Systems, methods, and compositions for generating a high-resolution spatial map of a distribution of targets of a sample are described. Processes for generating the spatial map can include: receiving the sample at a substrate having a distribution of functionalized particles, each having a stochastic barcode sequence paired with a position on the substrate; promoting interactions between the distribution of targets of the sample and the distribution of functionalized particles upon transmitting heat to a surface of the substrate opposite the distribution of functionalized particles; applying a set of reactions to the sample at the substrate, obtaining a set of sequences of a population of molecules generated from the set of reactions, the set of sequences associated with the distribution of targets labeled using the stochastic barcode sequences of the distribution of functionalized particles, and returning a set of positions of the distribution of targets upon processing the set of sequences.

Systems, methods, and compositions for generating a high-resolution spatial map of a distribution of targets of a sample are described. Processes for generating the spatial map can include: receiving the sample at a substrate having a distribution of functionalized particles, each having a stochastic barcode sequence paired with a position on the substrate; promoting interactions between the distribution of targets of the sample and the distribution of functionalized particles upon transmitting heat to a surface of the substrate opposite the distribution of functionalized particles; applying a set of reactions to the sample at the substrate, obtaining a set of sequences of a population of molecules generated from the set of reactions, the set of sequences associated with the distribution of targets labeled using the stochastic barcode sequences of the distribution of functionalized particles, and returning a set of positions of the distribution of targets upon processing the set of sequences.

A device for extracting a nucleic acid from a sample liquid includes a heating element configured to be connected to an extraction nucleic acid. The extraction nucleic acid is at least partly complementary to the nucleic acid to be extracted from the sample liquid. The heating element is heatable to a temperature that is equal to or higher than a denaturing temperature of the nucleic acid bound to the extraction nucleic acid.

A device for extracting a nucleic acid from a sample liquid includes a heating element configured to be connected to an extraction nucleic acid. The extraction nucleic acid is at least partly complementary to the nucleic acid to be extracted from the sample liquid. The heating element is heatable to a temperature that is equal to or higher than a denaturing temperature of the nucleic acid bound to the extraction nucleic acid.

A nucleic acid amplification method using a solid-phase carrier according to the present invention comprises: capturing a target nucleic acid comprising mRNA on a solid-phase carrier; carrying out complementary-strand synthesis on the solid phase; carrying out exonuclease treatment to degrade and remove unreacted target- capturing nucleic acid on the solid phase; and then carrying out mRNA degradation and homopolymer addition by TdT reaction in the presence of a chain-terminating nucleotide triphosphate. According to the method of the present invention, cDNA can be stably and highly efficiently amplified even from a small amount of sample even in cases where the ratio of the amount of enzyme to the DNA substrate on the solid phase is excessive, where the reaction time is excessive, and/or where reagents show lot-to-lot variation. Further, the amplification method of the present invention can broaden the range of applications of techniques in which analysis using a specific-binding molecule labeled with an oligonucleic acid such as a DNA-labeled antibody and analysis of transcripts are carried out simultaneously.

A nucleic acid amplification method using a solid-phase carrier according to the present invention comprises: capturing a target nucleic acid comprising mRNA on a solid-phase carrier; carrying out complementary-strand synthesis on the solid phase; carrying out exonuclease treatment to degrade and remove unreacted target- capturing nucleic acid on the solid phase; and then carrying out mRNA degradation and homopolymer addition by TdT reaction in the presence of a chain-terminating nucleotide triphosphate. According to the method of the present invention, cDNA can be stably and highly efficiently amplified even from a small amount of sample even in cases where the ratio of the amount of enzyme to the DNA substrate on the solid phase is excessive, where the reaction time is excessive, and/or where reagents show lot-to-lot variation. Further, the amplification method of the present invention can broaden the range of applications of techniques in which analysis using a specific-binding molecule labeled with an oligonucleic acid such as a DNA-labeled antibody and analysis of transcripts are carried out simultaneously.

The present disclosure provides materials and methods to link imaging and sequencing measurements of a single cell. Sequencing information can be linked with phenotypic measurements that are not directly encoded in the genome such as morphological features, protein expression & localization, organelle dynamics, or the metabolic composition of a cell.

The present disclosure provides materials and methods to link imaging and sequencing measurements of a single cell. Sequencing information can be linked with phenotypic measurements that are not directly encoded in the genome such as morphological features, protein expression & localization, organelle dynamics, or the metabolic composition of a cell.

Described herein are solid supports and methods for depleting library fragments prepared from unwanted RNA sequences and/or enriching library fragments prepared from desired RNA sequences. These methods may incorporate microfluidics and flowcells for greater ease of use. Libraries enriched or depleted with the present methods may be used for sequencing. Also described are probes and methods for enzymatic depletion of ribosomal RNA from human microbiome samples.

Described herein are solid supports and methods for depleting library fragments prepared from unwanted RNA sequences and/or enriching library fragments prepared from desired RNA sequences. These methods may incorporate microfluidics and flowcells for greater ease of use. Libraries enriched or depleted with the present methods may be used for sequencing. Also described are probes and methods for enzymatic depletion of ribosomal RNA from human microbiome samples.