and

(b) instructions for operating said scanner according to said programming.

27. The kit of claim 26, further comprising an array.

17. A method for obtaining information about an array, comprising:

encoding information on an array using one or more array information features; and

providing information for decoding said encoded information.

18. The method of claim 17, wherein said array is shipped in the absence of said information.

19. The method of claim 17, wherein said array information is provided from a location remote to said array.

28. A kit for use with an array scanner, said kit comprising:

(a) an array comprising array information features; and

(b) instructions for obtaining information for decoding encoded array information encoded by said array information features.