Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: The present disclosure provides a method for analyzing a polyribonucleotide, wherein the polyribonucleotide is an mRNA molecule with a poly(A) tail, said method comprising: (a) obtaining a labeled polyribonucleotide by GI tailing; followed by (b) providing a second molecule comprising a first primer recognition sequence followed by a sequence of C nucleotide residues linked to a sequence of T nucleotide residues; followed by (c) obtaining a complex of said labeled polyribonucleotide and said second molecule; followed by (d) obtaining an extended second molecule by (d1) extending the 3? end of the second molecule by synthesizing a sequence that is complementary to the labeled polyribonucleotide; followed by (d2) extending the 3? end of the second molecule by adding at least 1 to 5 C nucleotide residues, followed by a second primer recognition sequence; said method providing information on entire polyribonucleotides, in particular mRNA isoforms and their respective poly(A) tails.

Abstract: The present invention relates to a computer-implemented analysis of spatial abundance of poly-A containing RNA in a tissue sample, comprising the steps of: (i) obtaining imaging data and the sequencing data, (ii) registering the imaging data and detecting the beads, and employing a first machine learning method to obtain a first barcode set from the imaging data, (iii) processing the sequencing data to obtain a second barcode set from the sequencing data, (iv) processing the first and second barcode sets by an optimal transport framework and/or supervised machine learning to match the data sets to each other and to obtain matched barcodes, (v) outputting based on the matched barcodes a matrix holding the expression values for each gene that was identified in each bead found in the data.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: The present disclosure provides a method for analyzing a polyribonucleotide, wherein the polyribonucleotide is an mRNA molecule with a poly(A) tail, said method comprising: (a) obtaining a labeled polyribonucleotide by GI tailing; followed by (b) providing a second molecule comprising a first primer recognition sequence followed by a sequence of C nucleotide residues linked to a sequence of T nucleotide residues; followed by (c) obtaining a complex of said labeled polyribonucleotide and said second molecule; followed by (d) obtaining an extended second molecule by (d1) extending the 3? end of the second molecule by synthesizing a sequence that is complementary to the labeled polyribonucleotide; followed by (d2) extending the 3? end of the second molecule by adding at least 1 to 5 C nucleotide residues, followed by a second primer recognition sequence; said method providing information on entire polyribonucleotides, in particular mRNA isoforms and their respective poly(A) tails.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.