Provided herein is a method for sample analysis. In some embodiments, the method may involve: (a) incubating a nucleic acid sample with a terminal transferase and a cyclooctene-functionalized nucleotide to produced cyclooctene-functionalized nucleic acid molecules; (b) tethering the cyclooctene-functionalized nucleic acid molecules to a tetrazine-functionalized support via an Alder cycloaddition reaction; (c) performing at least two separate primer extension reactions using the tethered nucleic acid molecules as a template to produce multiple distinct sets of primer extension products; (d) separately analyzing the sets of primer extension products using different methods to produce multiple data sets; and (e) integrating the data sets.

Provided herein is a method for sample analysis. In some embodiments, the method may involve: (a) incubating a nucleic acid sample with a terminal transferase and a cyclooctene-functionalized nucleotide to produced cyclooctene-functionalized nucleic acid molecules; (b) tethering the cyclooctene-functionalized nucleic acid molecules to a tetrazine-functionalized support via an Alder cycloaddition reaction; (c) performing at least two separate primer extension reactions using the tethered nucleic acid molecules as a template to produce multiple distinct sets of primer extension products; (d) separately analyzing the sets of primer extension products using different methods to produce multiple data sets; and (e) integrating the data sets.

The invention is directed to methods and apparatus for parallel enzymatic synthesis of polynucleotides in an array of reaction chambers using a tem-plate-free polymerase that has sequence-dependent coupling efficiencies. Whenever sequences causing low efficiency coupling occur at a 3′ end of a growing chain of a polynucleotide being synthesized, one or more additional coupling cy-cies without de-protection steps are inserted into synthesis plans to provide additional time for completing the coupling reaction at that position of the polynucleotide.

The invention is directed to methods and apparatus for parallel enzymatic synthesis of polynucleotides in an array of reaction chambers using a tem-plate-free polymerase that has sequence-dependent coupling efficiencies. Whenever sequences causing low efficiency coupling occur at a 3′ end of a growing chain of a polynucleotide being synthesized, one or more additional coupling cy-cies without de-protection steps are inserted into synthesis plans to provide additional time for completing the coupling reaction at that position of the polynucleotide.

Provided herein are methods of identifying the spatial location of a nucleic acid in a biological sample. In some embodiments, the methods employ a template switching oligonucleotide. In some embodiments, the methods extend the capture probe to create a complementary DNA (cDNA) molecule of a capture analyte and produce second strand in one reaction.

Provided herein are methods of identifying the spatial location of a nucleic acid in a biological sample. In some embodiments, the methods employ a template switching oligonucleotide. In some embodiments, the methods extend the capture probe to create a complementary DNA (cDNA) molecule of a capture analyte and produce second strand in one reaction.

The invention relates to improved methods of enzymatic solid-supported nucleic acid synthesis that make use of terminal deoxynucleotidyl transferase (TdT) enzymes or modified terminal deoxynucleotidyl transferase (TdT) enzymes on polyacrylamide type supports. The invention further relates to the use of kits comprising said enzymes in a method of solid-supported nucleic acid synthesis.

The invention relates to improved methods of enzymatic solid-supported nucleic acid synthesis that make use of terminal deoxynucleotidyl transferase (TdT) enzymes or modified terminal deoxynucleotidyl transferase (TdT) enzymes on polyacrylamide type supports. The invention further relates to the use of kits comprising said enzymes in a method of solid-supported nucleic acid synthesis.

The invention relates to the use of polyphosphate containing species in a method of nucleic acid synthesis, to methods of nucleic acid synthesis, and to the use of kits comprising said polyphosphate containing species. The invention also relates to the use of polyphosphate containing species for the capping of 3′-terminal hydroxyl moieties using terminal transferases.

The invention relates to the use of polyphosphate containing species in a method of nucleic acid synthesis, to methods of nucleic acid synthesis, and to the use of kits comprising said polyphosphate containing species. The invention also relates to the use of polyphosphate containing species for the capping of 3′-terminal hydroxyl moieties using terminal transferases.