Method of constructing a spatially barcoded surface
AssigneeCellanome, Inc.
InventorsAnirudh VENUGOPAL, Paul KITABJIAN, Ali AGAH
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Abstract
A method of making a barcoded surface includes synthesizing a plurality of arrays arranged in rows and columns. Each array can include a plurality of discrete reaction sites with a first oligonucleotide containing a first unique array barcode sequence. The first unique array barcode sequences of the first oligonucleotides corresponds to a mapped discrete reaction site location within the array. A second oligonucleotide can be coupled to the first oligonucleotide that contains a second unique barcode sequence. The first unique barcode sequences of the second oligonucleotides corresponds to a mapped first sub-group location within the plurality of arrays.
Claims26
A method of making a barcoded surface, the method comprising:
- synthesizing a plurality of arrays, wherein:
- (i) each array comprises a plurality of discrete reaction sites,
- (ii) each discrete reaction site comprises a first oligonucleotide coupled to a surface of a solid support at a 5′ end of the first oligonucleotide,
- (iii) the surface comprises an uncoated region in between neighboring arrays, the uncoated region comprising an area where no first oligonucleotides are coupled to the surface,
- (iv) the first oligonucleotide includes a first unique array barcode sequence for each discrete reaction site location within the array,
- (v) each of the first unique array barcode sequences of the first oligonucleotides corresponds to a mapped discrete reaction site location within the array;
- and
- disposing a liquid containing a second oligonucleotide onto each array of the plurality of arrays where a portion of the uncoated region in between the neighboring arrays is not covered by the liquid containing the second oligonucleotide, wherein:
- (vi) the second oligonucleotide couples to the first oligonucleotide to form a first surface oligonucleotide complex,
- (vii) the second oligonucleotide includes a second unique barcode sequence, the second unique barcode sequence including a same sequence within a first sub-group of the plurality of arrays and a different sequence between each of the first sub-groups of the plurality of arrays,
- (viii) each of the second unique barcode sequences of the second oligonucleotides corresponds to a mapped first sub-group location within the plurality of arrays.
A flow cell configured to capture cells from a biological sample in a hydrogel cage comprising:
- (a) an inlet configured for receiving a liquid;
- (b) an outlet configured outputting the liquid;
- (c) a top layer;
- (d) a spacer layer having a cut-out portion;
- and
- (e) a bottom layer, wherein the top layer and the bottom layer are in an opposing relationship with the spacer layer in between the top layer and the bottom layer, wherein the top layer, the bottom layer, and the cut-out portion cooperate to form a channel, wherein the inlet and the outlet are in liquid communication with the channel allowing liquid flow through the channel, the bottom layer comprising a plurality of arrays, wherein
- (i) each array comprises a plurality of discrete sites where a spatial barcode oligonucleotide is coupled to a surface on the bottom layer at each of the discrete sites, wherein the spatial barcode oligonucleotide comprises:
- a first oligonucleotide and a second oligonucleotide,
- (ii) the surface includes an uncoated region in between neighboring arrays, the uncoated region comprising an area where no spatial barcode oligonucleotides are coupled to the surface,
- (iii) the first oligonucleotide includes a first unique array barcode sequence for each discrete site location within the array,
- (iv) the first unique array barcode sequence of the first oligonucleotide corresponds to a mapped discrete site location within the array;
- (v) the second oligonucleotide includes a second unique barcode sequence, the second unique barcode sequence including a same sequence within a first sub-group of the plurality of arrays and a different sequence between each of the first sub-groups of the plurality of arrays, and
- (vi) the second unique barcode sequence of the second oligonucleotide corresponds to a mapped first sub-group location within the plurality of arrays.
Dependencies are inferred from the claim text.