Systems, methods, and compositions provided herein relate to preparation of beads encapsulating long DNA fragments for high-throughput spatial indexing. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.

An example of a kit includes a flow cell assembly. The flow cell assembly includes a reaction chamber, a temperature controlled flow channel in selective fluid communication with an inlet of the reaction chamber, and a filter positioned in the temperature controlled flow channel. The reaction chamber includes depressions separated by interstitial regions and capture primers attached within each of the depressions. The filter is i) to block concentrated biological sample-polymer complexes generated in the temperature controlled flow channel at a first temperature, and ii) to allow passage of concentrated biological sample and polymer released from the complexes in the temperature controlled flow channel at a second temperature.

An example of a kit includes a flow cell assembly. The flow cell assembly includes a reaction chamber, a temperature controlled flow channel in selective fluid communication with an inlet of the reaction chamber, and a filter positioned in the temperature controlled flow channel. The reaction chamber includes depressions separated by interstitial regions and capture primers attached within each of the depressions. The filter is i) to block concentrated biological sample-polymer complexes generated in the temperature controlled flow channel at a first temperature, and ii) to allow passage of concentrated biological sample and polymer released from the complexes in the temperature controlled flow channel at a second temperature.

The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.

The present disclosure relates to methods and kits for generating single cell barcodes and imparting them to the constituent molecules within a single cell. Additionally, methods to overlay sample barcode and spatial barcode information onto the single cell barcodes are also described. Generation of single cell barcodes is achieved by labeling the genomic DNA of a cell/nucleus with a small handful, preferably just a one or two cellular barcode probes (CBP) that can be amplified and propagated to label the constituent molecules within the cell. The disclosure finds utility in applications such as characterization of cellular heterogeneity, comprehensive profiling of tissue composition, characterization of adherent cells, discovery of new cell subtypes and functions of individual cells in the context of its microenvironment, and others.

Methods of capturing multiple analytes from a biological sample onto a substrate include: (a) positioning a first substrate that includes a plurality of capture probes with respect to a second substrate on which a biological sample that includes multiple analytes is disposed, where the first substrate is permeable; (b) delivering a first fluid to a first surface of the first substrate, where the first surface is opposite to a second surface of the first substrate that faces the second substrate; (c) allowing the first fluid to pass through the first substrate and contact the biological sample; (d) capturing a first one of the multiple analytes with one or more of the capture probes; (e) delivering a second fluid to the first surface of the first substrate; (f) allowing the second fluid to pass through the first substrate and contact the biological sample; and (g) capturing a second one of the multiple analytes with one or more of the capture probes. Other methods of capturing analytes from a biological sample are also described herein.

Methods of capturing multiple analytes from a biological sample onto a substrate include: (a) positioning a first substrate that includes a plurality of capture probes with respect to a second substrate on which a biological sample that includes multiple analytes is disposed, where the first substrate is permeable; (b) delivering a first fluid to a first surface of the first substrate, where the first surface is opposite to a second surface of the first substrate that faces the second substrate; (c) allowing the first fluid to pass through the first substrate and contact the biological sample; (d) capturing a first one of the multiple analytes with one or more of the capture probes; (e) delivering a second fluid to the first surface of the first substrate; (f) allowing the second fluid to pass through the first substrate and contact the biological sample; and (g) capturing a second one of the multiple analytes with one or more of the capture probes. Other methods of capturing analytes from a biological sample are also described herein.

The present invention provides methods and composition suitable for stabilizing cell-containing samples such as blood samples. The stabilizers used are primary or secondary carboxylic acid amides.

The present invention provides methods and composition suitable for stabilizing cell-containing samples such as blood samples. The stabilizers used are primary or secondary carboxylic acid amides.

Methods for determining a location of a feature on an array include: (a) providing a first array with a first plurality of features immobilized on a first substrate; (b) providing a second array with a second plurality of features immobilized on a second substrate; (c) aligning the first array with the second array; (d) hybridizing a first barcoded oligonucleotide of the first array to a second barcoded oligonucleotide of the second array, thereby producing a combined nucleic acid that includes first and second spatial barcodes; (e) determining all or a portion of the sequence of the combined nucleic acid; and (f) identifying the second barcoded oligonucleotide associated with the first barcoded oligonucleotide in the combined nucleic acid, and determining the location of a second feature in the second array.