Disclosed herein are methods for tracking solutions, (e.g., reaction conditions in solutions). In some embodiments, the method comprises: contacting a first lanthanide-chelator complex to a first solution to generate a first barcoded solution, wherein the first lanthanide-chelator complex comprises a first lanthanide chelated by a first chelator; contacting a second lanthanide-chelator complex to a second solution to generate a second barcoded solution, wherein the second lanthanide-chelator complex comprises a second lanthanide chelated by a second chelator; mixing the first barcoded solution and the second barcoded solution to form one or more mixtures; and identifying the first lanthanide ions in the mass spectrum and the second lanthanide ions in the mass spectrum to track the condition of each of the one or more mixtures.

Disclosed is an adaptor for sequencing DNAs at ultratrace levels and its uses. The adaptor contains, from 5′terminus to 3′terminus, a Tag sequence, PolyNs, a first stem sequencing, a first loop sequence, dUTP(s), a second loop sequence, and a second stem sequence, wherein the second stem sequence is complementary to the first stem sequence when read in opposite directions, and the 5′terminus of the adaptor is phosphorylated. The adaptor is designed to form a hairpin structure itself in use and then ligated to a DNA molecule of interest, so that adaptor-adaptor ligation can be effectively avoided, eliminating the inefficient adaptor-DNA ligation problem. Such an adaptor is especially suitable for library construction and sequencing of DNAs at ultratrace levels, laying a good basis for accurate sequencing of ctDNAs.

Disclosed is an adaptor for sequencing DNAs at ultratrace levels and its uses. The adaptor contains, from 5′terminus to 3′terminus, a Tag sequence, PolyNs, a first stem sequencing, a first loop sequence, dUTP(s), a second loop sequence, and a second stem sequence, wherein the second stem sequence is complementary to the first stem sequence when read in opposite directions, and the 5′terminus of the adaptor is phosphorylated. The adaptor is designed to form a hairpin structure itself in use and then ligated to a DNA molecule of interest, so that adaptor-adaptor ligation can be effectively avoided, eliminating the inefficient adaptor-DNA ligation problem. Such an adaptor is especially suitable for library construction and sequencing of DNAs at ultratrace levels, laying a good basis for accurate sequencing of ctDNAs.

A barcoded transposase complex and an application thereof in high-throughput sequencing. Provided is a transposase recognition element, having the following structure: X(m)Y(f)N(n), in which X(m) represents a transposase recognition region of a double-stranded nucleic acid structure, Y(f) represents a spacer region of a single-stranded DNA structure, and N(n) represents a sample barcode of a single-stranded DNA structure. The high-molecular-weight DNA is processed using the barcoded transposase complex, to obtain a lot of barcoded DNA fragments. The barcoded DNA fragments obtained from each high-molecular-weight DNA are mixed to obtain a mixing sample. A carrier having a molecular barcode is adopted to capture. An exonuclease is adopted for processing, and then transposase is released. StLFR technology is adopted to construct a DNA library. The barcoded transposase complex can be applied to hybrid sequencing of a high-throughput sequencing platform.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides instrumentation and automated methods for creating cell surface display libraries, where the cells of the library display engineered peptides on their cell surfaces for identification of antigens that bind to T-cell receptors. The engineered peptides may be putative antigens or binding regions of the T-cell receptors.

The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications, including cell lineage analysis. Cell lineage analysis may comprise the use of one or more lineage tracing nucleic acid molecules. The disclosed methods may comprise using a lineage tracing nucleic acid molecule to identify a biological particle with one or more progenitor cells.

Methods related to concealment of genetic information present within nucleic acid sequences, wherein individual nucleic acid molecules are barcoded. In some embodiments barcoding occurs before, after, or during enrichment. Barcoded nucleic acids are then combined with control barcoded nucleic acids. Different methods are provided for barcoding and pooling to conceal different types of genetic information present within nucleic acids.