Office Action 2: Notice of Allowance (2025-02-05)

CLAIMS:
LISTING OF THE CLAIMS

1\. (Previously Presented) A method of generating a spatial transcriptomics gene expression image having subcellular resolution, comprising:a. providing a flat array surface comprising high density clusters of probes, wherein each probe comprises a spatial barcode sequence and a capture domain, and wherein a location of each cluster on said flat array surface is known;
b. contacting said flat array surface with a tissue section under conditions such that RNA from cells in said tissue section hybridizes to said capture domain of said probes;
c. reverse transcribing target sequences from said RNA on 3' ends of said probes;
d. generating second strand copies of said probes and eluting said second strand copies from said array;
e. generating a sequencing library from eluted second strand copies;
f. sequencing said sequencing library to generate sequencing data; and
g. generating a spatial transcriptomics gene expression image having subcellular resolution from said sequencing data.

2\. (Original) The method of claim 1, wherein each probe in a given cluster comprises an identical spatial barcode sequence, and wherein said spatial barcode sequence for each cluster is unique.

3\. (Original) The method of claim 1, wherein said flat array surface comprises 0.5-2 million clusters per 1mm2 of surface.

4\. (Original) The method of claim 3, wherein said flat array surface comprises about 1.5 million clusters per 1mm2 of surface.

5\. (Original) The method of claim 1, wherein each cluster comprises at least 200 probes.

6\. (Previously Presented) The method of claim 1, wherein each cluster comprises at least 500 probes.

7\. (Previously Presented) The method of claim 1, wherein each cluster comprises at least 800 probes.

8\. (Previously Presented) The method of claim 1, wherein each cluster has a diameter of 500-1200nm.

9\. (Original) The method of claim 8, wherein each cluster has an average diameter of 0.6pm.

10\. (Original) The method of claim 1, wherein said flat array surface comprises a material selected from glass, silicon, poly-L-lysine coated materials, nitrocellulose, polystyrene,cyclic olefin copolymers (COCs), cyclic olefin polymers (COPs), polyacrylamide,
polypropylene, polyethylene and polycarbonate.

11\. (Original) The method of claim 1, wherein said capture domain is identical for each probe.

12\. (Original) The method of claim 1, wherein said capture domain comprises a poly-T oligonucleotide comprising at least 10 deoxythymidine residues.

13\. (Original) The method of claim 1, wherein each probe further comprises a sequencing barcode.

14\. (Original) The method of claim 1, wherein each probe further comprises one or more filler sequences.

15\. (Original) The method of claim 1, wherein each probe further comprises a unique molecular identifier (UMI) barcode sequence.

16\. (Original) The method of claim 1, wherein each probe further comprises a cleavage domain comprising a binding site for a restriction endonuclease.

17\. (Original) The method of claim 1, further comprising imaging the tissue before or after reverse transcribing target sequences from said RNA on 3' ends of said probes.

18\. (Original) The method of claim 17, further comprising correlating the identified location of each cluster on said flat array surface with a corresponding location within said tissue section.

19\. (Previously Presented) The method of claim 1, wherein the distance between centers of said clusters is 1 pm or less.

20\. (Previously Presented) The method of claim 1, wherein said clusters are produced by bridge amplification.

OFFICE ACTION:
EXAMINER’S COMMENTS
1.	The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2.	The terminal disclaimer filed on 01/21/25 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of US ‘480 has been reviewed and is accepted.  The terminal disclaimer has been recorded.
3.

APPLICANT REBUTTAL: REMARKS
1. Preliminary Remarks
Claims 1-20 are pending and under active consideration. No claims are amended or cancelled herein.
2. Patentability Remarks
The Examiner objects to the specification and indicates that the continuation information must be updated to indicate the issue of the parent application. The specification is updated herein to address this change.
The Examiner rejects claims 1-20 on the grounds of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11,713,480. Submitted herewith is a terminal disclaimer over the '480 patent. Reconsideration of the rejection is respectfully requested.
Conclusion