Abstract: Nucleic acid molecule constructs, methods of making such construct, and methods of sequencing using such constructs are described herein. The nucleic acid molecule constructs can include a template sequence and a copy of the template sequence, along with a sequencing primer region associated with the template sequence and a copy of the sequencing primer region associated with the copy of the template sequence, which allows the template sequence and the copy of the template sequence to be simultaneously sequenced. Also described are methods of using the nucleic acid molecule constructs for methylation sequencing.

Abstract: Described herein is a composition, comprising: a first strand comprising a first portion and a first copy portion, wherein the first copy portion is a copy of the first portion except that substantially all cytosine bases in the first copy portion are methylated; and a second strand comprising a second portion and a second copy portion, wherein the second copy portion is a copy of the second portion except that substantially all cytosine bases in the second copy portion are methylated. In some implementations, at least one cytosine base in the first portion or the second portion is not methylated.

Abstract: Provided herein are methods, systems, compositions, and kits that can determine spatial information between a plurality of analytes in a sample by tagging such analytes with tags, where identities and/or locations of such tags are previously unknown prior to tagging. Each of a plurality of analyte sequences may be tagged with multiple spatial tags, such that each analyte sequence is associated with a set of two or more spatial tags. The sets of spatial tags may be analyzed to generate a map of analyte sequences. The map may comprise information about the respective absolute positions of each of a set of sequences with respect to a reference sequence. The map may comprise information about the respective probability cloud (or likely location) of each of a set of sequences with respect to a reference sequence.

Abstract: Despite the advance of screening technology, omic-based studies with spatial resolution still requires laborious efforts, hampering the analysis of biology and disease. The present disclosure provides methods, systems, reagents, and platforms to increase the throughput of analyte screening with spatial resolution.